diff --git a/recipes/bioconda-utils/meta.yaml b/recipes/bioconda-utils/meta.yaml index 03186fa281bac..1b05d619627aa 100644 --- a/recipes/bioconda-utils/meta.yaml +++ b/recipes/bioconda-utils/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.15.3" %} -{% set sha256 = "68c23754259fe7102edcc6c89ad55cf5a7ecfd453a2ea0f4e82a290129e4603c" %} +{% set version = "0.15.2" %} +{% set sha256 = "a51b1b8e872be08c5f69aaeb55c36379ef4f08039ce51abcabc8167b8577dda2" %} package: name: bioconda-utils diff --git a/recipes/bioconductor-a4/build.sh b/recipes/bioconductor-a4/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-a4/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4/meta.yaml b/recipes/bioconductor-a4/meta.yaml new file mode 100644 index 0000000000000..42d6a2cac7379 --- /dev/null +++ b/recipes/bioconductor-a4/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.30.0" %} +{% set name = "a4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4e44a4273b805b3fda0cbbd476566c25 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MLP, nlcv, ALL, Cairo +requirements: + host: + - 'bioconductor-a4base >=1.30.0,<1.31.0' + - 'bioconductor-a4classif >=1.30.0,<1.31.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-a4reporting >=1.30.0,<1.31.0' + - r-base + run: + - 'bioconductor-a4base >=1.30.0,<1.31.0' + - 'bioconductor-a4classif >=1.30.0,<1.31.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-a4reporting >=1.30.0,<1.31.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Automated Affymetrix Array Analysis Umbrella Package' + diff --git a/recipes/bioconductor-a4base/build.sh b/recipes/bioconductor-a4base/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-a4base/build.sh +++ b/recipes/bioconductor-a4base/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4base/meta.yaml b/recipes/bioconductor-a4base/meta.yaml index c833fa4cefc4a..6056bbc7ad27c 100644 --- a/recipes/bioconductor-a4base/meta.yaml +++ b/recipes/bioconductor-a4base/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "a4Base" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,36 +10,37 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ed117190a960d4e69725cf5fd1f2c7c785a5258c06eb897d80f0a57626ae7520 + md5: a8238f64848e4f0974867b0a5f3dc920 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic # Suggests: Cairo, ALL requirements: host: - - 'bioconductor-a4core >=1.28.0,<1.30.0' - - 'bioconductor-a4preproc >=1.28.0,<1.30.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-glmnet - r-gplots - r-mpm run: - - 'bioconductor-a4core >=1.28.0,<1.30.0' - - 'bioconductor-a4preproc >=1.28.0,<1.30.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-glmnet - r-gplots @@ -48,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis' extra: identifiers: - biotools:a4base - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4base + path: recipes/bioconductor-a4base + version: 1.28.0 + diff --git a/recipes/bioconductor-a4classif/build.sh b/recipes/bioconductor-a4classif/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-a4classif/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4classif/meta.yaml b/recipes/bioconductor-a4classif/meta.yaml new file mode 100644 index 0000000000000..310ad67c2e993 --- /dev/null +++ b/recipes/bioconductor-a4classif/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.30.0" %} +{% set name = "a4Classif" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f3c574a15569caf4bc36badf16e2403a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ALL +requirements: + host: + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - r-base + - r-glmnet + - r-pamr + - r-rocr + - r-varselrf + run: + - 'bioconductor-a4core >=1.30.0,<1.31.0' + - 'bioconductor-a4preproc >=1.30.0,<1.31.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - r-base + - r-glmnet + - r-pamr + - r-rocr + - r-varselrf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Automated Affymetrix Array Analysis Classification Package' + diff --git a/recipes/bioconductor-a4core/build.sh b/recipes/bioconductor-a4core/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-a4core/build.sh +++ b/recipes/bioconductor-a4core/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4core/meta.yaml b/recipes/bioconductor-a4core/meta.yaml index 8ec76f661a614..1a8c96f6c1344 100644 --- a/recipes/bioconductor-a4core/meta.yaml +++ b/recipes/bioconductor-a4core/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "a4Core" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3e71939ec82a11b5d9be7e28e744903fde2a3e58aa4ecc65138c7e8eaec4ac6b + md5: 1c18ebb284225195642263519f84089b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-glmnet run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-glmnet test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis Core Package' extra: identifiers: - biotools:a4core - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4core + path: recipes/bioconductor-a4core + version: 1.28.0 + diff --git a/recipes/bioconductor-a4preproc/build.sh b/recipes/bioconductor-a4preproc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-a4preproc/build.sh +++ b/recipes/bioconductor-a4preproc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4preproc/meta.yaml b/recipes/bioconductor-a4preproc/meta.yaml index 93c0437982550..e2c637e3f572b 100644 --- a/recipes/bioconductor-a4preproc/meta.yaml +++ b/recipes/bioconductor-a4preproc/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "a4Preproc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 84408d2da7e19431824560f1cd9cdd952539550dcfe5607b244220cc88e71042 + md5: 79f088fcd94c8cf56ca40b40a59b8e97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis Preprocessing Package' extra: identifiers: - biotools:a4preproc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4preproc + path: recipes/bioconductor-a4preproc + version: 1.28.0 + diff --git a/recipes/bioconductor-a4reporting/build.sh b/recipes/bioconductor-a4reporting/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-a4reporting/build.sh +++ b/recipes/bioconductor-a4reporting/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-a4reporting/meta.yaml b/recipes/bioconductor-a4reporting/meta.yaml index ad23a41ee502c..cc3f99a348bab 100644 --- a/recipes/bioconductor-a4reporting/meta.yaml +++ b/recipes/bioconductor-a4reporting/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "a4Reporting" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 103e43eaff7834e74c85faf79b7af28a81fb33f148181989d8cf68aea1ccbd43 + md5: 4a7eb752a3ac2e746930c0166c248d3d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' - r-base - r-xtable run: - - 'bioconductor-annaffy >=1.52.0,<1.54.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' - r-base - r-xtable test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Automated Affymetrix Array Analysis Reporting Package' extra: identifiers: - biotools:a4reporting - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-a4reporting + path: recipes/bioconductor-a4reporting + version: 1.28.0 + diff --git a/recipes/bioconductor-abadata/meta.yaml b/recipes/bioconductor-abadata/meta.yaml index e1d12b07d83a4..bb3879f1e95e1 100644 --- a/recipes/bioconductor-abadata/meta.yaml +++ b/recipes/bioconductor-abadata/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ABAData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9fa25de3474c152697a6092a2599d57572c5af84101d861c8737afa1ade46734 + md5: 617a2967ed10a6b1f90406420a28545e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, ABAEnrichment requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Provides the data for the gene expression enrichment analysis conducted in the package ''ABAEnrichment''. The package includes three datasets which are derived from the Allen Brain Atlas: (1) Gene expression data from Human Brain (adults) averaged across donors, (2) Gene expression data from the Developing Human Brain pooled into five age categories and averaged across donors and (3) a developmental effect score based on the Developing Human Brain expression data. All datasets are restricted to protein coding genes.' - +extra: + parent_recipe: + name: bioconductor-abadata + path: recipes/bioconductor-abadata + version: 1.10.0 diff --git a/recipes/bioconductor-abadata/post-link.sh b/recipes/bioconductor-abadata/post-link.sh index c126642788f2f..50b809e3ecd35 100644 --- a/recipes/bioconductor-abadata/post-link.sh +++ b/recipes/bioconductor-abadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ABAData_1.10.0.tar.gz" +FN="ABAData_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ABAData_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/ABAData_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ABAData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/ABAData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-abadata/bioconductor-abadata_1.12.0_src_all.tar.gz" ) -MD5="cb4096c89b74d15232d431ffd41485f8" +MD5="617a2967ed10a6b1f90406420a28545e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-abaenrichment/build.sh b/recipes/bioconductor-abaenrichment/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-abaenrichment/build.sh +++ b/recipes/bioconductor-abaenrichment/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-abaenrichment/meta.yaml b/recipes/bioconductor-abaenrichment/meta.yaml index 7f0fa306cedbf..68af8a5a138eb 100644 --- a/recipes/bioconductor-abaenrichment/meta.yaml +++ b/recipes/bioconductor-abaenrichment/meta.yaml @@ -1,31 +1,34 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ABAEnrichment" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dc12cd6e10754bc0f49a84c6d8c4614bb65322009c02db2bdb8d0aaa2d019703 + md5: f5934cab26c8b62087ed9242aa0cbf8a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-abadata >=1.10.0,<1.12.0' + - 'bioconductor-abadata >=1.12.0,<1.13.0' + - 'bioconductor-gofuncr >=1.2.0,<1.3.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' - 'r-gtools >=3.5.0' - 'r-rcpp >=0.11.5' run: - - 'bioconductor-abadata >=1.10.0,<1.12.0' + - 'bioconductor-abadata >=1.12.0,<1.13.0' + - 'bioconductor-gofuncr >=1.2.0,<1.3.0' - r-base - 'r-data.table >=1.10.4' - 'r-gplots >=2.14.2' @@ -39,9 +42,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function ''aba_enrich'' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. ''aba_enrich'' interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like ''get_expression'' and ''plot_expression'' facilitate exploring the expression data. From version 1.3.5 onwards genomic regions can be provided as input, too; and from version 1.5.9 onwards the function ''get_annotated_genes'' offers an easy way to obtain annotations of genes to enriched or user-defined brain regions.' + summary: 'The package ABAEnrichment is designed to test for enrichment of user defined candidate genes in the set of expressed genes in different human brain regions. The core function ''aba_enrich'' integrates the expression of the candidate gene set (averaged across donors) and the structural information of the brain using an ontology, both provided by the Allen Brain Atlas project. ''aba_enrich'' interfaces the ontology enrichment software FUNC to perform the statistical analyses. Additional functions provided in this package like ''get_expression'' and ''plot_expression'' facilitate exploring the expression data, and besides the standard candidate vs. background gene set enrichment, also three additional tests are implemented, e.g. for cases when genes are ranked instead of divided into candidate and background.' extra: identifiers: - biotools:abaenrichment + parent_recipe: + name: bioconductor-abaenrichment + path: recipes/bioconductor-abaenrichment + version: 1.10.0 + diff --git a/recipes/bioconductor-abarray/build.sh b/recipes/bioconductor-abarray/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-abarray/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-abarray/meta.yaml b/recipes/bioconductor-abarray/meta.yaml new file mode 100644 index 0000000000000..19e12280a1143 --- /dev/null +++ b/recipes/bioconductor-abarray/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.50.0" %} +{% set name = "ABarray" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 84761cfa2828e57c5ef0daa712f741d8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, LPE +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'Automated pipline to perform gene expression analysis for Applied Biosystems Genome Survey Microarray (AB1700) data format. Functions include data preprocessing, filtering, control probe analysis, statistical analysis in one single function. A GUI interface is also provided. The raw data, processed data, graphics output and statistical results are organized into folders according to the analysis settings used.' + diff --git a/recipes/bioconductor-abseqr/build.sh b/recipes/bioconductor-abseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-abseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-abseqr/meta.yaml b/recipes/bioconductor-abseqr/meta.yaml new file mode 100644 index 0000000000000..e2a7fcfd264d3 --- /dev/null +++ b/recipes/bioconductor-abseqr/meta.yaml @@ -0,0 +1,70 @@ +{% set version = "1.0.0" %} +{% set name = "abseqR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de9e8be03e84433a1fc776c563ec4426 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +# SystemRequirements: pandoc (>= 1.19.2.1) +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - r-base + - r-circlize + - r-flexdashboard + - r-ggcorrplot + - r-ggdendro + - r-ggplot2 + - r-gridextra + - r-knitr + - r-plotly + - r-plyr + - r-png + - r-rcolorbrewer + - r-reshape2 + - r-rmarkdown + - r-stringr + - r-vegan + - r-venndiagram + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - r-base + - r-circlize + - r-flexdashboard + - r-ggcorrplot + - r-ggdendro + - r-ggplot2 + - r-gridextra + - r-knitr + - r-plotly + - r-plyr + - r-png + - r-rcolorbrewer + - r-reshape2 + - r-rmarkdown + - r-stringr + - r-vegan + - r-venndiagram +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'AbSeq is a comprehensive bioinformatic pipeline for the analysis of sequencing datasets generated from antibody libraries and abseqR is one of its packages. abseqR empowers the users of abseqPy (https://github.com/malhamdoosh/abseqPy) with plotting and reporting capabilities and allows them to generate interactive HTML reports for the convenience of viewing and sharing with other researchers. Additionally, abseqR extends abseqPy to compare multiple repertoire analyses and perform further downstream analysis on its output.' + diff --git a/recipes/bioconductor-absseq/build.sh b/recipes/bioconductor-absseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-absseq/build.sh +++ b/recipes/bioconductor-absseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-absseq/meta.yaml b/recipes/bioconductor-absseq/meta.yaml index 2e9c8c1182675..9fabb26ead2d6 100644 --- a/recipes/bioconductor-absseq/meta.yaml +++ b/recipes/bioconductor-absseq/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.0" %} {% set name = "ABSSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ba8585d98a89573cece046d30bf59cc9c9ef8042a68c6d75546f74e6755c156 + md5: 030589f236271c0cfa666af69b74e223 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: edgeR requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-locfit test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Inferring differential expression genes by absolute counts difference between two groups, utilizing Negative binomial distribution and moderating fold-change according to heterogeneity of dispersion across expression level.' extra: identifiers: - biotools:absseq + parent_recipe: + name: bioconductor-absseq + path: recipes/bioconductor-absseq + version: 1.34.1 + diff --git a/recipes/bioconductor-acde/build.sh b/recipes/bioconductor-acde/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-acde/build.sh +++ b/recipes/bioconductor-acde/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-acde/meta.yaml b/recipes/bioconductor-acde/meta.yaml index 18613c4e27530..2ba01cd6a1028 100644 --- a/recipes/bioconductor-acde/meta.yaml +++ b/recipes/bioconductor-acde/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "acde" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: efe908ae1b6f31a719a6de6755dbd1e885d83f9844260d2f0856a9b7a7b889c3 + md5: f5bf1b85bb7436813020a5aec3765d12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a multivariate inferential analysis method for detecting differentially expressed genes in gene expression data. It uses artificial components, close to the data''s principal components but with an exact interpretation in terms of differential genetic expression, to identify differentially expressed genes while controlling the false discovery rate (FDR). The methods on this package are described in the vignette or in the article ''Multivariate Method for Inferential Identification of Differentially Expressed Genes in Gene Expression Experiments'' by J. P. Acosta, L. Lopez-Kleine and S. Restrepo (2015, pending publication).' extra: identifiers: - biotools:acde - doi:10.1007/978-0-387-49317-6_9 + parent_recipe: + name: bioconductor-acde + path: recipes/bioconductor-acde + version: 1.10.0 + diff --git a/recipes/bioconductor-ace/build.sh b/recipes/bioconductor-ace/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ace/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ace/meta.yaml b/recipes/bioconductor-ace/meta.yaml new file mode 100644 index 0000000000000..4c4fb59a45bf5 --- /dev/null +++ b/recipes/bioconductor-ace/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "ACE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 20953839cc1ce4ab6b8a3689954c3c74 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Uses segmented copy number data to estimate tumor cell percentage and produce copy number plots displaying absolute copy numbers.' + diff --git a/recipes/bioconductor-acgh/build.sh b/recipes/bioconductor-acgh/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-acgh/build.sh +++ b/recipes/bioconductor-acgh/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-acgh/meta.yaml b/recipes/bioconductor-acgh/meta.yaml index 9b02efde5f943..095c8593716a9 100644 --- a/recipes/bioconductor-acgh/meta.yaml +++ b/recipes/bioconductor-acgh/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "aCGH" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: be3bb6a3584612c0c51a96b0c2d0847e7d5bcb806f48e2182f2b578c8f955ce1 + md5: 4bdcf0503d13c9393ea12593e769d165 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-cluster - r-survival run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-cluster - r-survival @@ -37,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions for reading aCGH data from image analysis output files and clone information files, creation of aCGH S3 objects for storing these data. Basic methods for accessing/replacing, subsetting, printing and plotting aCGH objects.' extra: identifiers: - biotools:acgh - doi:10.1093/bioinformatics/bti677 + parent_recipe: + name: bioconductor-acgh + path: recipes/bioconductor-acgh + version: 1.58.0 + diff --git a/recipes/bioconductor-acme/build.sh b/recipes/bioconductor-acme/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-acme/build.sh +++ b/recipes/bioconductor-acme/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-acme/meta.yaml b/recipes/bioconductor-acme/meta.yaml index 7bac099299623..747a7761320d0 100644 --- a/recipes/bioconductor-acme/meta.yaml +++ b/recipes/bioconductor-acme/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "ACME" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 68f30578cc39397ebe5d1d4cd0d46daa4a1d99af0d15b78abb9bd777369a3227 + md5: 02fba578c93d2cf28d7f548400bae520 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base build: - {{ compiler('c') }} @@ -32,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'ACME (Algorithms for Calculating Microarray Enrichment) is a set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing "enrichment". It does not rely on a specific array technology (although the array should be a "tiling" array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory.' extra: identifiers: - biotools:acme + parent_recipe: + name: bioconductor-acme + path: recipes/bioconductor-acme + version: 2.36.0 + diff --git a/recipes/bioconductor-adacgh2/build.sh b/recipes/bioconductor-adacgh2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adacgh2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adacgh2/meta.yaml b/recipes/bioconductor-adacgh2/meta.yaml new file mode 100644 index 0000000000000..73cf53ff509c6 --- /dev/null +++ b/recipes/bioconductor-adacgh2/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "2.22.0" %} +{% set name = "ADaCGH2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cd000cb277c242ba358cade134fc5a4d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: CGHregions, Cairo, limma +requirements: + host: + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-snapcgh >=1.52.0,<1.53.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + - r-bit + - r-cluster + - r-ff + - r-ffbase + - r-waveslim + run: + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-snapcgh >=1.52.0,<1.53.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + - r-bit + - r-cluster + - r-ff + - r-ffbase + - r-waveslim + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Analysis and plotting of array CGH data. Allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.' + diff --git a/recipes/bioconductor-adaptest/build.sh b/recipes/bioconductor-adaptest/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-adaptest/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adaptest/meta.yaml b/recipes/bioconductor-adaptest/meta.yaml new file mode 100644 index 0000000000000..8ee6327b13445 --- /dev/null +++ b/recipes/bioconductor-adaptest/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.2.0" %} +{% set name = "adaptest" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1535857a21f2819c2930aded9d404325 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, Matrix, SuperLearner, earth, gam, nnls, airway, rmarkdown, knitr, BiocStyle +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-calibrate + - 'r-origami >=1.0.0' + - r-tmle + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-calibrate + - 'r-origami >=1.0.0' + - r-tmle +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Data-adaptive test statistics represent a general methodology for performing multiple hypothesis testing on effects sizes while maintaining honest statistical inference when operating in high-dimensional settings (). The utilities provided here extend the use of this general methodology to many common data analytic challenges that arise in modern computational and genomic biology.' + diff --git a/recipes/bioconductor-adme16cod.db/meta.yaml b/recipes/bioconductor-adme16cod.db/meta.yaml new file mode 100644 index 0000000000000..a8c10c48572b6 --- /dev/null +++ b/recipes/bioconductor-adme16cod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "adme16cod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3902516a40a503302ef732143b2394b9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink ADME Rat 16-Assay Bioarray annotation data (chip adme16cod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-adme16cod.db/post-link.sh b/recipes/bioconductor-adme16cod.db/post-link.sh new file mode 100644 index 0000000000000..bc38bb05eb812 --- /dev/null +++ b/recipes/bioconductor-adme16cod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="adme16cod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/adme16cod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/adme16cod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-adme16cod.db/bioconductor-adme16cod.db_3.4.0_src_all.tar.gz" +) +MD5="3902516a40a503302ef732143b2394b9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-adme16cod.db/pre-unlink.sh b/recipes/bioconductor-adme16cod.db/pre-unlink.sh new file mode 100644 index 0000000000000..77490d1696680 --- /dev/null +++ b/recipes/bioconductor-adme16cod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ adme16cod.db diff --git a/recipes/bioconductor-adsplit/build.sh b/recipes/bioconductor-adsplit/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-adsplit/build.sh +++ b/recipes/bioconductor-adsplit/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-adsplit/meta.yaml b/recipes/bioconductor-adsplit/meta.yaml index 985d911d24ecb..69252cc0de95d 100644 --- a/recipes/bioconductor-adsplit/meta.yaml +++ b/recipes/bioconductor-adsplit/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "adSplit" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5886e5d91dfa9c5bd859a0c6d158036a74dc8413f4874bc9fa7bbca46852257e + md5: a5cd67644a93b10c454e0584b002e08d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: golubEsets (>= 1.0), vsn (>= 1.5.0), hu6800.db (>= 1.8.1) requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - 'r-cluster >=1.9.1' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - 'r-cluster >=1.9.1' build: @@ -41,8 +42,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements clustering of microarray gene expression profiles according to functional annotations. For each term genes are annotated to, splits into two subclasses are computed and a significance of the supporting gene set is determined.' - +extra: + parent_recipe: + name: bioconductor-adsplit + path: recipes/bioconductor-adsplit + version: 1.50.0 diff --git a/recipes/bioconductor-affixcan/build.sh b/recipes/bioconductor-affixcan/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-affixcan/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affixcan/meta.yaml b/recipes/bioconductor-affixcan/meta.yaml new file mode 100644 index 0000000000000..dfd673e9a880b --- /dev/null +++ b/recipes/bioconductor-affixcan/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "AffiXcan" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 20b361ce24b3fbf71f7d3a032655a98d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Impute a GReX (Genetically Regulated Expression) for a set of genes in a sample of individuals, using a method based on the Total Binding Affinity (TBA). Statistical models to impute GReX can be trained with a training dataset where the real total expression values are known.' + diff --git a/recipes/bioconductor-affxparser/build.sh b/recipes/bioconductor-affxparser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affxparser/build.sh +++ b/recipes/bioconductor-affxparser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affxparser/meta.yaml b/recipes/bioconductor-affxparser/meta.yaml index 18e5489453824..99184ff5fc6c7 100644 --- a/recipes/bioconductor-affxparser/meta.yaml +++ b/recipes/bioconductor-affxparser/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "affxparser" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: de99cca0efd768fe216b1775b4942d12786d3a630cc2685cef933377f2140ffb + md5: 1c7cbf0945cc1504d16ba19d68b0f192 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: R.oo (>= 1.22.0), R.utils (>= 2.7.0), AffymetrixDataTestFiles requirements: host: - r-base @@ -29,8 +30,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' - summary: 'Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix'' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.' - + summary: 'Package for parsing Affymetrix files (CDF, CEL, CHP, BPMAP, BAR). It provides methods for fast and memory efficient parsing of Affymetrix files using the Affymetrix'' Fusion SDK. Both ASCII- and binary-based files are supported. Currently, there are methods for reading chip definition file (CDF) and a cell intensity file (CEL). These files can be read either in full or in part. For example, probe signals from a few probesets can be extracted very quickly from a set of CEL files into a convenient list structure.' +extra: + parent_recipe: + name: bioconductor-affxparser + path: recipes/bioconductor-affxparser + version: 1.52.0 diff --git a/recipes/bioconductor-affy/build.sh b/recipes/bioconductor-affy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affy/build.sh +++ b/recipes/bioconductor-affy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affy/conda_build_config.yaml b/recipes/bioconductor-affy/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affy/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affy/meta.yaml b/recipes/bioconductor-affy/meta.yaml index 92b0d60752a38..11864893d1214 100644 --- a/recipes/bioconductor-affy/meta.yaml +++ b/recipes/bioconductor-affy/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "affy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 26cef02431581909471bb637ba03c736fde6787699593c9c0ea2bea8cb41b86b + md5: 0f37ad355a3b6a6b501c65a3deec2d41 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: tkWidgets (>= 1.19.0), affydata, widgetTools requirements: host: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-biocmanager run: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-biocmanager build: - {{ compiler('c') }} - automake @@ -41,9 +42,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'The package contains functions for exploratory oligonucleotide array analysis. The dependence on tkWidgets only concerns few convenience functions. ''affy'' is fully functional without it.' extra: identifiers: - biotools:affy + parent_recipe: + name: bioconductor-affy + path: recipes/bioconductor-affy + version: 1.58.0 + diff --git a/recipes/bioconductor-affycomp/build.sh b/recipes/bioconductor-affycomp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affycomp/build.sh +++ b/recipes/bioconductor-affycomp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affycomp/meta.yaml b/recipes/bioconductor-affycomp/meta.yaml index 92cdde798083c..2755a2e54757a 100644 --- a/recipes/bioconductor-affycomp/meta.yaml +++ b/recipes/bioconductor-affycomp/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "affycomp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3bd3f4f9ba63776a9549add57b11c74d2126ea1c14793bec6a8b53d9df7b4dc9 + md5: 76bd3762a9a1589fd157be1a543de1d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: splines, affycompData requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains functions that can be used to compare expression measures for Affymetrix Oligonucleotide Arrays.' extra: identifiers: - biotools:affycomp - doi:10.1093/bioinformatics/btg410 + parent_recipe: + name: bioconductor-affycomp + path: recipes/bioconductor-affycomp + version: 1.56.0 + diff --git a/recipes/bioconductor-affycompatible/build.sh b/recipes/bioconductor-affycompatible/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affycompatible/build.sh +++ b/recipes/bioconductor-affycompatible/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affycompatible/meta.yaml b/recipes/bioconductor-affycompatible/meta.yaml index cb2f1afa4482f..85f2057e51217 100644 --- a/recipes/bioconductor-affycompatible/meta.yaml +++ b/recipes/bioconductor-affycompatible/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "AffyCompatible" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a431003b26362db8565aa83c474cd8b3f8c29a2bab34ca0a85689f520a4cf0cb + md5: 7d2ab32e48872dcba0cdf268543d15c9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - 'r-rcurl >=0.8-1' - 'r-xml >=2.8-1' run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - 'r-rcurl >=0.8-1' - 'r-xml >=2.8-1' @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides an interface to Affymetrix chip annotation and sample attribute files. The package allows an easy way for users to download and manage local data bases of Affynmetrix NetAffx annotation files. The package also provides access to GeneChip Operating System (GCOS) and GeneChip Command Console (AGCC)-compatible sample annotation files.' extra: identifiers: - biotools:affycompatible - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affycompatible + path: recipes/bioconductor-affycompatible + version: 1.40.0 + diff --git a/recipes/bioconductor-affycompdata/meta.yaml b/recipes/bioconductor-affycompdata/meta.yaml new file mode 100644 index 0000000000000..28c67a3e46440 --- /dev/null +++ b/recipes/bioconductor-affycompdata/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "affycompData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7dd3ccd7ee103e5fabc1beb000d08af2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affycomp >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-affycomp >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data needed by the affycomp package.' + diff --git a/recipes/bioconductor-affycompdata/post-link.sh b/recipes/bioconductor-affycompdata/post-link.sh new file mode 100644 index 0000000000000..f9d3ac54f36da --- /dev/null +++ b/recipes/bioconductor-affycompdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="affycompData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/affycompData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/affycompData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affycompdata/bioconductor-affycompdata_1.20.0_src_all.tar.gz" +) +MD5="7dd3ccd7ee103e5fabc1beb000d08af2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affycompdata/pre-unlink.sh b/recipes/bioconductor-affycompdata/pre-unlink.sh new file mode 100644 index 0000000000000..6f70a9f1b2848 --- /dev/null +++ b/recipes/bioconductor-affycompdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ affycompData diff --git a/recipes/bioconductor-affycontam/build.sh b/recipes/bioconductor-affycontam/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affycontam/build.sh +++ b/recipes/bioconductor-affycontam/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affycontam/conda_build_config.yaml b/recipes/bioconductor-affycontam/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affycontam/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affycontam/meta.yaml b/recipes/bioconductor-affycontam/meta.yaml index 5daf7ca87f605..5fa9abbf6345b 100644 --- a/recipes/bioconductor-affycontam/meta.yaml +++ b/recipes/bioconductor-affycontam/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "affyContam" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: afc3e450d15878232ad906959da83cd71b24516b35b86b718f37f600db78bd29 + md5: a2f70361f7e473c963c0e46202b8004f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affydata >=1.28.0,<1.30.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affydata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affydata >=1.28.0,<1.30.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affydata >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'structured corruption of cel file data to demonstrate QA effectiveness' extra: identifiers: - biotools:affycontam - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affycontam + path: recipes/bioconductor-affycontam + version: 1.38.0 + diff --git a/recipes/bioconductor-affycoretools/build.sh b/recipes/bioconductor-affycoretools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affycoretools/build.sh +++ b/recipes/bioconductor-affycoretools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affycoretools/conda_build_config.yaml b/recipes/bioconductor-affycoretools/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affycoretools/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affycoretools/meta.yaml b/recipes/bioconductor-affycoretools/meta.yaml index caaccedaebb87..e201766063164 100644 --- a/recipes/bioconductor-affycoretools/meta.yaml +++ b/recipes/bioconductor-affycoretools/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.52.2" %} +{% set version = "1.54.0" %} {% set name = "affycoretools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 463446ea737148d9273378fb9c0823daebe36a00e3489db7431e7714fd294691 + md5: f9ed1862b102e59df1f5177ce547cecc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata, hgfocuscdf, BiocStyle, knitr, hgu95av2.db, rgl, rmarkdown requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-reportingtools >=2.20.0,<2.22.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-reportingtools >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-ggplot2 @@ -38,17 +40,17 @@ requirements: - r-rsqlite - r-xtable run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-reportingtools >=2.20.0,<2.22.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-reportingtools >=2.22.0,<2.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-ggplot2 @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Various wrapper functions that have been written to streamline the more common analyses that a core Biostatistician might see.' extra: identifiers: - biotools:affycoretools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affycoretools + path: recipes/bioconductor-affycoretools + version: 1.52.2 + diff --git a/recipes/bioconductor-affydata/conda_build_config.yaml b/recipes/bioconductor-affydata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affydata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affydata/meta.yaml b/recipes/bioconductor-affydata/meta.yaml index 87b08e0c5f6e5..7b19a399ae92c 100644 --- a/recipes/bioconductor-affydata/meta.yaml +++ b/recipes/bioconductor-affydata/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "affydata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 70ba50c00b2739b59de4191ec17f4faef9341e53576f7e065a5b4649de966ab0 + md5: c4edc5ad12670675bc7fc5b993f29a36 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2cdf, hgu133acdf requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Example datasets of a slightly large size. They represent ''real world examples'', unlike the artificial examples included in the package affy.' - +extra: + parent_recipe: + name: bioconductor-affydata + path: recipes/bioconductor-affydata + version: 1.28.0 diff --git a/recipes/bioconductor-affydata/post-link.sh b/recipes/bioconductor-affydata/post-link.sh index c6919eeb1f0f2..8f860f057ea33 100644 --- a/recipes/bioconductor-affydata/post-link.sh +++ b/recipes/bioconductor-affydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="affydata_1.28.0.tar.gz" +FN="affydata_1.30.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/affydata_1.28.0.tar.gz" - "https://bioarchive.galaxyproject.org/affydata_1.28.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.28.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/affydata_1.30.0.tar.gz" + "https://bioarchive.galaxyproject.org/affydata_1.30.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affydata/bioconductor-affydata_1.30.0_src_all.tar.gz" ) -MD5="e1e5523f0ee6fd8be2900b693b9bb73d" +MD5="c4edc5ad12670675bc7fc5b993f29a36" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-affyexpress/build.sh b/recipes/bioconductor-affyexpress/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affyexpress/build.sh +++ b/recipes/bioconductor-affyexpress/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyexpress/conda_build_config.yaml b/recipes/bioconductor-affyexpress/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affyexpress/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affyexpress/meta.yaml b/recipes/bioconductor-affyexpress/meta.yaml index 54d55d3514f9a..5884954d13242 100644 --- a/recipes/bioconductor-affyexpress/meta.yaml +++ b/recipes/bioconductor-affyexpress/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "AffyExpress" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5e78e275fc2d2bb191f2ce2c6e908ee420050443f89241c205275f20a5a6042c + md5: 4afe8bb6ec8b571cacfd6faa5cb7284c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: simpleaffy, R2HTML, affyPLM, hgu95av2cdf, hgu95av2, test3cdf, genefilter, estrogen, annaffy, gcrma requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The purpose of this package is to provide a comprehensive and easy-to-use tool for quality assessment and to identify differentially expressed genes in the Affymetrix gene expression data.' extra: identifiers: - biotools:affyexpress - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affyexpress + path: recipes/bioconductor-affyexpress + version: 1.46.0 + diff --git a/recipes/bioconductor-affyhgu133a2expr/meta.yaml b/recipes/bioconductor-affyhgu133a2expr/meta.yaml new file mode 100644 index 0000000000000..3895b1ab1fbf9 --- /dev/null +++ b/recipes/bioconductor-affyhgu133a2expr/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "Affyhgu133A2Expr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5944ee99dfc56eaedd6ca8a95dfd59dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Contains pre-built human (GPL571) databases of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' + diff --git a/recipes/bioconductor-affyhgu133a2expr/post-link.sh b/recipes/bioconductor-affyhgu133a2expr/post-link.sh new file mode 100644 index 0000000000000..ce7e4b9518b66 --- /dev/null +++ b/recipes/bioconductor-affyhgu133a2expr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Affyhgu133A2Expr_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133A2Expr_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133A2Expr_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133a2expr/bioconductor-affyhgu133a2expr_1.18.0_src_all.tar.gz" +) +MD5="5944ee99dfc56eaedd6ca8a95dfd59dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affyhgu133a2expr/pre-unlink.sh b/recipes/bioconductor-affyhgu133a2expr/pre-unlink.sh new file mode 100644 index 0000000000000..b6d22f3345aeb --- /dev/null +++ b/recipes/bioconductor-affyhgu133a2expr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Affyhgu133A2Expr diff --git a/recipes/bioconductor-affyhgu133aexpr/meta.yaml b/recipes/bioconductor-affyhgu133aexpr/meta.yaml new file mode 100644 index 0000000000000..129f700b224b2 --- /dev/null +++ b/recipes/bioconductor-affyhgu133aexpr/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "Affyhgu133aExpr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9254b9cb76829110172cb80b01921ddc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Contains pre-built human (GPL96) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' + diff --git a/recipes/bioconductor-affyhgu133aexpr/post-link.sh b/recipes/bioconductor-affyhgu133aexpr/post-link.sh new file mode 100644 index 0000000000000..930322bc4de5c --- /dev/null +++ b/recipes/bioconductor-affyhgu133aexpr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Affyhgu133aExpr_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133aExpr_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133aExpr_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133aexpr/bioconductor-affyhgu133aexpr_1.20.0_src_all.tar.gz" +) +MD5="9254b9cb76829110172cb80b01921ddc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affyhgu133aexpr/pre-unlink.sh b/recipes/bioconductor-affyhgu133aexpr/pre-unlink.sh new file mode 100644 index 0000000000000..7ffa4d678284a --- /dev/null +++ b/recipes/bioconductor-affyhgu133aexpr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Affyhgu133aExpr diff --git a/recipes/bioconductor-affyhgu133plus2expr/meta.yaml b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml new file mode 100644 index 0000000000000..d302bae8fc2c5 --- /dev/null +++ b/recipes/bioconductor-affyhgu133plus2expr/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.16.0" %} +{% set name = "Affyhgu133Plus2Expr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 86ff16e83ac8445c7242525e1cbc146a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Contains pre-built human (GPL570) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO and preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' + diff --git a/recipes/bioconductor-affyhgu133plus2expr/post-link.sh b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh new file mode 100644 index 0000000000000..2d7cab54a13ce --- /dev/null +++ b/recipes/bioconductor-affyhgu133plus2expr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Affyhgu133Plus2Expr_1.16.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affyhgu133Plus2Expr_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affyhgu133Plus2Expr_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affyhgu133plus2expr/bioconductor-affyhgu133plus2expr_1.16.0_src_all.tar.gz" +) +MD5="86ff16e83ac8445c7242525e1cbc146a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affyhgu133plus2expr/pre-unlink.sh b/recipes/bioconductor-affyhgu133plus2expr/pre-unlink.sh new file mode 100644 index 0000000000000..84e539b33be68 --- /dev/null +++ b/recipes/bioconductor-affyhgu133plus2expr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Affyhgu133Plus2Expr diff --git a/recipes/bioconductor-affyilm/build.sh b/recipes/bioconductor-affyilm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affyilm/build.sh +++ b/recipes/bioconductor-affyilm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyilm/conda_build_config.yaml b/recipes/bioconductor-affyilm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affyilm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affyilm/meta.yaml b/recipes/bioconductor-affyilm/meta.yaml index a468e62aee55e..ee2b7437346d0 100644 --- a/recipes/bioconductor-affyilm/meta.yaml +++ b/recipes/bioconductor-affyilm/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "affyILM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fd28cdbe08eb46ef5258a328621cfd648919d2d9d8f2568682305d9298bdc927 + md5: 87811dbf7c0589e74a9c5858811ffb61 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: AffymetrixDataTestFiles, hgfocusprobe requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'affyILM is a preprocessing tool which estimates gene expression levels for Affymetrix Gene Chips. Input from physical chemistry is employed to first background subtract intensities before calculating concentrations on behalf of the Langmuir model.' extra: identifiers: - biotools:affyilm - doi:10.1186/1748-7188-4-15 + parent_recipe: + name: bioconductor-affyilm + path: recipes/bioconductor-affyilm + version: 1.32.0 + diff --git a/recipes/bioconductor-affyio/build.sh b/recipes/bioconductor-affyio/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affyio/build.sh +++ b/recipes/bioconductor-affyio/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyio/meta.yaml b/recipes/bioconductor-affyio/meta.yaml index 857411b39d61e..190f270160157 100644 --- a/recipes/bioconductor-affyio/meta.yaml +++ b/recipes/bioconductor-affyio/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "affyio" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 56885f62402c8d68acca2f17fbdb3cd6af2356c50bb26c6cc1d779c8ace5056a + md5: 4f0bb750a68406e25541e19a5dd1f5a2 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Routines for parsing Affymetrix data files based upon file format information. Primary focus is on accessing the CEL and CDF file formats.' extra: identifiers: - biotools:affyio - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-affyio + path: recipes/bioconductor-affyio + version: 1.50.0 + diff --git a/recipes/bioconductor-affylmgui/build.sh b/recipes/bioconductor-affylmgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-affylmgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affylmgui/meta.yaml b/recipes/bioconductor-affylmgui/meta.yaml new file mode 100644 index 0000000000000..ae3b5d435abb4 --- /dev/null +++ b/recipes/bioconductor-affylmgui/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.56.0" %} +{% set name = "affylmGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c03dfb6477d26f31f544c7f60d3a0d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-biocmanager + - r-r2html + - r-tkrplot + - r-xtable + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-biocmanager + - r-r2html + - r-tkrplot + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'A Graphical User Interface (GUI) for analysis of Affymetrix microarray gene expression data using the affy and limma packages.' + diff --git a/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml new file mode 100644 index 0000000000000..607f37d6567dc --- /dev/null +++ b/recipes/bioconductor-affymetrixdatatestfiles/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.20.0" %} +{% set name = "AffymetrixDataTestFiles" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ba84883ca62f5f7b73d9cd3fa1f36a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-2.1 + summary: 'This package contains annotation data files and sample data files of Affymetrix file formats. The files originate from the Affymetrix'' Fusion SDK distribution and other official sources.' + diff --git a/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh new file mode 100644 index 0000000000000..14b0334c71899 --- /dev/null +++ b/recipes/bioconductor-affymetrixdatatestfiles/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AffymetrixDataTestFiles_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AffymetrixDataTestFiles_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/AffymetrixDataTestFiles_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affymetrixdatatestfiles/bioconductor-affymetrixdatatestfiles_0.20.0_src_all.tar.gz" +) +MD5="9ba84883ca62f5f7b73d9cd3fa1f36a5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affymetrixdatatestfiles/pre-unlink.sh b/recipes/bioconductor-affymetrixdatatestfiles/pre-unlink.sh new file mode 100644 index 0000000000000..bb938c8ee0afe --- /dev/null +++ b/recipes/bioconductor-affymetrixdatatestfiles/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AffymetrixDataTestFiles diff --git a/recipes/bioconductor-affymoe4302expr/meta.yaml b/recipes/bioconductor-affymoe4302expr/meta.yaml new file mode 100644 index 0000000000000..02977b3d0e0ea --- /dev/null +++ b/recipes/bioconductor-affymoe4302expr/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "Affymoe4302Expr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e21ed8d45f198ac957d5343b48dd8d2c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Contains pre-built mouse (GPL1261) database of gene expression profiles. The gene expression data was downloaded from NCBI GEO, preprocessed and normalized consistently. The biological context of each sample was recorded and manually verified based on the sample description in GEO.' + diff --git a/recipes/bioconductor-affymoe4302expr/post-link.sh b/recipes/bioconductor-affymoe4302expr/post-link.sh new file mode 100644 index 0000000000000..6eedcfc633997 --- /dev/null +++ b/recipes/bioconductor-affymoe4302expr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Affymoe4302Expr_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Affymoe4302Expr_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Affymoe4302Expr_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-affymoe4302expr/bioconductor-affymoe4302expr_1.20.0_src_all.tar.gz" +) +MD5="e21ed8d45f198ac957d5343b48dd8d2c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-affymoe4302expr/pre-unlink.sh b/recipes/bioconductor-affymoe4302expr/pre-unlink.sh new file mode 100644 index 0000000000000..2d832316c7166 --- /dev/null +++ b/recipes/bioconductor-affymoe4302expr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Affymoe4302Expr diff --git a/recipes/bioconductor-affypara/build.sh b/recipes/bioconductor-affypara/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-affypara/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affypara/meta.yaml b/recipes/bioconductor-affypara/meta.yaml new file mode 100644 index 0000000000000..32f3362f5b2b8 --- /dev/null +++ b/recipes/bioconductor-affypara/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.42.0" %} +{% set name = "affyPara" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7a05c33daf0b6393e7ff928bf134b47f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: affydata +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'r-aplpack >=1.1.1' + - r-base + - 'r-snow >=0.2-3' + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'r-aplpack >=1.1.1' + - r-base + - 'r-snow >=0.2-3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The package contains parallelized functions for exploratory oligonucleotide array analysis. The package is designed for large numbers of microarray data.' + diff --git a/recipes/bioconductor-affypdnn/build.sh b/recipes/bioconductor-affypdnn/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affypdnn/build.sh +++ b/recipes/bioconductor-affypdnn/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affypdnn/conda_build_config.yaml b/recipes/bioconductor-affypdnn/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affypdnn/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affypdnn/meta.yaml b/recipes/bioconductor-affypdnn/meta.yaml index a0d5c9ec481a6..1a4224db0ee10 100644 --- a/recipes/bioconductor-affypdnn/meta.yaml +++ b/recipes/bioconductor-affypdnn/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "affypdnn" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dbf8564c32f3d21415d3af05fc2aa699aad74ad5b6b7fe228cd657d9b2c185f6 + md5: cc5feb90eb660fee35c0cab8846cb443 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The package contains functions to perform the PDNN method described by Li Zhang et al.' extra: identifiers: - biotools:affypdnn + parent_recipe: + name: bioconductor-affypdnn + path: recipes/bioconductor-affypdnn + version: 1.54.0 + diff --git a/recipes/bioconductor-affyplm/build.sh b/recipes/bioconductor-affyplm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affyplm/build.sh +++ b/recipes/bioconductor-affyplm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyplm/conda_build_config.yaml b/recipes/bioconductor-affyplm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affyplm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affyplm/meta.yaml b/recipes/bioconductor-affyplm/meta.yaml index 4f33493ff8be3..01cd75976bef9 100644 --- a/recipes/bioconductor-affyplm/meta.yaml +++ b/recipes/bioconductor-affyplm/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "affyPLM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 94ca54deabc2b4be06f22e3a4c0a824336dd27853ea275701d2f69f4e66778a3 + md5: 4d9e87db1f232700fec8543fc83fd8be build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affydata, MASS requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -40,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package that extends and improves the functionality of the base affy package. Routines that make heavy use of compiled code for speed. Central focus is on implementation of methods for fitting probe-level models and tools using these models. PLM based quality assessment tools.' extra: identifiers: - biotools:affyplm + parent_recipe: + name: bioconductor-affyplm + path: recipes/bioconductor-affyplm + version: 1.56.0 + diff --git a/recipes/bioconductor-affyqcreport/build.sh b/recipes/bioconductor-affyqcreport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-affyqcreport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyqcreport/meta.yaml b/recipes/bioconductor-affyqcreport/meta.yaml new file mode 100644 index 0000000000000..4137ab14dc2ca --- /dev/null +++ b/recipes/bioconductor-affyqcreport/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.60.0" %} +{% set name = "affyQCReport" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 639c5ee5befbf01b8f090eacc2a81f67 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: tkWidgets (>= 1.5.23), affydata (>= 1.4.1) +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - r-base + - r-lattice + - r-rcolorbrewer + - r-xtable + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - r-base + - r-lattice + - r-rcolorbrewer + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'This package creates a QC report for an AffyBatch object. The report is intended to allow the user to quickly assess the quality of a set of arrays in an AffyBatch object.' + diff --git a/recipes/bioconductor-affyrnadegradation/build.sh b/recipes/bioconductor-affyrnadegradation/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-affyrnadegradation/build.sh +++ b/recipes/bioconductor-affyrnadegradation/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml b/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-affyrnadegradation/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-affyrnadegradation/meta.yaml b/recipes/bioconductor-affyrnadegradation/meta.yaml index 1e5469e30d177..0d3ba3a05941d 100644 --- a/recipes/bioconductor-affyrnadegradation/meta.yaml +++ b/recipes/bioconductor-affyrnadegradation/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "AffyRNADegradation" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fa67369354eb2c3a7675da1c0cdb2780b164f3fff06bdd4d17960f0bfc947960 + md5: cad1f5fe8dd49d21d9409975dfb9bb32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: AmpAffyExample requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package helps with the assessment and correction of RNA degradation effects in Affymetrix 3'' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation.' extra: identifiers: - biotools:affyrnadegradation + parent_recipe: + name: bioconductor-affyrnadegradation + path: recipes/bioconductor-affyrnadegradation + version: 1.26.0 + diff --git a/recipes/bioconductor-ag.db/meta.yaml b/recipes/bioconductor-ag.db/meta.yaml new file mode 100644 index 0000000000000..7cbe76c1e1b56 --- /dev/null +++ b/recipes/bioconductor-ag.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "ag.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e5913da38fe4487202306cacd885840d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Arabidopsis Genome Array annotation data (chip ag) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ag.db/post-link.sh b/recipes/bioconductor-ag.db/post-link.sh new file mode 100644 index 0000000000000..4918e248e708b --- /dev/null +++ b/recipes/bioconductor-ag.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ag.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ag.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/ag.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ag.db/bioconductor-ag.db_3.2.3_src_all.tar.gz" +) +MD5="e5913da38fe4487202306cacd885840d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ag.db/pre-unlink.sh b/recipes/bioconductor-ag.db/pre-unlink.sh new file mode 100644 index 0000000000000..46824017fd279 --- /dev/null +++ b/recipes/bioconductor-ag.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ag.db diff --git a/recipes/bioconductor-agcdf/meta.yaml b/recipes/bioconductor-agcdf/meta.yaml new file mode 100644 index 0000000000000..31a6de20756c8 --- /dev/null +++ b/recipes/bioconductor-agcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "agcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5dd14bc6a6d2729f5e7b170105c78e48 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the AG.CDF file.' + diff --git a/recipes/bioconductor-agcdf/post-link.sh b/recipes/bioconductor-agcdf/post-link.sh new file mode 100644 index 0000000000000..bf5d8be1dec95 --- /dev/null +++ b/recipes/bioconductor-agcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="agcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/agcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/agcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-agcdf/bioconductor-agcdf_2.18.0_src_all.tar.gz" +) +MD5="5dd14bc6a6d2729f5e7b170105c78e48" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-agcdf/pre-unlink.sh b/recipes/bioconductor-agcdf/pre-unlink.sh new file mode 100644 index 0000000000000..6124227a503e3 --- /dev/null +++ b/recipes/bioconductor-agcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ agcdf diff --git a/recipes/bioconductor-agdex/build.sh b/recipes/bioconductor-agdex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-agdex/build.sh +++ b/recipes/bioconductor-agdex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-agdex/meta.yaml b/recipes/bioconductor-agdex/meta.yaml index 8d4ca0774e088..c19c605bfeba7 100644 --- a/recipes/bioconductor-agdex/meta.yaml +++ b/recipes/bioconductor-agdex/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "AGDEX" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 31c07d465d469691f644762d42e8d76d3ca1b60c12583184c70a63a657097c30 + md5: 0a82c526b05e7fbac77480ea0a93b42c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL Version 2 or later' summary: 'A tool to evaluate agreement of differential expression for cross-species genomics' extra: identifiers: - biotools:agdex - doi:10.1093/bioinformatics/btr362 + parent_recipe: + name: bioconductor-agdex + path: recipes/bioconductor-agdex + version: 1.28.0 + diff --git a/recipes/bioconductor-agilp/build.sh b/recipes/bioconductor-agilp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-agilp/build.sh +++ b/recipes/bioconductor-agilp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-agilp/meta.yaml b/recipes/bioconductor-agilp/meta.yaml index 9be07d3451d13..aae07b7866fb1 100644 --- a/recipes/bioconductor-agilp/meta.yaml +++ b/recipes/bioconductor-agilp/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "agilp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4d285b0934d55ae9e523c73f47995d2e5d6f20122b9edfeb14dd4d0f3377d578 + md5: c9c79b9c0a8bf313d6426266e1cac965 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,8 +26,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'More about what it does (maybe more than one line)' - +extra: + parent_recipe: + name: bioconductor-agilp + path: recipes/bioconductor-agilp + version: 3.12.0 diff --git a/recipes/bioconductor-agimicrorna/build.sh b/recipes/bioconductor-agimicrorna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-agimicrorna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-agimicrorna/meta.yaml b/recipes/bioconductor-agimicrorna/meta.yaml new file mode 100644 index 0000000000000..46da78c9dbd89 --- /dev/null +++ b/recipes/bioconductor-agimicrorna/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.32.0" %} +{% set name = "AgiMicroRna" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c28be6c85e4bf0e0fdfd1bf17df43814 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: geneplotter,marray,gplots,gtools,gdata,codelink +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affycoretools >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affycoretools >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Processing and Analysis of Agilent microRNA data' + diff --git a/recipes/bioconductor-agprobe/meta.yaml b/recipes/bioconductor-agprobe/meta.yaml new file mode 100644 index 0000000000000..5bb5c0e0a8b1e --- /dev/null +++ b/recipes/bioconductor-agprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "agprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 08f7527d4c8a30d8b2f86016a53f075a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was AG\_probe\_tab.' + diff --git a/recipes/bioconductor-agprobe/post-link.sh b/recipes/bioconductor-agprobe/post-link.sh new file mode 100644 index 0000000000000..95d7df3c4a9a0 --- /dev/null +++ b/recipes/bioconductor-agprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="agprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/agprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/agprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-agprobe/bioconductor-agprobe_2.18.0_src_all.tar.gz" +) +MD5="08f7527d4c8a30d8b2f86016a53f075a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-agprobe/pre-unlink.sh b/recipes/bioconductor-agprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3a4a4810687aa --- /dev/null +++ b/recipes/bioconductor-agprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ agprobe diff --git a/recipes/bioconductor-ahcytobands/meta.yaml b/recipes/bioconductor-ahcytobands/meta.yaml new file mode 100644 index 0000000000000..afc5050a6952f --- /dev/null +++ b/recipes/bioconductor-ahcytobands/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.99.0" %} +{% set name = "AHCytoBands" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87b801fe5699cae422a661711272c0a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Supplies AnnotationHub with CytoBand information from UCSC. There is a track for each major organism. Giemsa-stained bands are commonly used to decorate chromosomal overviews in visualizations of genomic data.' + diff --git a/recipes/bioconductor-ahcytobands/post-link.sh b/recipes/bioconductor-ahcytobands/post-link.sh new file mode 100644 index 0000000000000..06fe7624f755e --- /dev/null +++ b/recipes/bioconductor-ahcytobands/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AHCytoBands_0.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/AHCytoBands_0.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/AHCytoBands_0.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ahcytobands/bioconductor-ahcytobands_0.99.0_src_all.tar.gz" +) +MD5="87b801fe5699cae422a661711272c0a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ahcytobands/pre-unlink.sh b/recipes/bioconductor-ahcytobands/pre-unlink.sh new file mode 100644 index 0000000000000..f57517a22c2eb --- /dev/null +++ b/recipes/bioconductor-ahcytobands/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AHCytoBands diff --git a/recipes/bioconductor-ahensdbs/meta.yaml b/recipes/bioconductor-ahensdbs/meta.yaml new file mode 100644 index 0000000000000..a8c37920286d0 --- /dev/null +++ b/recipes/bioconductor-ahensdbs/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.8" %} +{% set name = "AHEnsDbs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a325efcf47764e6a2fd3945661016c17 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, AnnotationHub (>= 2.7.13) +requirements: + host: + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Supplies AnnotationHub with EnsDb Ensembl-based annotation databases for all species. EnsDb SQLite databases are generated separately from Ensembl MySQL databases using functions from the ensembldb package employing the Ensembl Perl API.' + diff --git a/recipes/bioconductor-ahensdbs/post-link.sh b/recipes/bioconductor-ahensdbs/post-link.sh new file mode 100644 index 0000000000000..3eb5320c7550f --- /dev/null +++ b/recipes/bioconductor-ahensdbs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AHEnsDbs_1.0.8.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/AHEnsDbs_1.0.8.tar.gz" + "https://bioarchive.galaxyproject.org/AHEnsDbs_1.0.8.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ahensdbs/bioconductor-ahensdbs_1.0.8_src_all.tar.gz" +) +MD5="a325efcf47764e6a2fd3945661016c17" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ahensdbs/pre-unlink.sh b/recipes/bioconductor-ahensdbs/pre-unlink.sh new file mode 100644 index 0000000000000..5399d6c93bfcc --- /dev/null +++ b/recipes/bioconductor-ahensdbs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AHEnsDbs diff --git a/recipes/bioconductor-aims/build.sh b/recipes/bioconductor-aims/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-aims/build.sh +++ b/recipes/bioconductor-aims/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aims/meta.yaml b/recipes/bioconductor-aims/meta.yaml index 62de11a8ae348..c0888345bc2ad 100644 --- a/recipes/bioconductor-aims/meta.yaml +++ b/recipes/bioconductor-aims/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "AIMS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 633ddb32cd9f751d3cfbaad515cbe5dc69cacec97a5024d8e43dde4f9d1225a6 + md5: 18bf55f45ea1074d8b125d9f540af410 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: breastCancerVDX, hgu133a.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package contains the AIMS implementation. It contains necessary functions to assign the five intrinsic molecular subtypes (Luminal A, Luminal B, Her2-enriched, Basal-like, Normal-like). Assignments could be done on individual samples as well as on dataset of gene expression data.' extra: identifiers: - biotools:aims - doi:10.1093/jnci/dju357 + parent_recipe: + name: bioconductor-aims + path: recipes/bioconductor-aims + version: 1.12.0 + diff --git a/recipes/bioconductor-airway/meta.yaml b/recipes/bioconductor-airway/meta.yaml new file mode 100644 index 0000000000000..45f30594abc1f --- /dev/null +++ b/recipes/bioconductor-airway/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2.0" %} +{% set name = "airway" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1b539cecd5b5a3b3550b659ec1f21b89 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, GEOquery +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package provides a RangedSummarizedExperiment object of read counts in genes for an RNA-Seq experiment on four human airway smooth muscle cell lines treated with dexamethasone. Details on the gene model and read counting procedure are provided in the package vignette. The citation for the experiment is: Himes BE, Jiang X, Wagner P, Hu R, Wang Q, Klanderman B, Whitaker RM, Duan Q, Lasky-Su J, Nikolos C, Jester W, Johnson M, Panettieri R Jr, Tantisira KG, Weiss ST, Lu Q. ''RNA-Seq Transcriptome Profiling Identifies CRISPLD2 as a Glucocorticoid Responsive Gene that Modulates Cytokine Function in Airway Smooth Muscle Cells.'' PLoS One. 2014 Jun 13;9(6):e99625. PMID: 24926665. GEO: GSE52778.' + diff --git a/recipes/bioconductor-airway/post-link.sh b/recipes/bioconductor-airway/post-link.sh new file mode 100644 index 0000000000000..c81a400d94cd4 --- /dev/null +++ b/recipes/bioconductor-airway/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="airway_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/airway_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/airway_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-airway/bioconductor-airway_1.2.0_src_all.tar.gz" +) +MD5="1b539cecd5b5a3b3550b659ec1f21b89" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-airway/pre-unlink.sh b/recipes/bioconductor-airway/pre-unlink.sh new file mode 100644 index 0000000000000..fcfd7e2b6780f --- /dev/null +++ b/recipes/bioconductor-airway/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ airway diff --git a/recipes/bioconductor-aldex2/build.sh b/recipes/bioconductor-aldex2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-aldex2/build.sh +++ b/recipes/bioconductor-aldex2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aldex2/meta.yaml b/recipes/bioconductor-aldex2/meta.yaml index a3cf135518c91..70229a6dbc71b 100644 --- a/recipes/bioconductor-aldex2/meta.yaml +++ b/recipes/bioconductor-aldex2/meta.yaml @@ -1,45 +1,52 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ALDEx2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0580de52ddb83195ed5c1938d64ddef3dbbb385677ba96605fa0c122ce244d4e + md5: c9538d59388ff431ba6ad0eb409b6247 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'A differential abundance analysis for the comparison of two or more conditions. Useful for analyzing data from standard RNA-seq or meta-RNA-seq assays as well as selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, optimized for three or more experimental replicates. The method infers biological and sampling variation to calculate the expected false discovery rate, given the variation, based on a Wilcox rank test or Welch t-test (via aldex.ttest), or a glm and Kruskal-Wallis test (via aldex.glm). Reports p-values and Benjamini-Hochberg corrected p-values.' extra: identifiers: - biotools:aldex2 + parent_recipe: + name: bioconductor-aldex2 + path: recipes/bioconductor-aldex2 + version: 1.12.0 + diff --git a/recipes/bioconductor-all/meta.yaml b/recipes/bioconductor-all/meta.yaml index 7d547d997efba..71b3660102990 100644 --- a/recipes/bioconductor-all/meta.yaml +++ b/recipes/bioconductor-all/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "ALL" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_{{ name|lower }}.tar.gz' - sha256: 329fab87700c03b8f82841782f3dbd8f1f578905539144afa128f1e39e71126b + md5: 815e7ffa1cb6eb8d71d29a5f450ff804 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: rpart requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Data of T- and B-cell Acute Lymphocytic Leukemia from the Ritz Laboratory at the DFCI (includes Apr 2004 versions)' - +extra: + parent_recipe: + name: bioconductor-all + path: recipes/bioconductor-all + version: 1.22.0 diff --git a/recipes/bioconductor-all/post-link.sh b/recipes/bioconductor-all/post-link.sh index ddbefaa54c10b..52efd5a566822 100644 --- a/recipes/bioconductor-all/post-link.sh +++ b/recipes/bioconductor-all/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ALL_1.22.0.tar.gz" +FN="ALL_1.24.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ALL_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/ALL_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ALL_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/ALL_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-all/bioconductor-all_1.24.0_src_all.tar.gz" ) -MD5="c762f0d3cce828ef717525c45832ab8c" +MD5="815e7ffa1cb6eb8d71d29a5f450ff804" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-allelicimbalance/build.sh b/recipes/bioconductor-allelicimbalance/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-allelicimbalance/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-allelicimbalance/meta.yaml b/recipes/bioconductor-allelicimbalance/meta.yaml new file mode 100644 index 0000000000000..597b3436bc087 --- /dev/null +++ b/recipes/bioconductor-allelicimbalance/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.20.0" %} +{% set name = "AllelicImbalance" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6a2b9b7e9957cf227690060862bd280c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-gridextra + - r-lattice + - r-latticeextra + - r-nlme + - r-seqinr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-gridextra + - r-lattice + - r-latticeextra + - r-nlme + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides a framework for allelic specific expression investigation using RNA-seq data.' + diff --git a/recipes/bioconductor-allenpvc/meta.yaml b/recipes/bioconductor-allenpvc/meta.yaml new file mode 100644 index 0000000000000..d2f86a5626605 --- /dev/null +++ b/recipes/bioconductor-allenpvc/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "allenpvc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e77a28b830842ee034930432e95fdfaf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: CC0 + summary: 'Celular taxonomy of the primary visual cortex in adult mice based on single cell RNA-sequencing from a study performed by the Allen Institute for Brain Science. In said study 49 transcriptomic cell types are identified.' + diff --git a/recipes/bioconductor-allenpvc/post-link.sh b/recipes/bioconductor-allenpvc/post-link.sh new file mode 100644 index 0000000000000..98f33105d04c2 --- /dev/null +++ b/recipes/bioconductor-allenpvc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="allenpvc_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/allenpvc_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/allenpvc_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-allenpvc/bioconductor-allenpvc_1.0.0_src_all.tar.gz" +) +MD5="e77a28b830842ee034930432e95fdfaf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-allenpvc/pre-unlink.sh b/recipes/bioconductor-allenpvc/pre-unlink.sh new file mode 100644 index 0000000000000..986f4d31ad538 --- /dev/null +++ b/recipes/bioconductor-allenpvc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ allenpvc diff --git a/recipes/bioconductor-allmll/meta.yaml b/recipes/bioconductor-allmll/meta.yaml new file mode 100644 index 0000000000000..a50031f6ba3bc --- /dev/null +++ b/recipes/bioconductor-allmll/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.22.0" %} +{% set name = "ALLMLL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fc9e850c94ac9ec9c377f5e8843e7673 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides probe-level data for 20 HGU133A and 20 HGU133B arrays which are a subset of arrays from a large ALL study. The data is for the MLL arrays. This data was published in Mary E. Ross, Xiaodong Zhou, Guangchun Song, Sheila A. Shurtleff, Kevin Girtman, W. Kent Williams, Hsi-Che Liu, Rami Mahfouz, Susana C. Raimondi, Noel Lenny, Anami Patel, and James R. Downing (2003) Classification of pediatric acute lymphoblastic leukemia by gene expression profiling Blood 102: 2951-2959' + diff --git a/recipes/bioconductor-allmll/post-link.sh b/recipes/bioconductor-allmll/post-link.sh new file mode 100644 index 0000000000000..f725e86035a27 --- /dev/null +++ b/recipes/bioconductor-allmll/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ALLMLL_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ALLMLL_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ALLMLL_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-allmll/bioconductor-allmll_1.22.0_src_all.tar.gz" +) +MD5="fc9e850c94ac9ec9c377f5e8843e7673" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-allmll/pre-unlink.sh b/recipes/bioconductor-allmll/pre-unlink.sh new file mode 100644 index 0000000000000..0e7130138282b --- /dev/null +++ b/recipes/bioconductor-allmll/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ALLMLL diff --git a/recipes/bioconductor-alpine/build.sh b/recipes/bioconductor-alpine/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-alpine/build.sh +++ b/recipes/bioconductor-alpine/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alpine/meta.yaml b/recipes/bioconductor-alpine/meta.yaml index 864d6079e47bb..bfe30b46fcdff 100644 --- a/recipes/bioconductor-alpine/meta.yaml +++ b/recipes/bioconductor-alpine/meta.yaml @@ -1,49 +1,51 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "alpine" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 42372a9247cde09da3b466b26a11e73b30f44e555e08210a0dbab67fb33e337a + md5: 2f5f6264027f585b0c8a25a7d90095a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat, alpineData, rtracklayer, ensembldb, BSgenome.Hsapiens.NCBI.GRCh38, RColorBrewer requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-speedglm - r-stringr run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-speedglm - r-stringr @@ -51,9 +53,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.' extra: identifiers: - biotools:alpine + parent_recipe: + name: bioconductor-alpine + path: recipes/bioconductor-alpine + version: 1.6.0 + diff --git a/recipes/bioconductor-alpinedata/meta.yaml b/recipes/bioconductor-alpinedata/meta.yaml new file mode 100644 index 0000000000000..af5d3c973159b --- /dev/null +++ b/recipes/bioconductor-alpinedata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.8.0" %} +{% set name = "alpineData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 56b8097bf76942789ec2694ad0fa51e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicAlignments, knitr +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'A small subset of paired-end RNA-seq reads from four samples of the GEUVADIS project.' + diff --git a/recipes/bioconductor-alpinedata/post-link.sh b/recipes/bioconductor-alpinedata/post-link.sh new file mode 100644 index 0000000000000..c06a2fe90d186 --- /dev/null +++ b/recipes/bioconductor-alpinedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="alpineData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/alpineData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/alpineData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alpinedata/bioconductor-alpinedata_1.8.0_src_all.tar.gz" +) +MD5="56b8097bf76942789ec2694ad0fa51e7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-alpinedata/pre-unlink.sh b/recipes/bioconductor-alpinedata/pre-unlink.sh new file mode 100644 index 0000000000000..f9d5c047414c2 --- /dev/null +++ b/recipes/bioconductor-alpinedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ alpineData diff --git a/recipes/bioconductor-alsace/build.sh b/recipes/bioconductor-alsace/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-alsace/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-alsace/meta.yaml b/recipes/bioconductor-alsace/meta.yaml new file mode 100644 index 0000000000000..ba72c0d0ef0c7 --- /dev/null +++ b/recipes/bioconductor-alsace/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.18.0" %} +{% set name = "alsace" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a26103b4ba914dab96374e4e7be3b78b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: lattice, knitr +requirements: + host: + - r-als + - r-base + - 'r-ptw >=1.0.6' + run: + - r-als + - r-base + - 'r-ptw >=1.0.6' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Alternating Least Squares (or Multivariate Curve Resolution) for analytical chemical data, in particular hyphenated data where the first direction is a retention time axis, and the second a spectral axis. Package builds on the basic als function from the ALS package and adds functionality for high-throughput analysis, including definition of time windows, clustering of profiles, retention time correction, etcetera.' + diff --git a/recipes/bioconductor-altcdfenvs/build.sh b/recipes/bioconductor-altcdfenvs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-altcdfenvs/build.sh +++ b/recipes/bioconductor-altcdfenvs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-altcdfenvs/conda_build_config.yaml b/recipes/bioconductor-altcdfenvs/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-altcdfenvs/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-altcdfenvs/meta.yaml b/recipes/bioconductor-altcdfenvs/meta.yaml index 36c2babbd3e96..dd1cf79935093 100644 --- a/recipes/bioconductor-altcdfenvs/meta.yaml +++ b/recipes/bioconductor-altcdfenvs/meta.yaml @@ -1,47 +1,54 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "altcdfenvs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ddba4b59069c284eea7b2ca54a9f1ed0c46dc514e64db4badeb43cdd5a4fea33 + md5: 3d5ddd23cc69e649a27a607a98d5d4dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: plasmodiumanophelescdf, hgu95acdf, hgu133aprobe, hgu133a.db, hgu133acdf, Rgraphviz, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-makecdfenv >=1.56.0,<1.58.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-makecdfenv >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-makecdfenv >=1.56.0,<1.58.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-makecdfenv >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Convenience data structures and functions to handle cdfenvs' extra: identifiers: - biotools:altcdfenvs + parent_recipe: + name: bioconductor-altcdfenvs + path: recipes/bioconductor-altcdfenvs + version: 2.42.0 + diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml new file mode 100644 index 0000000000000..574be0bd566f8 --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg19/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.1" %} +{% set name = "alternativeSplicingEvents.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e694353233e7d5d3abd22bfb5887513 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: data.frame, dplyr, GenomicRanges, S4Vectors +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.' + diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh b/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh new file mode 100644 index 0000000000000..c926ecd7596ea --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="alternativeSplicingEvents.hg19_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/alternativeSplicingEvents.hg19_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg19_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg19/bioconductor-alternativesplicingevents.hg19_1.0.1_src_all.tar.gz" +) +MD5="3e694353233e7d5d3abd22bfb5887513" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-alternativesplicingevents.hg19/pre-unlink.sh b/recipes/bioconductor-alternativesplicingevents.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..44843587cb29b --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ alternativeSplicingEvents.hg19 diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml new file mode 100644 index 0000000000000..a58a7d4bdab8f --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg38/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.1" %} +{% set name = "alternativeSplicingEvents.hg38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ce2e10cfe00ec4451670e1fd18d2e37 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: dplyr, GenomicRanges, S4Vectors +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Data frame containing alternative splicing events. The splicing events were compiled from the annotation files used by the alternative splicing quantification tools MISO, VAST-TOOLS, SUPPA and rMATS.' + diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh b/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh new file mode 100644 index 0000000000000..6e4e45d2d7b67 --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="alternativeSplicingEvents.hg38_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/alternativeSplicingEvents.hg38_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/alternativeSplicingEvents.hg38_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-alternativesplicingevents.hg38/bioconductor-alternativesplicingevents.hg38_1.0.1_src_all.tar.gz" +) +MD5="9ce2e10cfe00ec4451670e1fd18d2e37" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-alternativesplicingevents.hg38/pre-unlink.sh b/recipes/bioconductor-alternativesplicingevents.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..82b97d63c5523 --- /dev/null +++ b/recipes/bioconductor-alternativesplicingevents.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ alternativeSplicingEvents.hg38 diff --git a/recipes/bioconductor-amountain/build.sh b/recipes/bioconductor-amountain/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-amountain/build.sh +++ b/recipes/bioconductor-amountain/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-amountain/meta.yaml b/recipes/bioconductor-amountain/meta.yaml index cadeb659b66a5..7e5c0b42dede3 100644 --- a/recipes/bioconductor-amountain/meta.yaml +++ b/recipes/bioconductor-amountain/meta.yaml @@ -1,28 +1,28 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "AMOUNTAIN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 94d402f778f446eba3c9a75c6ebb8fb7443153652534e1911f1c761c9a0f2edd + md5: 394ae847017425e30abdaf18107b02b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, qgraph, knitr, rmarkdown +# SystemRequirements: gsl requirements: host: - r-base - - openblas run: - r-base - - openblas build: - {{ compiler('c') }} - make @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A pure data-driven gene network, weighted gene co-expression network (WGCN) could be constructed only from expression profile. Different layers in such networks may represent different time points, multiple conditions or various species. AMOUNTAIN aims to search active modules in multi-layer WGCN using a continuous optimization approach.' extra: identifiers: - biotools:amountain - doi:10.1101/056952 + parent_recipe: + name: bioconductor-amountain + path: recipes/bioconductor-amountain + version: 1.6.0 + diff --git a/recipes/bioconductor-ampaffyexample/meta.yaml b/recipes/bioconductor-ampaffyexample/meta.yaml new file mode 100644 index 0000000000000..30d81a0845bf1 --- /dev/null +++ b/recipes/bioconductor-ampaffyexample/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.22.0" %} +{% set name = "AmpAffyExample" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89fc3d6d5cff3852ec8b8748898bf8af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: hgu133acdf +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'Six arrays. Three from amplified RNA, three from the typical procedure.' + diff --git a/recipes/bioconductor-ampaffyexample/post-link.sh b/recipes/bioconductor-ampaffyexample/post-link.sh new file mode 100644 index 0000000000000..dfeecc7c3b58c --- /dev/null +++ b/recipes/bioconductor-ampaffyexample/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AmpAffyExample_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AmpAffyExample_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/AmpAffyExample_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ampaffyexample/bioconductor-ampaffyexample_1.22.0_src_all.tar.gz" +) +MD5="89fc3d6d5cff3852ec8b8748898bf8af" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ampaffyexample/pre-unlink.sh b/recipes/bioconductor-ampaffyexample/pre-unlink.sh new file mode 100644 index 0000000000000..8e5b863a6bd0c --- /dev/null +++ b/recipes/bioconductor-ampaffyexample/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AmpAffyExample diff --git a/recipes/bioconductor-amplican/build.sh b/recipes/bioconductor-amplican/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-amplican/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-amplican/meta.yaml b/recipes/bioconductor-amplican/meta.yaml new file mode 100644 index 0000000000000..90545d0347209 --- /dev/null +++ b/recipes/bioconductor-amplican/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.4.0" %} +{% set name = "amplican" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 10c9662fb6df49f5d796ae7a40287749 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, GenomicAlignments +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - 'r-clustercrit >=1.2.7' + - 'r-data.table >=1.10.4-3' + - 'r-dplyr >=0.7.2' + - 'r-ggforce >=0.1.2' + - 'r-ggplot2 >=2.2.0' + - 'r-ggthemes >=3.4.0' + - 'r-gridextra >=2.2.1' + - 'r-gtable >=0.2.0' + - 'r-knitr >=1.16' + - 'r-matrix >=1.2-10' + - 'r-matrixstats >=0.52.2' + - 'r-rmarkdown >=1.6' + - 'r-stringr >=1.2.0' + - 'r-waffle >=0.7.0' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - 'r-clustercrit >=1.2.7' + - 'r-data.table >=1.10.4-3' + - 'r-dplyr >=0.7.2' + - 'r-ggforce >=0.1.2' + - 'r-ggplot2 >=2.2.0' + - 'r-ggthemes >=3.4.0' + - 'r-gridextra >=2.2.1' + - 'r-gtable >=0.2.0' + - 'r-knitr >=1.16' + - 'r-matrix >=1.2-10' + - 'r-matrixstats >=0.52.2' + - 'r-rmarkdown >=1.6' + - 'r-stringr >=1.2.0' + - 'r-waffle >=0.7.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: '`amplican` performs alignment of the amplicon reads, normalizes gathered data, calculates multiple statistics (e.g. cut rates, frameshifts) and presents results in form of aggregated reports. Data and statistics can be broken down by experiments, barcodes, user defined groups, guides and amplicons allowing for quick identification of potential problems.' + diff --git a/recipes/bioconductor-ampliqueso/build.sh b/recipes/bioconductor-ampliqueso/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ampliqueso/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ampliqueso/meta.yaml b/recipes/bioconductor-ampliqueso/meta.yaml new file mode 100644 index 0000000000000..1b420a3438f7f --- /dev/null +++ b/recipes/bioconductor-ampliqueso/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.20.0" %} +{% set name = "ampliQueso" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 568c03956831cb1c2af20d9c8c78f0a0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-rnaseqmap >=2.40.0,<2.41.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gplots + - r-knitr + - r-rgl + - r-samr + - r-statmod + - r-xtable + run: + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-rnaseqmap >=2.40.0,<2.41.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gplots + - r-knitr + - r-rgl + - r-samr + - r-statmod + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq' + diff --git a/recipes/bioconductor-analysispageserver/build.sh b/recipes/bioconductor-analysispageserver/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-analysispageserver/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-analysispageserver/meta.yaml b/recipes/bioconductor-analysispageserver/meta.yaml new file mode 100644 index 0000000000000..3e67c394a509f --- /dev/null +++ b/recipes/bioconductor-analysispageserver/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.16.0" %} +{% set name = "AnalysisPageServer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 85095095c94e346b6c74c85b3a8ee6dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, XML, knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-log4r + - r-rjson + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-log4r + - r-rjson + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AnalysisPageServer is a modular system that enables sharing of customizable R analyses via the web.' + diff --git a/recipes/bioconductor-anamir/build.sh b/recipes/bioconductor-anamir/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anamir/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anamir/meta.yaml b/recipes/bioconductor-anamir/meta.yaml new file mode 100644 index 0000000000000..e187018ff2244 --- /dev/null +++ b/recipes/bioconductor-anamir/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.10.0" %} +{% set name = "anamiR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0743887caa63267607e4165602f90951 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, data.table +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-gage >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-agricolae + - r-base + - r-dbi + - r-gplots + - r-rmysql + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-gage >=2.32.0,<2.33.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-agricolae + - r-base + - r-dbi + - r-gplots + - r-rmysql +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package is intended to identify potential interactions of miRNA-target gene interactions from miRNA and mRNA expression data. It contains functions for statistical test, databases of miRNA-target gene interaction and functional analysis.' + diff --git a/recipes/bioconductor-anaquin/build.sh b/recipes/bioconductor-anaquin/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anaquin/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anaquin/meta.yaml b/recipes/bioconductor-anaquin/meta.yaml new file mode 100644 index 0000000000000..33d9502ce3ccf --- /dev/null +++ b/recipes/bioconductor-anaquin/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "2.6.0" %} +{% set name = "Anaquin" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8f1bc0e8a7c1e4762e4c561b8461f068 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, rmarkdown +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - 'r-ggplot2 >=2.2.0' + - r-knitr + - r-locfit + - r-plyr + - r-rocr + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - 'r-ggplot2 >=2.2.0' + - r-knitr + - r-locfit + - r-plyr + - r-rocr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'The project is intended to support the use of sequins (synthetic sequencing spike-in controls) owned and made available by the Garvan Institute of Medical Research. The goal is to provide a standard open source library for quantitative analysis, modelling and visualization of spike-in controls.' + diff --git a/recipes/bioconductor-aneufinder/build.sh b/recipes/bioconductor-aneufinder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-aneufinder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aneufinder/meta.yaml b/recipes/bioconductor-aneufinder/meta.yaml new file mode 100644 index 0000000000000..2df5118ba3de4 --- /dev/null +++ b/recipes/bioconductor-aneufinder/meta.yaml @@ -0,0 +1,76 @@ +{% set version = "1.10.1" %} +{% set name = "AneuFinder" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aef30798edd6bd379f288ef13dce3cc8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, BiocStyle, testthat, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 +requirements: + host: + - 'bioconductor-aneufinderdata >=1.10.0,<1.11.0' + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-cowplot + - r-doparallel + - r-ecp + - r-foreach + - r-ggdendro + - r-ggplot2 + - r-ggrepel + - r-mclust + - r-reordercluster + - r-reshape2 + run: + - 'bioconductor-aneufinderdata >=1.10.0,<1.11.0' + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-cowplot + - r-doparallel + - r-ecp + - r-foreach + - r-ggdendro + - r-ggplot2 + - r-ggrepel + - r-mclust + - r-reordercluster + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'AneuFinder implements functions for copy-number detection, breakpoint detection, and karyotype and heterogeneity analysis in single-cell whole genome sequencing and strand-seq data.' + diff --git a/recipes/bioconductor-aneufinderdata/meta.yaml b/recipes/bioconductor-aneufinderdata/meta.yaml new file mode 100644 index 0000000000000..6240769b088de --- /dev/null +++ b/recipes/bioconductor-aneufinderdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.10.0" %} +{% set name = "AneuFinderData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aeee3783942cb420cfb1a39dbbe1b9cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Whole-genome single cell sequencing data for demonstration purposes in the AneuFinder package.' + diff --git a/recipes/bioconductor-aneufinderdata/post-link.sh b/recipes/bioconductor-aneufinderdata/post-link.sh new file mode 100644 index 0000000000000..aaaaf625be0f2 --- /dev/null +++ b/recipes/bioconductor-aneufinderdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AneuFinderData_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AneuFinderData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/AneuFinderData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-aneufinderdata/bioconductor-aneufinderdata_1.10.0_src_all.tar.gz" +) +MD5="aeee3783942cb420cfb1a39dbbe1b9cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-aneufinderdata/pre-unlink.sh b/recipes/bioconductor-aneufinderdata/pre-unlink.sh new file mode 100644 index 0000000000000..10890c69f9213 --- /dev/null +++ b/recipes/bioconductor-aneufinderdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AneuFinderData diff --git a/recipes/bioconductor-anf/build.sh b/recipes/bioconductor-anf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anf/meta.yaml b/recipes/bioconductor-anf/meta.yaml new file mode 100644 index 0000000000000..15c18397f9b07 --- /dev/null +++ b/recipes/bioconductor-anf/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "ANF" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 78709ee747b31ed759c515fd36ae9960 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ExperimentHub, SNFtool, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-igraph + - r-mass + - r-rcolorbrewer + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-igraph + - r-mass + - r-rcolorbrewer + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package is used for complex patient clustering by integrating multi-omic data through affinity network fusion.' + diff --git a/recipes/bioconductor-annaffy/build.sh b/recipes/bioconductor-annaffy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annaffy/build.sh +++ b/recipes/bioconductor-annaffy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annaffy/meta.yaml b/recipes/bioconductor-annaffy/meta.yaml index f0365ca0d2535..ee605741c842a 100644 --- a/recipes/bioconductor-annaffy/meta.yaml +++ b/recipes/bioconductor-annaffy/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "annaffy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a981787b7c682d2a65ef5001d2417038e401f24e3a8796b05c7ff33fcc376a72 + md5: 1417af7e94aa576c88bb823ac42e6f9e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db, multtest, tcltk requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-dbi test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for handling data from Bioconductor Affymetrix annotation data packages. Produces compact HTML and text reports including experimental data and URL links to many online databases. Allows searching biological metadata using various criteria.' extra: identifiers: - biotools:annaffy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annaffy + path: recipes/bioconductor-annaffy + version: 1.52.0 + diff --git a/recipes/bioconductor-annmap/build.sh b/recipes/bioconductor-annmap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annmap/build.sh +++ b/recipes/bioconductor-annmap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annmap/meta.yaml b/recipes/bioconductor-annmap/meta.yaml index 42c68a1e87e3a..bc8906fc165a3 100644 --- a/recipes/bioconductor-annmap/meta.yaml +++ b/recipes/bioconductor-annmap/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "annmap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 60b56b634842ceafdbb54aa6d89e00fd082ad93a96d0793544fb7e53e14031af + md5: 004c0c2fc7fe6be4898c97449f568b62 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, rjson, Gviz requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-dbi - r-digest - r-lattice - 'r-rmysql >=0.6-0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-dbi - r-digest @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'annmap provides annotation mappings for Affymetrix exon arrays and coordinate based queries to support deep sequencing data analysis. Database access is hidden behind the API which provides a set of functions such as genesInRange(), geneToExon(), exonDetails(), etc. Functions to plot gene architecture and BAM file data are also provided. Underlying data are from Ensembl.' extra: identifiers: - biotools:annmap - doi:10.1093/nar/gkm779 + parent_recipe: + name: bioconductor-annmap + path: recipes/bioconductor-annmap + version: 1.22.0 + diff --git a/recipes/bioconductor-annotate/build.sh b/recipes/bioconductor-annotate/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotate/build.sh +++ b/recipes/bioconductor-annotate/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotate/meta.yaml b/recipes/bioconductor-annotate/meta.yaml index 5ff04c8078f1f..bc5133133297c 100644 --- a/recipes/bioconductor-annotate/meta.yaml +++ b/recipes/bioconductor-annotate/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "annotate" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4e3234694c5f1b2713b64e0e548e1e9a4d21d02d24e638280dea90e0b767b6e2 + md5: ffa9213f171f22054d4e323f0c1bf99d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db, genefilter, Biostrings (>= 2.25.10), IRanges, rae230a.db, rae230aprobe, tkWidgets, GO.db, org.Hs.eg.db, org.Mm.eg.db, hom.Hs.inp.db, humanCHRLOC, Rgraphviz, RUnit, requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-dbi - r-rcurl - r-xml - r-xtable run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-dbi - r-rcurl @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Using R enviroments for annotation.' extra: identifiers: - biotools:annotate - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotate + path: recipes/bioconductor-annotate + version: 1.58.0 + diff --git a/recipes/bioconductor-annotationdbi/build.sh b/recipes/bioconductor-annotationdbi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationdbi/build.sh +++ b/recipes/bioconductor-annotationdbi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationdbi/meta.yaml b/recipes/bioconductor-annotationdbi/meta.yaml index 454a2688e63ec..f562b0826bd17 100644 --- a/recipes/bioconductor-annotationdbi/meta.yaml +++ b/recipes/bioconductor-annotationdbi/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.42.1" %} +{% set version = "1.44.0" %} {% set name = "AnnotationDbi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2c2ce448f8512e9b9247dc1f1e2e8da6f53c7e8637e52bb200782310e95fd329 + md5: 65b98cea76650046e4287a093092269a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db, GO.db, org.Sc.sgd.db, org.At.tair.db, KEGG.db, RUnit, TxDb.Hsapiens.UCSC.hg19.knownGene, hom.Hs.inp.db, org.Hs.eg.db, reactome.db, AnnotationForge, graph, EnsDb.Hsapiens.v75, BiocStyle, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-rsqlite @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides user interface and database connection code for annotation data packages using SQLite data storage.' extra: identifiers: - biotools:annotationdbi - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationdbi + path: recipes/bioconductor-annotationdbi + version: 1.42.1 + diff --git a/recipes/bioconductor-annotationfilter/build.sh b/recipes/bioconductor-annotationfilter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationfilter/build.sh +++ b/recipes/bioconductor-annotationfilter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationfilter/meta.yaml b/recipes/bioconductor-annotationfilter/meta.yaml index 9b5266d8bf890..bad6ae7e2302b 100644 --- a/recipes/bioconductor-annotationfilter/meta.yaml +++ b/recipes/bioconductor-annotationfilter/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "AnnotationFilter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ac95ad4d99b3cdea41a085926b0c791298eea6512da9d1db7fb3cf29bbb1ef1 + md5: 607d1a6cc3e97499cb79ff01e24f03c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat, RSQLite, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-lazyeval run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-lazyeval test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides class and other infrastructure to implement filters for manipulating Bioconductor annotation resources. The filters will be used by ensembldb, Organism.dplyr, and other packages.' - +extra: + parent_recipe: + name: bioconductor-annotationfilter + path: recipes/bioconductor-annotationfilter + version: 1.4.0 diff --git a/recipes/bioconductor-annotationforge/build.sh b/recipes/bioconductor-annotationforge/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationforge/build.sh +++ b/recipes/bioconductor-annotationforge/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationforge/meta.yaml b/recipes/bioconductor-annotationforge/meta.yaml index bb3c506b132ed..f1130276e6f62 100644 --- a/recipes/bioconductor-annotationforge/meta.yaml +++ b/recipes/bioconductor-annotationforge/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.22.2" %} +{% set version = "1.24.0" %} {% set name = "AnnotationForge" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f92570578af4c8b025e696198c58adb5f97c108f4c662f0b37d2fbbbedf1759e + md5: 2f5509af2751bdbc94f0f08b2ec6950e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, httr, GenomeInfoDb (>= 1.17.1), Biostrings, affy, hgu95av2.db, human.db0, org.Hs.eg.db, Homo.sapiens, hom.Hs.inp.db, GO.db, BiocStyle, knitr, BiocManager requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-rcurl - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dbi - r-rcurl @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides code for generating Annotation packages and their databases. Packages produced are intended to be used with AnnotationDbi.' extra: identifiers: - biotools:annotationforge - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationforge + path: recipes/bioconductor-annotationforge + version: 1.22.2 + diff --git a/recipes/bioconductor-annotationfuncs/build.sh b/recipes/bioconductor-annotationfuncs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationfuncs/build.sh +++ b/recipes/bioconductor-annotationfuncs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationfuncs/meta.yaml b/recipes/bioconductor-annotationfuncs/meta.yaml index df43fc0ca40ed..e88a768e1eb90 100644 --- a/recipes/bioconductor-annotationfuncs/meta.yaml +++ b/recipes/bioconductor-annotationfuncs/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "AnnotationFuncs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3cf31a5ae8258c5734345b65b9f3cc707405ac811c105e6b09d0c61dd999c0a8 + md5: 80fb2ac0e0b19ff0abdce58fc2c53933 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Bt.eg.db, GO.db, org.Hs.eg.db, hom.Hs.inp.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions for handling translating between different identifieres using the Biocore Data Team data-packages (e.g. org.Bt.eg.db).' extra: identifiers: - biotools:annotationfuncs - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationfuncs + path: recipes/bioconductor-annotationfuncs + version: 1.30.0 + diff --git a/recipes/bioconductor-annotationhub/build.sh b/recipes/bioconductor-annotationhub/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationhub/build.sh +++ b/recipes/bioconductor-annotationhub/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationhub/conda_build_config.yaml b/recipes/bioconductor-annotationhub/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-annotationhub/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-annotationhub/meta.yaml b/recipes/bioconductor-annotationhub/meta.yaml index 21f5b0a0b1e22..31999e10b97ea 100644 --- a/recipes/bioconductor-annotationhub/meta.yaml +++ b/recipes/bioconductor-annotationhub/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "2.12.1" %} +{% set version = "2.14.2" %} {% set name = "AnnotationHub" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cf58bade5dd676504108fbad9248dcdf6306e9e613f17d48808ce230d3119a0a + md5: 2a7eb910fdde802fbbdf5e126368971b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: IRanges, GenomicRanges, GenomeInfoDb, VariantAnnotation, Rsamtools, rtracklayer, BiocStyle, knitr, AnnotationForge, rBiopaxParser, RUnit, GenomicFeatures, MSnbase, mzR, Biostrings, SummarizedExperiment, ExperimentHub, gdsfmt requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-curl - r-httr - r-rsqlite - r-yaml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-curl - r-httr - r-rsqlite @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a client for the Bioconductor AnnotationHub web resource. The AnnotationHub web resource provides a central location where genomic files (e.g., VCF, bed, wig) and other resources from standard locations (e.g., UCSC, Ensembl) can be discovered. The resource includes metadata about each resource, e.g., a textual description, tags, and date of modification. The client creates and manages a local cache of files retrieved by the user, helping with quick and reproducible access.' extra: identifiers: - biotools:annotationhub - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationhub + path: recipes/bioconductor-annotationhub + version: 2.12.1 + diff --git a/recipes/bioconductor-annotationhubdata/build.sh b/recipes/bioconductor-annotationhubdata/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationhubdata/build.sh +++ b/recipes/bioconductor-annotationhubdata/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationhubdata/conda_build_config.yaml b/recipes/bioconductor-annotationhubdata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-annotationhubdata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-annotationhubdata/meta.yaml b/recipes/bioconductor-annotationhubdata/meta.yaml index 95bb9f5a7e5e2..16a36b2d552bd 100644 --- a/recipes/bioconductor-annotationhubdata/meta.yaml +++ b/recipes/bioconductor-annotationhubdata/meta.yaml @@ -1,42 +1,43 @@ -{% set version = "1.10.3" %} +{% set version = "1.12.0" %} {% set name = "AnnotationHubData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e91b48c7db39456601090dd66e6209023e849a2ccc0d49acab63b066806163f3 + md5: 523c97f501f82a3ea206a80e4d99c3e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, knitr, BiocStyle, grasp2db, GenomeInfoDbData requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationforge >=1.22.2,<1.24.0' - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-dbi - 'r-futile.logger >=1.3.0' - r-jsonlite @@ -44,25 +45,24 @@ requirements: - r-rsqlite - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationforge >=1.22.2,<1.24.0' - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-dbi - 'r-futile.logger >=1.3.0' - r-jsonlite @@ -73,10 +73,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'These recipes convert a wide variety and a growing number of public bioinformatic data sets into easily-used standard Bioconductor data structures.' extra: identifiers: - biotools:annotationhubdata - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-annotationhubdata + path: recipes/bioconductor-annotationhubdata + version: 1.10.3 + diff --git a/recipes/bioconductor-annotationtools/build.sh b/recipes/bioconductor-annotationtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-annotationtools/build.sh +++ b/recipes/bioconductor-annotationtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotationtools/meta.yaml b/recipes/bioconductor-annotationtools/meta.yaml index 9b20d11433e18..fe0cc657d1862 100644 --- a/recipes/bioconductor-annotationtools/meta.yaml +++ b/recipes/bioconductor-annotationtools/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "annotationTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 48894ee4377fe07205f98b7de47e5e246a5efcc1754a53ee2ea7a2d8c6518342 + md5: 9371efaf0751aa8d26710245cba18825 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Functions to annotate microarrays, find orthologs, and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file database (plain text files).' extra: identifiers: - biotools:annotationtools + parent_recipe: + name: bioconductor-annotationtools + path: recipes/bioconductor-annotationtools + version: 1.54.0 + diff --git a/recipes/bioconductor-annotatr/build.sh b/recipes/bioconductor-annotatr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-annotatr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-annotatr/meta.yaml b/recipes/bioconductor-annotatr/meta.yaml new file mode 100644 index 0000000000000..3c10b576a5f7a --- /dev/null +++ b/recipes/bioconductor-annotatr/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.8.0" %} +{% set name = "annotatr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e91b2cc81be539c201d2c518d37b764f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, devtools, knitr, org.Dm.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, rmarkdown, roxygen2, testthat, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Ggallus.UCSC.galGal5.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-readr + - r-reshape2 + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-readr + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Given a set of genomic sites/regions (e.g. ChIP-seq peaks, CpGs, differentially methylated CpGs or regions, SNPs, etc.) it is often of interest to investigate the intersecting genomic annotations. Such annotations include those relating to gene models (promoters, 5''UTRs, exons, introns, and 3''UTRs), CpGs (CpG islands, CpG shores, CpG shelves), or regulatory sequences such as enhancers. The annotatr package provides an easy way to summarize and visualize the intersection of genomic sites/regions with genomic annotations.' + diff --git a/recipes/bioconductor-anopheles.db0/meta.yaml b/recipes/bioconductor-anopheles.db0/meta.yaml new file mode 100644 index 0000000000000..098d9ce54a397 --- /dev/null +++ b/recipes/bioconductor-anopheles.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "anopheles.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c19b72aa3fa5aaefa84b3abf3cd5c303 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for anopheles, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-anopheles.db0/post-link.sh b/recipes/bioconductor-anopheles.db0/post-link.sh new file mode 100644 index 0000000000000..efe7988fa0ff1 --- /dev/null +++ b/recipes/bioconductor-anopheles.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="anopheles.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/anopheles.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/anopheles.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-anopheles.db0/bioconductor-anopheles.db0_3.7.1_src_all.tar.gz" +) +MD5="c19b72aa3fa5aaefa84b3abf3cd5c303" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-anopheles.db0/pre-unlink.sh b/recipes/bioconductor-anopheles.db0/pre-unlink.sh new file mode 100644 index 0000000000000..43e3eb2a62fa6 --- /dev/null +++ b/recipes/bioconductor-anopheles.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ anopheles.db0 diff --git a/recipes/bioconductor-anota/build.sh b/recipes/bioconductor-anota/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-anota/build.sh +++ b/recipes/bioconductor-anota/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anota/meta.yaml b/recipes/bioconductor-anota/meta.yaml index 224b317675b6f..0c3f57ac7a038 100644 --- a/recipes/bioconductor-anota/meta.yaml +++ b/recipes/bioconductor-anota/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "anota" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 275fb5af3c9d8dce6fe1fb2e5b5b402d7ebac2b7e9260fd7b206b96098dbf726 + md5: c3cc7015b78f0b9283107019ce4fd4ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Genome wide studies of translational control is emerging as a tool to study verious biological conditions. The output from such analysis is both the mRNA level (e.g. cytosolic mRNA level) and the levl of mRNA actively involved in translation (the actively translating mRNA level) for each mRNA. The standard analysis of such data strives towards identifying differential translational between two or more sample classes - i.e. differences in actively translated mRNA levels that are independent of underlying differences in cytosolic mRNA levels. This package allows for such analysis using partial variances and the random variance model. As 10s of thousands of mRNAs are analyzed in parallell the library performs a number of tests to assure that the data set is suitable for such analysis.' extra: identifiers: - biotools:anota - doi:10.1093/bioinformatics/btr146 + parent_recipe: + name: bioconductor-anota + path: recipes/bioconductor-anota + version: 1.28.0 + diff --git a/recipes/bioconductor-anota2seq/build.sh b/recipes/bioconductor-anota2seq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-anota2seq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-anota2seq/meta.yaml b/recipes/bioconductor-anota2seq/meta.yaml new file mode 100644 index 0000000000000..f0171ad91ed6e --- /dev/null +++ b/recipes/bioconductor-anota2seq/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.0" %} +{% set name = "anota2seq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5841a54f1413e576c45b5aec77d03c98 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle,knitr +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rcolorbrewer + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'anota2seq provides analysis of translational efficiency and differential expression analysis for polysome-profiling and ribosome-profiling studies (two or more sample classes) quantified by RNA sequencing or DNA-microarray. Polysome-profiling and ribosome-profiling typically generate data for two RNA sources; translated mRNA and total mRNA. Analysis of differential expression is used to estimate changes within each RNA source (i.e. translated mRNA or total mRNA). Analysis of translational efficiency aims to identify changes in translation efficiency leading to altered protein levels that are independent of total mRNA levels (i.e. changes in translated mRNA that are independent of levels of total mRNA) or buffering, a mechanism regulating translational efficiency so that protein levels remain constant despite fluctuating total mRNA levels (i.e. changes in total mRNA that are independent of levels of translated mRNA). anota2seq applies analysis of partial variance and the random variance model to fulfill these tasks.' + diff --git a/recipes/bioconductor-antiprofiles/build.sh b/recipes/bioconductor-antiprofiles/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-antiprofiles/build.sh +++ b/recipes/bioconductor-antiprofiles/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-antiprofiles/meta.yaml b/recipes/bioconductor-antiprofiles/meta.yaml index 9aa2c0f3baf78..cf16d177f6200 100644 --- a/recipes/bioconductor-antiprofiles/meta.yaml +++ b/recipes/bioconductor-antiprofiles/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "antiProfiles" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d40b1a3f3495b3b1ed59f05253c88b3caa78ad845e16ad5154bfdc1907456d99 + md5: 5f45e664940f6ea8925cb91e62f3e6e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: antiProfilesData, RColorBrewer requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Implements gene expression anti-profiles as described in Corrada Bravo et al., BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272.' extra: identifiers: - biotools:antiprofiles - doi:10.1186/1471-2105-13-272 + parent_recipe: + name: bioconductor-antiprofiles + path: recipes/bioconductor-antiprofiles + version: 1.20.0 + diff --git a/recipes/bioconductor-antiprofilesdata/meta.yaml b/recipes/bioconductor-antiprofilesdata/meta.yaml new file mode 100644 index 0000000000000..8a06586e49aff --- /dev/null +++ b/recipes/bioconductor-antiprofilesdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "antiProfilesData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6db261abb425b57ede7976f9b0a0ca90 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: frma, GEOquery, GEOmetadb +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Colon normal tissue and cancer samples used in Corrada Bravo, et al. gene expression anti-profiles paper: BMC Bioinformatics 2012, 13:272 doi:10.1186/1471-2105-13-272. Measurements are z-scores obtained from the GeneExpression Barcode in the ''frma'' package' + diff --git a/recipes/bioconductor-antiprofilesdata/post-link.sh b/recipes/bioconductor-antiprofilesdata/post-link.sh new file mode 100644 index 0000000000000..93eda78912940 --- /dev/null +++ b/recipes/bioconductor-antiprofilesdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="antiProfilesData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/antiProfilesData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/antiProfilesData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-antiprofilesdata/bioconductor-antiprofilesdata_1.18.0_src_all.tar.gz" +) +MD5="6db261abb425b57ede7976f9b0a0ca90" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-antiprofilesdata/pre-unlink.sh b/recipes/bioconductor-antiprofilesdata/pre-unlink.sh new file mode 100644 index 0000000000000..bf51213a57515 --- /dev/null +++ b/recipes/bioconductor-antiprofilesdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ antiProfilesData diff --git a/recipes/bioconductor-apcomplex/build.sh b/recipes/bioconductor-apcomplex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-apcomplex/build.sh +++ b/recipes/bioconductor-apcomplex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-apcomplex/meta.yaml b/recipes/bioconductor-apcomplex/meta.yaml index f0d24c1cccf1a..7ea71bf3ed35b 100644 --- a/recipes/bioconductor-apcomplex/meta.yaml +++ b/recipes/bioconductor-apcomplex/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "apComplex" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 805d761773a9494b6904c9af82b9246259471fbf24ddb3a16709716673c80610 + md5: 82bb7fd1f58e41e1479feac11932084b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions to estimate a bipartite graph of protein complex membership using AP-MS data.' extra: identifiers: - biotools:apcomplex - doi:10.1093/bioinformatics/bti567 + parent_recipe: + name: bioconductor-apcomplex + path: recipes/bioconductor-apcomplex + version: 2.46.0 + diff --git a/recipes/bioconductor-apeglm/build.sh b/recipes/bioconductor-apeglm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-apeglm/build.sh +++ b/recipes/bioconductor-apeglm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-apeglm/meta.yaml b/recipes/bioconductor-apeglm/meta.yaml index 0328e89e91a41..af0e48b9f6e7e 100644 --- a/recipes/bioconductor-apeglm/meta.yaml +++ b/recipes/bioconductor-apeglm/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.1" %} {% set name = "apeglm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecdf6d18246532d74973ed8eb1262d6451dbd7656710164e9a17b1f3fd5391ca + md5: 9ea5ccdba700813f59686a9fef116c26 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: DESeq2, airway, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-emdbook - r-rcpp - r-rcppeigen - r-rcppnumerical run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-emdbook - r-rcpp @@ -41,8 +42,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'apeglm provides Bayesian shrinkage estimators for effect sizes for a variety of GLM models, using approximation of the posterior for individual coefficients.' - +extra: + parent_recipe: + name: bioconductor-apeglm + path: recipes/bioconductor-apeglm + version: 1.2.1 diff --git a/recipes/bioconductor-appreci8r/build.sh b/recipes/bioconductor-appreci8r/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-appreci8r/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-appreci8r/meta.yaml b/recipes/bioconductor-appreci8r/meta.yaml new file mode 100644 index 0000000000000..55c526695043c --- /dev/null +++ b/recipes/bioconductor-appreci8r/meta.yaml @@ -0,0 +1,93 @@ +{% set version = "1.0.0" %} +{% set name = "appreci8R" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 425813a17e39960bc786393fbf3ac7ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GO.db, org.Hs.eg.db +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-cosmic.67 >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' + - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - r-base + - r-dt + - r-openxlsx + - r-rentrez + - r-rsnps + - r-seqinr + - r-shiny + - r-shinyjs + - r-stringr + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-cosmic.67 >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mafdb.1kgenomes.phase3.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.exac.r1.0.hs37d5 >=3.7.0,<3.8.0' + - 'bioconductor-mafdb.gnomadex.r2.0.1.hs37d5 >=3.8.0,<3.9.0' + - 'bioconductor-polyphen.hsapiens.dbsnp131 >=1.0.0,<1.1.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sift.hsapiens.dbsnp137 >=1.0.0,<1.1.0' + - 'bioconductor-snplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37 >=0.99.0,<0.100.0' + - r-base + - r-dt + - r-openxlsx + - r-rentrez + - r-rsnps + - r-seqinr + - r-shiny + - r-shinyjs + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'The appreci8R is an R version of our appreci8-algorithm - A Pipeline for PREcise variant Calling Integrating 8 tools. Variant calling results of our standard appreci8-tools (GATK, Platypus, VarScan, FreeBayes, LoFreq, SNVer, samtools and VarDict), as well as up to 5 additional tools is combined, evaluated and filtered.' + diff --git a/recipes/bioconductor-arabidopsis.db0/meta.yaml b/recipes/bioconductor-arabidopsis.db0/meta.yaml new file mode 100644 index 0000000000000..a84d7b2e2d56a --- /dev/null +++ b/recipes/bioconductor-arabidopsis.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "arabidopsis.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1366b9a8107e13d674be15d742537f2a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for arabidopsis, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-arabidopsis.db0/post-link.sh b/recipes/bioconductor-arabidopsis.db0/post-link.sh new file mode 100644 index 0000000000000..ac39216e6583f --- /dev/null +++ b/recipes/bioconductor-arabidopsis.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="arabidopsis.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/arabidopsis.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/arabidopsis.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-arabidopsis.db0/bioconductor-arabidopsis.db0_3.7.1_src_all.tar.gz" +) +MD5="1366b9a8107e13d674be15d742537f2a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-arabidopsis.db0/pre-unlink.sh b/recipes/bioconductor-arabidopsis.db0/pre-unlink.sh new file mode 100644 index 0000000000000..ef09dd83efae7 --- /dev/null +++ b/recipes/bioconductor-arabidopsis.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ arabidopsis.db0 diff --git a/recipes/bioconductor-aracne.networks/meta.yaml b/recipes/bioconductor-aracne.networks/meta.yaml new file mode 100644 index 0000000000000..11203b2eba781 --- /dev/null +++ b/recipes/bioconductor-aracne.networks/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.8.0" %} +{% set name = "aracne.networks" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1dd61303e99861938db45495480b8dea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package contains ARACNe-inferred networks from TCGA tumor datasets. It also contains a function to export them into plain-text format.' + diff --git a/recipes/bioconductor-aracne.networks/post-link.sh b/recipes/bioconductor-aracne.networks/post-link.sh new file mode 100644 index 0000000000000..87e22c1ba0a6d --- /dev/null +++ b/recipes/bioconductor-aracne.networks/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="aracne.networks_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/aracne.networks_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/aracne.networks_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-aracne.networks/bioconductor-aracne.networks_1.8.0_src_all.tar.gz" +) +MD5="1dd61303e99861938db45495480b8dea" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-aracne.networks/pre-unlink.sh b/recipes/bioconductor-aracne.networks/pre-unlink.sh new file mode 100644 index 0000000000000..9fb983ae2a2da --- /dev/null +++ b/recipes/bioconductor-aracne.networks/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ aracne.networks diff --git a/recipes/bioconductor-aroma.light/build.sh b/recipes/bioconductor-aroma.light/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-aroma.light/build.sh +++ b/recipes/bioconductor-aroma.light/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aroma.light/meta.yaml b/recipes/bioconductor-aroma.light/meta.yaml index 2fec743665902..54963819b8447 100644 --- a/recipes/bioconductor-aroma.light/meta.yaml +++ b/recipes/bioconductor-aroma.light/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "3.10.0" %} +{% set version = "3.12.0" %} {% set name = "aroma.light" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 767638cd7ba45f730052158941d5c7ed29987fbb3bb9718aac09339e358fbab7 + md5: f98a7b55b903ecd0334b7d3afed5ce95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: princurve (>= 2.1.2) requirements: host: - r-base - - 'r-matrixstats >=0.52.2' + - 'r-matrixstats >=0.54.0' - 'r-r.methodss3 >=1.7.1' - - 'r-r.oo >=1.21.0' - - 'r-r.utils >=2.6.0' + - 'r-r.oo >=1.22.0' + - 'r-r.utils >=2.7.0' run: - r-base - - 'r-matrixstats >=0.52.2' + - 'r-matrixstats >=0.54.0' - 'r-r.methodss3 >=1.7.1' - - 'r-r.oo >=1.21.0' - - 'r-r.utils >=2.6.0' + - 'r-r.oo >=1.22.0' + - 'r-r.utils >=2.7.0' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Methods for microarray analysis that take basic data types such as matrices and lists of vectors. These methods can be used standalone, be utilized in other packages, or be wrapped up in higher-level classes.' extra: identifiers: - biotools:aroma.light + parent_recipe: + name: bioconductor-aroma.light + path: recipes/bioconductor-aroma.light + version: 3.10.0 + diff --git a/recipes/bioconductor-arrayexpress/build.sh b/recipes/bioconductor-arrayexpress/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-arrayexpress/build.sh +++ b/recipes/bioconductor-arrayexpress/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arrayexpress/conda_build_config.yaml b/recipes/bioconductor-arrayexpress/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-arrayexpress/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-arrayexpress/meta.yaml b/recipes/bioconductor-arrayexpress/meta.yaml index 68216a6735196..fb77dbc20ed6e 100644 --- a/recipes/bioconductor-arrayexpress/meta.yaml +++ b/recipes/bioconductor-arrayexpress/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ArrayExpress" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 98c8297309653266cfd37d47405222380f45bada6e8e72ae84e801f4653d23b9 + md5: 718b770b408424f6141d1ce8c818b00a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affy requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' - r-base - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' - r-base - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet' - +extra: + parent_recipe: + name: bioconductor-arrayexpress + path: recipes/bioconductor-arrayexpress + version: 1.40.0 diff --git a/recipes/bioconductor-arrayexpresshts/build.sh b/recipes/bioconductor-arrayexpresshts/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-arrayexpresshts/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arrayexpresshts/meta.yaml b/recipes/bioconductor-arrayexpresshts/meta.yaml new file mode 100644 index 0000000000000..880534dcd9426 --- /dev/null +++ b/recipes/bioconductor-arrayexpresshts/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.32.0" %} +{% set name = "ArrayExpressHTS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dcb1ef59f60151a8a83f63c2d42ab28a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-bitops + - r-hmisc + - r-r2html + - r-rcolorbrewer + - r-rjava + - r-sampling + - r-sendmailr + - r-snow + - r-svmisc + - r-xml + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-bitops + - r-hmisc + - r-r2html + - r-rcolorbrewer + - r-rjava + - r-sampling + - r-sendmailr + - r-snow + - r-svmisc + - r-xml + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'RNA-Seq processing pipeline for public ArrayExpress experiments or local datasets' + diff --git a/recipes/bioconductor-arraymvout/build.sh b/recipes/bioconductor-arraymvout/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-arraymvout/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arraymvout/meta.yaml b/recipes/bioconductor-arraymvout/meta.yaml new file mode 100644 index 0000000000000..c4351cae7e2b7 --- /dev/null +++ b/recipes/bioconductor-arraymvout/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.40.0" %} +{% set name = "arrayMvout" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c9c9ec7b5f1774bab6514b85fb9db8a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MAQCsubset, mvoutData, lumiBarnes, affyPLM, affydata, hgu133atagcdf +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affycontam >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-mdqc >=1.44.0,<1.45.0' + - 'bioconductor-parody >=1.40.0,<1.41.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affycontam >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-mdqc >=1.44.0,<1.45.0' + - 'bioconductor-parody >=1.40.0,<1.41.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package supports the application of diverse quality metrics to AffyBatch instances, summarizing these metrics via PCA, and then performing parametric outlier detection on the PCs to identify aberrant arrays with a fixed Type I error rate' + diff --git a/recipes/bioconductor-arrayquality/build.sh b/recipes/bioconductor-arrayquality/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-arrayquality/build.sh +++ b/recipes/bioconductor-arrayquality/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arrayquality/meta.yaml b/recipes/bioconductor-arrayquality/meta.yaml index 444d913fb941c..1bfe93385a325 100644 --- a/recipes/bioconductor-arrayquality/meta.yaml +++ b/recipes/bioconductor-arrayquality/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "arrayQuality" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 437f1d57604f411ab9e55416f30658fef284c795dce682429a5884a028b38680 + md5: e217db056836d45c77da1fa228ea7d87 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: mclust, MEEBOdata, HEEBOdata requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-gridbase - r-hexbin - r-rcolorbrewer run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-gridbase - r-hexbin @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for performing print-run and array level quality assessment.' extra: identifiers: - biotools:arrayquality - doi:10.1093/bioinformatics/btn647 + parent_recipe: + name: bioconductor-arrayquality + path: recipes/bioconductor-arrayquality + version: 1.58.0 + diff --git a/recipes/bioconductor-arrayqualitymetrics/build.sh b/recipes/bioconductor-arrayqualitymetrics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-arrayqualitymetrics/build.sh +++ b/recipes/bioconductor-arrayqualitymetrics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml b/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-arrayqualitymetrics/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-arrayqualitymetrics/meta.yaml b/recipes/bioconductor-arrayqualitymetrics/meta.yaml index cbb80e0d3b7e6..837e3d81435b0 100644 --- a/recipes/bioconductor-arrayqualitymetrics/meta.yaml +++ b/recipes/bioconductor-arrayqualitymetrics/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "3.36.0" %} +{% set version = "3.38.0" %} {% set name = "arrayQualityMetrics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d31f0bea123391dd118e7d91e8a8074a40e2ca6c32631062b4ea81dd35ffcd5e + md5: c85ba7444832fd3da35ebeb206ac5dbc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALLMLL, CCl4, BiocStyle, knitr requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyplm >=1.56.0,<1.58.0' - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' @@ -36,13 +38,13 @@ requirements: - r-setrng - r-xml run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyplm >=1.56.0,<1.58.0' - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - 'r-cairo >=1.4-6' - 'r-gridsvg >=1.4-3' @@ -57,9 +59,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'This package generates microarray quality metrics reports for data in Bioconductor microarray data containers (ExpressionSet, NChannelSet, AffyBatch). One and two color array platforms are supported.' extra: identifiers: - biotools:arrayqualitymetrics + parent_recipe: + name: bioconductor-arrayqualitymetrics + path: recipes/bioconductor-arrayqualitymetrics + version: 3.36.0 + diff --git a/recipes/bioconductor-arraytools/build.sh b/recipes/bioconductor-arraytools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-arraytools/build.sh +++ b/recipes/bioconductor-arraytools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arraytools/conda_build_config.yaml b/recipes/bioconductor-arraytools/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-arraytools/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-arraytools/meta.yaml b/recipes/bioconductor-arraytools/meta.yaml index a079e1dbbbbcc..7e326f1e73f9c 100644 --- a/recipes/bioconductor-arraytools/meta.yaml +++ b/recipes/bioconductor-arraytools/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "ArrayTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 109f61ec070ace944b3d7a3fea37aa73f95887a218c908e52e08464a27f14f0c + md5: 2111784fb075319520ca6b6f1add616b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: simpleaffy, R2HTML, affydata, affyPLM, genefilter, annaffy, gcrma, hugene10sttranscriptcluster.db requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-xtable run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-xtable test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package is designed to provide solutions for quality assessment and to detect differentially expressed genes for the Affymetrix GeneChips, including both 3'' -arrays and gene 1.0-ST arrays. The package generates comprehensive analysis reports in HTML format. Hyperlinks on the report page will lead to a series of QC plots, processed data, and differentially expressed gene lists. Differentially expressed genes are reported in tabular format with annotations hyperlinked to online biological databases.' extra: identifiers: - biotools:arraytools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-arraytools + path: recipes/bioconductor-arraytools + version: 1.40.0 + diff --git a/recipes/bioconductor-arraytv/build.sh b/recipes/bioconductor-arraytv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-arraytv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arraytv/meta.yaml b/recipes/bioconductor-arraytv/meta.yaml new file mode 100644 index 0000000000000..f3df951222fc6 --- /dev/null +++ b/recipes/bioconductor-arraytv/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "ArrayTV" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5cf6ce896c57f219ee738b6d9dfa8a7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RColorBrewer, crlmm, ff, BSgenome.Hsapiens.UCSC.hg18,BSgenome.Hsapiens.UCSC.hg19, lattice, latticeExtra, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-foreach + run: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-foreach +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Wave correction for genotyping and copy number arrays' + diff --git a/recipes/bioconductor-arrmdata/meta.yaml b/recipes/bioconductor-arrmdata/meta.yaml index f91b2fb0ac509..1cb3170c45b91 100644 --- a/recipes/bioconductor-arrmdata/meta.yaml +++ b/recipes/bioconductor-arrmdata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "ARRmData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2a05e8d5260c51e8fcf9485ac2232aaeee995568d6e7d74dc5a42247e81893f6 + md5: 16ccdc6a5bc334b90c45e81103075a58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Raw Beta values from 36 samples across 3 groups from Illumina 450k methylation arrays' - +extra: + parent_recipe: + name: bioconductor-arrmdata + path: recipes/bioconductor-arrmdata + version: 1.16.0 diff --git a/recipes/bioconductor-arrmdata/post-link.sh b/recipes/bioconductor-arrmdata/post-link.sh index 313fe0283fccf..95d96b40cfdaa 100644 --- a/recipes/bioconductor-arrmdata/post-link.sh +++ b/recipes/bioconductor-arrmdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ARRmData_1.16.0.tar.gz" +FN="ARRmData_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ARRmData_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/ARRmData_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ARRmData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ARRmData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-arrmdata/bioconductor-arrmdata_1.18.0_src_all.tar.gz" ) -MD5="fce3b1d71d92cf8bf62a52a490543f58" +MD5="16ccdc6a5bc334b90c45e81103075a58" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-arrmnormalization/build.sh b/recipes/bioconductor-arrmnormalization/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-arrmnormalization/build.sh +++ b/recipes/bioconductor-arrmnormalization/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-arrmnormalization/meta.yaml b/recipes/bioconductor-arrmnormalization/meta.yaml index e2510d7585ec5..3e8cf3285e30c 100644 --- a/recipes/bioconductor-arrmnormalization/meta.yaml +++ b/recipes/bioconductor-arrmnormalization/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "ARRmNormalization" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 321e66bf19cab82cf9b53f203cfe43f6981c7190a02bb7d8460c069b54bc56f2 + md5: 0007af10085c49def9f420ab8a14bfa0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-arrmdata >=1.16.0,<1.18.0' + - 'bioconductor-arrmdata >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-arrmdata >=1.16.0,<1.18.0' + - 'bioconductor-arrmdata >=1.18.0,<1.19.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Perform the Adaptive Robust Regression method (ARRm) for the normalization of methylation data from the Illumina Infinium HumanMethylation 450k assay.' extra: identifiers: - biotools:arrmnormalization - doi:10.1186/s13059-014-0503-2 + parent_recipe: + name: bioconductor-arrmnormalization + path: recipes/bioconductor-arrmnormalization + version: 1.20.0 + diff --git a/recipes/bioconductor-artms/build.sh b/recipes/bioconductor-artms/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-artms/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-artms/meta.yaml b/recipes/bioconductor-artms/meta.yaml new file mode 100644 index 0000000000000..7d5833dbdd442 --- /dev/null +++ b/recipes/bioconductor-artms/meta.yaml @@ -0,0 +1,101 @@ +{% set version = "1.0.1" %} +{% set name = "artMS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d58e7fb03b9626740a8d8ac919c8c03e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msstats >=3.14.0,<3.15.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - r-bit64 + - r-circlize + - r-cluster + - r-corrplot + - r-data.table + - r-dplyr + - r-factoextra + - r-factominer + - r-getopt + - r-ggdendro + - r-ggplot2 + - r-ggrepel + - r-gplots + - r-gprofiler + - r-openxlsx + - r-performanceanalytics + - r-pheatmap + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-seqinr + - r-stringr + - r-tidyr + - r-upsetr + - r-venndiagram + - r-yaml + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msstats >=3.14.0,<3.15.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - r-bit64 + - r-circlize + - r-cluster + - r-corrplot + - r-data.table + - r-dplyr + - r-factoextra + - r-factominer + - r-getopt + - r-ggdendro + - r-ggplot2 + - r-ggrepel + - r-gplots + - r-gprofiler + - r-openxlsx + - r-performanceanalytics + - r-pheatmap + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape2 + - r-seqinr + - r-stringr + - r-tidyr + - r-upsetr + - r-venndiagram + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3) + file LICENSE' + summary: 'artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON.' + diff --git a/recipes/bioconductor-asafe/build.sh b/recipes/bioconductor-asafe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-asafe/build.sh +++ b/recipes/bioconductor-asafe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-asafe/meta.yaml b/recipes/bioconductor-asafe/meta.yaml index 72d8f7f06045f..79a14cf565bfa 100644 --- a/recipes/bioconductor-asafe/meta.yaml +++ b/recipes/bioconductor-asafe/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ASAFE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da61cca0c5d5c1db943b56da27d7e33106888ac476fa1b84dd5478d1d6fb78df + md5: 514dbf478d594a68fd86ba799f35b51d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Given admixed individuals'' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.' extra: identifiers: - biotools:asafe - doi:10.1093/bioinformatics/btw220 + parent_recipe: + name: bioconductor-asafe + path: recipes/bioconductor-asafe + version: 1.6.0 + diff --git a/recipes/bioconductor-aseb/build.sh b/recipes/bioconductor-aseb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-aseb/build.sh +++ b/recipes/bioconductor-aseb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aseb/meta.yaml b/recipes/bioconductor-aseb/meta.yaml index 44c9feff16d24..a2764b6cf6d7d 100644 --- a/recipes/bioconductor-aseb/meta.yaml +++ b/recipes/bioconductor-aseb/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ASEB" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b91033ad3ddfae49c55eb1a65287f60d2246530c1e9c278c82736a26e66b3be3 + md5: 3051785401668b2ad729c669a876699e build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'ASEB is an R package to predict lysine sites that can be acetylated by a specific KAT-family.' extra: identifiers: - biotools:aseb - doi:10.1093/nar/gks437 + parent_recipe: + name: bioconductor-aseb + path: recipes/bioconductor-aseb + version: 1.24.0 + diff --git a/recipes/bioconductor-asgsca/build.sh b/recipes/bioconductor-asgsca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-asgsca/build.sh +++ b/recipes/bioconductor-asgsca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-asgsca/meta.yaml b/recipes/bioconductor-asgsca/meta.yaml index 089210b6f0429..9eb87d13cc87a 100644 --- a/recipes/bioconductor-asgsca/meta.yaml +++ b/recipes/bioconductor-asgsca/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ASGSCA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 49d5d156fd6bc3c159237072b85588c8375bd1edf33ba8e152c2fdd86586c18b + md5: 1a540dfd5b527f46d89a54056ea29339 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package provides tools to model and test the association between multiple genotypes and multiple traits, taking into account the prior biological knowledge. Genes, and clinical pathways are incorporated in the model as latent variables. The method is based on Generalized Structured Component Analysis (GSCA).' extra: identifiers: - biotools:asgsca - doi:10.1002/gepi.21872 + parent_recipe: + name: bioconductor-asgsca + path: recipes/bioconductor-asgsca + version: 1.14.0 + diff --git a/recipes/bioconductor-ashkenazimsonchr21/meta.yaml b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml new file mode 100644 index 0000000000000..a066f58e8bfdf --- /dev/null +++ b/recipes/bioconductor-ashkenazimsonchr21/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "AshkenazimSonChr21" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b565b952357149f37240f4fa62dfc425 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, VariantAnnotation +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SonVariantsChr21 is a dataset of annotated genomic variants coming from Complete Genomics whole genome sequencing. Data comes from GIAB project, Ashkenazim Trio, sample HG002 run 1. Both vcf and annotated data frame are provided.' + diff --git a/recipes/bioconductor-ashkenazimsonchr21/post-link.sh b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh new file mode 100644 index 0000000000000..05947210831fb --- /dev/null +++ b/recipes/bioconductor-ashkenazimsonchr21/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AshkenazimSonChr21_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AshkenazimSonChr21_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/AshkenazimSonChr21_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ashkenazimsonchr21/bioconductor-ashkenazimsonchr21_1.12.0_src_all.tar.gz" +) +MD5="b565b952357149f37240f4fa62dfc425" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ashkenazimsonchr21/pre-unlink.sh b/recipes/bioconductor-ashkenazimsonchr21/pre-unlink.sh new file mode 100644 index 0000000000000..cc4405a1bdc6e --- /dev/null +++ b/recipes/bioconductor-ashkenazimsonchr21/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AshkenazimSonChr21 diff --git a/recipes/bioconductor-asics/build.sh b/recipes/bioconductor-asics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-asics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-asics/meta.yaml b/recipes/bioconductor-asics/meta.yaml new file mode 100644 index 0000000000000..aa64cd7c8ba0f --- /dev/null +++ b/recipes/bioconductor-asics/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "ASICS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 96b660a838b9d9edcf46b98c866ce4c1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat, ASICSdata +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-plyr + - r-quadprog + - r-speaq + - r-zoo + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-plyr + - r-quadprog + - r-speaq + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'With a set of pure metabolite reference spectra, ASICS quantifies concentration of metabolites in a complex spectrum. The identification of metabolites is performed by fitting a mixture model to the spectra of the library with a sparse penalty. The method and its statistical properties are described in Tardivel et al. (2017) .' + diff --git a/recipes/bioconductor-asicsdata/meta.yaml b/recipes/bioconductor-asicsdata/meta.yaml new file mode 100644 index 0000000000000..eec44629ea8fa --- /dev/null +++ b/recipes/bioconductor-asicsdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "ASICSdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bb4f0522ab312de30adfa029a55e023b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: '1D NMR example spectra and additional data for use with the ASICS package. Raw 1D Bruker spectral data files were found in the MetaboLights database (https://www.ebi.ac.uk/metabolights/, study MTBLS1).' + diff --git a/recipes/bioconductor-asicsdata/post-link.sh b/recipes/bioconductor-asicsdata/post-link.sh new file mode 100644 index 0000000000000..d162b6f821b79 --- /dev/null +++ b/recipes/bioconductor-asicsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ASICSdata_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ASICSdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/ASICSdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-asicsdata/bioconductor-asicsdata_1.2.0_src_all.tar.gz" +) +MD5="bb4f0522ab312de30adfa029a55e023b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-asicsdata/pre-unlink.sh b/recipes/bioconductor-asicsdata/pre-unlink.sh new file mode 100644 index 0000000000000..fa34622c7351e --- /dev/null +++ b/recipes/bioconductor-asicsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ASICSdata diff --git a/recipes/bioconductor-aspli/build.sh b/recipes/bioconductor-aspli/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-aspli/build.sh +++ b/recipes/bioconductor-aspli/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aspli/meta.yaml b/recipes/bioconductor-aspli/meta.yaml index fb833992085e1..7308bea8912cf 100644 --- a/recipes/bioconductor-aspli/meta.yaml +++ b/recipes/bioconductor-aspli/meta.yaml @@ -1,56 +1,62 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ASpli" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 63987b36701915e6c764aca4f18b52abf3a0ef5087450d0d995de159b4b27abc + md5: f0c1e25d140f97ae3a5df84f8a8c190a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Integrative pipeline for the analysis of alternative splicing using RNAseq.' extra: identifiers: - biotools:aspli - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-aspli + path: recipes/bioconductor-aspli + version: 1.6.0 + diff --git a/recipes/bioconductor-assessorf/build.sh b/recipes/bioconductor-assessorf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-assessorf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-assessorf/meta.yaml b/recipes/bioconductor-assessorf/meta.yaml new file mode 100644 index 0000000000000..463e3a845fea2 --- /dev/null +++ b/recipes/bioconductor-assessorf/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.2" %} +{% set name = "AssessORF" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2e28b613ca3a146a5e719e2ce6366ccf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AssessORFData, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'In order to assess the quality of a set of predicted genes for a genome, evidence must first be mapped to that genome. Next, each gene must be categorized based on how strong the evidence is for or against that gene. The AssessORF package provides the functions and class structures necessary for accomplishing those tasks, using proteomic hits and evolutionarily conserved start codons as the forms of evidence.' + diff --git a/recipes/bioconductor-assessorfdata/meta.yaml b/recipes/bioconductor-assessorfdata/meta.yaml new file mode 100644 index 0000000000000..aea45562056d2 --- /dev/null +++ b/recipes/bioconductor-assessorfdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "AssessORFData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 53b9314533795f7344f755bccd72a1ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AssessORF, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - r-base + run: + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides access to mapping and results objects generated by the AssessORF package, as well as the genome sequences for the strains corresponding to those objects.' + diff --git a/recipes/bioconductor-assessorfdata/post-link.sh b/recipes/bioconductor-assessorfdata/post-link.sh new file mode 100644 index 0000000000000..4b1a394b96e2d --- /dev/null +++ b/recipes/bioconductor-assessorfdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="AssessORFData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/AssessORFData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/AssessORFData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-assessorfdata/bioconductor-assessorfdata_1.0.0_src_all.tar.gz" +) +MD5="53b9314533795f7344f755bccd72a1ec" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-assessorfdata/pre-unlink.sh b/recipes/bioconductor-assessorfdata/pre-unlink.sh new file mode 100644 index 0000000000000..6e2d299a82c77 --- /dev/null +++ b/recipes/bioconductor-assessorfdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ AssessORFData diff --git a/recipes/bioconductor-asset/build.sh b/recipes/bioconductor-asset/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-asset/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-asset/meta.yaml b/recipes/bioconductor-asset/meta.yaml new file mode 100644 index 0000000000000..8654243801b46 --- /dev/null +++ b/recipes/bioconductor-asset/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.0.0" %} +{% set name = "ASSET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 70928d9e0f7dac81d168732658f53b69 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + - r-mass + - r-msm + - r-rmeta + run: + - r-base + - r-mass + - r-msm + - r-rmeta +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 + file LICENSE' + summary: 'An R package for subset-based analysis of heterogeneous traits and subtypes' + diff --git a/recipes/bioconductor-assign/build.sh b/recipes/bioconductor-assign/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-assign/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-assign/meta.yaml b/recipes/bioconductor-assign/meta.yaml new file mode 100644 index 0000000000000..017c2c36b72ec --- /dev/null +++ b/recipes/bioconductor-assign/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.18.0" %} +{% set name = "ASSIGN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cd78a27ed8e521787729a557227ceba6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ggplot2 + - r-gplots + - r-msm + - r-rlab + - r-yaml + run: + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ggplot2 + - r-gplots + - r-msm + - r-rlab + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'ASSIGN is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples. ASSIGN employs a flexible Bayesian factor analysis approach that adapts predetermined pathway signatures derived either from knowledge-based literature or from perturbation experiments to the cell-/tissue-specific pathway signatures. The deregulation/activation level of each context-specific pathway is quantified to a score, which represents the extent to which a patient sample encompasses the pathway deregulation/activation signature.' + diff --git a/recipes/bioconductor-atacseqqc/build.sh b/recipes/bioconductor-atacseqqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-atacseqqc/build.sh +++ b/recipes/bioconductor-atacseqqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-atacseqqc/conda_build_config.yaml b/recipes/bioconductor-atacseqqc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-atacseqqc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-atacseqqc/meta.yaml b/recipes/bioconductor-atacseqqc/meta.yaml index f95b249a1d027..873cf16475d38 100644 --- a/recipes/bioconductor-atacseqqc/meta.yaml +++ b/recipes/bioconductor-atacseqqc/meta.yaml @@ -1,56 +1,58 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.2" %} {% set name = "ATACseqQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 543e52a8d1fadf2137a9d43ede8aa6f8e2a2959a6b44f64b6c3d19a2034f7e82 + md5: 37f36b10cb84e1730fad592e17d5015b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, phastCons100way.UCSC.hg19, MotifDb, trackViewer, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-motifstack >=1.24.1,<1.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-kernsmooth - r-preseqr - r-randomforest run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-motifstack >=1.24.1,<1.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-kernsmooth - r-preseqr @@ -59,8 +61,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'ATAC-seq, an assay for Transposase-Accessible Chromatin using sequencing, is a rapid and sensitive method for chromatin accessibility analysis. It was developed as an alternative method to MNase-seq, FAIRE-seq and DNAse-seq. Comparing to the other methods, ATAC-seq requires less amount of the biological samples and time to process. In the process of analyzing several ATAC-seq dataset produced in our labs, we learned some of the unique aspects of the quality assessment for ATAC-seq data.To help users to quickly assess whether their ATAC-seq experiment is successful, we developed ATACseqQC package partially following the guideline published in Nature Method 2013 (Greenleaf et al.), including diagnostic plot of fragment size distribution, proportion of mitochondria reads, nucleosome positioning pattern, and CTCF or other Transcript Factor footprints.' - +extra: + parent_recipe: + name: bioconductor-atacseqqc + path: recipes/bioconductor-atacseqqc + version: 1.4.3 diff --git a/recipes/bioconductor-ath1121501.db/meta.yaml b/recipes/bioconductor-ath1121501.db/meta.yaml new file mode 100644 index 0000000000000..eabfcb01990cd --- /dev/null +++ b/recipes/bioconductor-ath1121501.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "ath1121501.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ff9977848321463b27a379ed31fffbc3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.at.tair.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Arabidopsis ATH1 Genome Array annotation data (chip ath1121501) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ath1121501.db/post-link.sh b/recipes/bioconductor-ath1121501.db/post-link.sh new file mode 100644 index 0000000000000..bc78c065e4d59 --- /dev/null +++ b/recipes/bioconductor-ath1121501.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ath1121501.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/ath1121501.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501.db/bioconductor-ath1121501.db_3.2.3_src_all.tar.gz" +) +MD5="ff9977848321463b27a379ed31fffbc3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ath1121501.db/pre-unlink.sh b/recipes/bioconductor-ath1121501.db/pre-unlink.sh new file mode 100644 index 0000000000000..e8d92d388bae3 --- /dev/null +++ b/recipes/bioconductor-ath1121501.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ath1121501.db diff --git a/recipes/bioconductor-ath1121501cdf/meta.yaml b/recipes/bioconductor-ath1121501cdf/meta.yaml new file mode 100644 index 0000000000000..ccbfe821e5384 --- /dev/null +++ b/recipes/bioconductor-ath1121501cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ath1121501cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8b63798143219b7c1c2666a91a1a2440 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the ATH1-121501.CDF file.' + diff --git a/recipes/bioconductor-ath1121501cdf/post-link.sh b/recipes/bioconductor-ath1121501cdf/post-link.sh new file mode 100644 index 0000000000000..1be820ba446b5 --- /dev/null +++ b/recipes/bioconductor-ath1121501cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ath1121501cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ath1121501cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501cdf/bioconductor-ath1121501cdf_2.18.0_src_all.tar.gz" +) +MD5="8b63798143219b7c1c2666a91a1a2440" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ath1121501cdf/pre-unlink.sh b/recipes/bioconductor-ath1121501cdf/pre-unlink.sh new file mode 100644 index 0000000000000..dcdf5a9998be0 --- /dev/null +++ b/recipes/bioconductor-ath1121501cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ath1121501cdf diff --git a/recipes/bioconductor-ath1121501probe/meta.yaml b/recipes/bioconductor-ath1121501probe/meta.yaml new file mode 100644 index 0000000000000..23d2663830778 --- /dev/null +++ b/recipes/bioconductor-ath1121501probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ath1121501probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eeeae5e6550bb472ba3419d71bbd7dfb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was ATH1-121501\_probe\_tab.' + diff --git a/recipes/bioconductor-ath1121501probe/post-link.sh b/recipes/bioconductor-ath1121501probe/post-link.sh new file mode 100644 index 0000000000000..6eb81b3a5f721 --- /dev/null +++ b/recipes/bioconductor-ath1121501probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ath1121501probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ath1121501probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ath1121501probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ath1121501probe/bioconductor-ath1121501probe_2.18.0_src_all.tar.gz" +) +MD5="eeeae5e6550bb472ba3419d71bbd7dfb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ath1121501probe/pre-unlink.sh b/recipes/bioconductor-ath1121501probe/pre-unlink.sh new file mode 100644 index 0000000000000..4130790e54cfc --- /dev/null +++ b/recipes/bioconductor-ath1121501probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ath1121501probe diff --git a/recipes/bioconductor-attract/build.sh b/recipes/bioconductor-attract/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-attract/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-attract/meta.yaml b/recipes/bioconductor-attract/meta.yaml new file mode 100644 index 0000000000000..7cdf9a7b4d4d3 --- /dev/null +++ b/recipes/bioconductor-attract/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.34.0" %} +{% set name = "attract" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e01ada5c2cde36bc4f0ec78e81344a13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: illuminaHumanv1.db +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-base + - r-cluster + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-base + - r-cluster +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'This package contains the functions to find the gene expression modules that represent the drivers of Kauffman''s attractor landscape. The modules are the core attractor pathways that discriminate between different cell types of groups of interest. Each pathway has a set of synexpression groups, which show transcriptionally-coordinated changes in gene expression.' + diff --git a/recipes/bioconductor-aucell/build.sh b/recipes/bioconductor-aucell/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-aucell/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-aucell/meta.yaml b/recipes/bioconductor-aucell/meta.yaml new file mode 100644 index 0000000000000..b6a3e0ff7fa40 --- /dev/null +++ b/recipes/bioconductor-aucell/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "AUCell" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3342bbd472f405a1ef5ebeba04a5431b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocStyle, devtools, DT, GEOquery, knitr, NMF, plotly, R2HTML, rbokeh, rmarkdown, Rtsne, testthat, zoo +requirements: + host: + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-mixtools + - r-r.utils + - r-shiny + run: + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-mixtools + - r-r.utils + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'AUCell allows to identify cells with active gene sets (e.g. signatures, gene modules...) in single-cell RNA-seq data. AUCell uses the "Area Under the Curve" (AUC) to calculate whether a critical subset of the input gene set is enriched within the expressed genes for each cell. The distribution of AUC scores across all the cells allows exploring the relative expression of the signature. Since the scoring method is ranking-based, AUCell is independent of the gene expression units and the normalization procedure. In addition, since the cells are evaluated individually, it can easily be applied to bigger datasets, subsetting the expression matrix if needed.' + diff --git a/recipes/bioconductor-baalchip/build.sh b/recipes/bioconductor-baalchip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-baalchip/build.sh +++ b/recipes/bioconductor-baalchip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-baalchip/meta.yaml b/recipes/bioconductor-baalchip/meta.yaml index 8d98cd52e3777..3aa815d18e8f9 100644 --- a/recipes/bioconductor-baalchip/meta.yaml +++ b/recipes/bioconductor-baalchip/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "BaalChIP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 555c72cf38107f062d1ba406ce62fc8eb7af8b21f512e19a402fc96675a39db9 + md5: d2f63d691155d6831cae2aa3a10277a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-coda - r-doby @@ -32,11 +34,11 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-coda - r-doby @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package offers functions to process multiple ChIP-seq BAM files and detect allele-specific events. Computes allele counts at individual variants (SNPs/SNVs), implements extensive QC steps to remove problematic variants, and utilizes a bayesian framework to identify statistically significant allele- specific events. BaalChIP is able to account for copy number differences between the two alleles, a known phenotypical feature of cancer samples.' extra: identifiers: - biotools:baalchip - doi:10.1186/s13059-017-1165-7 + parent_recipe: + name: bioconductor-baalchip + path: recipes/bioconductor-baalchip + version: 1.6.0 + diff --git a/recipes/bioconductor-bac/build.sh b/recipes/bioconductor-bac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bac/build.sh +++ b/recipes/bioconductor-bac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bac/meta.yaml b/recipes/bioconductor-bac/meta.yaml index 4633e68afd1da..c5cc2ead24108 100644 --- a/recipes/bioconductor-bac/meta.yaml +++ b/recipes/bioconductor-bac/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 29b28af43c62c79a2737c19984c343d5f7b3a0e595417622cd47bbfb665706cf + md5: 1d862459cdf5b19fa4d1f45825a2ef46 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments' extra: identifiers: - biotools:bac - doi:10.1111/j.1541-0420.2007.00899.x + parent_recipe: + name: bioconductor-bac + path: recipes/bioconductor-bac + version: 1.40.0 + diff --git a/recipes/bioconductor-bacon/build.sh b/recipes/bioconductor-bacon/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bacon/build.sh +++ b/recipes/bioconductor-bacon/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bacon/meta.yaml b/recipes/bioconductor-bacon/meta.yaml index 121ca960209cc..08ec3dec23978 100644 --- a/recipes/bioconductor-bacon/meta.yaml +++ b/recipes/bioconductor-bacon/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "bacon" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: adce0d013825084694ad6b4842d6959037a13aa47b267b1ca9ef076caf1f68b0 + md5: 419715134113260537652291f755e901 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, testthat, roxygen2 requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-ellipse - r-ggplot2 run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-ellipse - r-ggplot2 @@ -34,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Bacon can be used to remove inflation and bias often observed in epigenome- and transcriptome-wide association studies. To this end bacon constructs an empirical null distribution using a Gibbs Sampling algorithm by fitting a three-component normal mixture on z-scores.' extra: identifiers: - biotools:bacon + parent_recipe: + name: bioconductor-bacon + path: recipes/bioconductor-bacon + version: 1.8.0 + diff --git a/recipes/bioconductor-bader/build.sh b/recipes/bioconductor-bader/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bader/build.sh +++ b/recipes/bioconductor-bader/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bader/meta.yaml b/recipes/bioconductor-bader/meta.yaml index 9a7ee53fb8551..60be4bc8f4223 100644 --- a/recipes/bioconductor-bader/meta.yaml +++ b/recipes/bioconductor-bader/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BADER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3558dfd520aad4fef475918a5101ddfee2e9db855cf99e084b7e32f6c7aeef15 + md5: 820c0d67f0eac42dda1b2747c96212a9 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: pasilla (>= 0.2.10) requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'For RNA sequencing count data, BADER fits a Bayesian hierarchical model. The algorithm returns the posterior probability of differential expression for each gene between two groups A and B. The joint posterior distribution of the variables in the model can be returned in the form of posterior samples, which can be used for further down-stream analyses such as gene set enrichment.' extra: identifiers: - biotools:bader - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bader + path: recipes/bioconductor-bader + version: 1.18.0 + diff --git a/recipes/bioconductor-badregionfinder/build.sh b/recipes/bioconductor-badregionfinder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-badregionfinder/build.sh +++ b/recipes/bioconductor-badregionfinder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-badregionfinder/meta.yaml b/recipes/bioconductor-badregionfinder/meta.yaml index 8db761c250624..ff5a909d02e51 100644 --- a/recipes/bioconductor-badregionfinder/meta.yaml +++ b/recipes/bioconductor-badregionfinder/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BadRegionFinder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78dab6e99f4fffa8d14b7dff8e50c26b0bbed864eec0a9cdb47891079630a5f2 + md5: 1e8c8450b18124340da912960d9a7d13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'BadRegionFinder is a package for identifying regions with a bad, acceptable and good coverage in sequence alignment data available as bam files. The whole genome may be considered as well as a set of target regions. Various visual and textual types of output are available.' extra: identifiers: - biotools:badregionfinder - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-badregionfinder + path: recipes/bioconductor-badregionfinder + version: 1.8.0 + diff --git a/recipes/bioconductor-bags/build.sh b/recipes/bioconductor-bags/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bags/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bags/meta.yaml b/recipes/bioconductor-bags/meta.yaml new file mode 100644 index 0000000000000..794a3f4c33e38 --- /dev/null +++ b/recipes/bioconductor-bags/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "2.22.0" %} +{% set name = "BAGS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2d000e29d269eb8f93a2eabcd1436182 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-breastcancervdx >=1.20.0,<1.21.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-breastcancervdx >=1.20.0,<1.21.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'R package providing functions to perform geneset significance analysis over simple cross-sectional data between 2 and 5 phenotypes of interest.' + diff --git a/recipes/bioconductor-ballgown/build.sh b/recipes/bioconductor-ballgown/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ballgown/build.sh +++ b/recipes/bioconductor-ballgown/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ballgown/meta.yaml b/recipes/bioconductor-ballgown/meta.yaml index e7a8fd184a5d7..35653c9318649 100644 --- a/recipes/bioconductor-ballgown/meta.yaml +++ b/recipes/bioconductor-ballgown/meta.yaml @@ -1,52 +1,59 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "ballgown" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 782a9760d27bb529238b1ecd3fa2f2c0f364ba8f861d7fad54bd127e2935a6d2 + md5: d71a9350866c532da0a81b77fe36628e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-rcolorbrewer test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for statistical analysis of assembled transcriptomes, including flexible differential expression analysis, visualization of transcript structures, and matching of assembled transcripts to annotation.' extra: identifiers: - biotools:ballgown - doi:10.1038/nbt.3172 + parent_recipe: + name: bioconductor-ballgown + path: recipes/bioconductor-ballgown + version: 2.12.0 + diff --git a/recipes/bioconductor-bamsignals/build.sh b/recipes/bioconductor-bamsignals/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bamsignals/build.sh +++ b/recipes/bioconductor-bamsignals/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bamsignals/meta.yaml b/recipes/bioconductor-bamsignals/meta.yaml index f6ddbff6c0951..925a1ea35b9dd 100644 --- a/recipes/bioconductor-bamsignals/meta.yaml +++ b/recipes/bioconductor-bamsignals/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "bamsignals" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fb552c89b77193ab47eba93c1cfd03547645100e18c5ee6a9838f24fc91d3890 + md5: 5d36b092f1a9e17de3b7f39ea838f7dc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat (>= 0.9), Rsamtools, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-rcpp >=0.10.6' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-rcpp >=0.10.6' build: @@ -41,10 +42,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package allows to efficiently obtain count vectors from indexed bam files. It counts the number of reads in given genomic ranges and it computes reads profiles and coverage profiles. It also handles paired-end data.' extra: identifiers: - biotools:bamsignals - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bamsignals + path: recipes/bioconductor-bamsignals + version: 1.12.1 + diff --git a/recipes/bioconductor-banocc/build.sh b/recipes/bioconductor-banocc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-banocc/build.sh +++ b/recipes/bioconductor-banocc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-banocc/meta.yaml b/recipes/bioconductor-banocc/meta.yaml index 9423e5a3a9b36..75502643ebb69 100644 --- a/recipes/bioconductor-banocc/meta.yaml +++ b/recipes/bioconductor-banocc/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "banocc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8e0e0edd7306bf239427155aa4a0ee667ac3f3e01baf8179ab462f8d6304c62e + md5: cd4ab19fdfec8ea813fedd55508ce94a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, methods, testthat +# SystemRequirements: C++11 requirements: host: - r-base - 'r-coda >=0.18.1' - r-mvtnorm - - 'r-rstan >=2.10.1' + - 'r-rstan >=2.17.4' - r-stringr run: - r-base - 'r-coda >=0.18.1' - r-mvtnorm - - 'r-rstan >=2.10.1' + - 'r-rstan >=2.17.4' - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'BAnOCC is a package designed for compositional data, where each sample sums to one. It infers the approximate covariance of the unconstrained data using a Bayesian model coded with `rstan`. It provides as output the `stanfit` object as well as posterior median and credible interval estimates for each correlation element.' - +extra: + parent_recipe: + name: bioconductor-banocc + path: recipes/bioconductor-banocc + version: 1.4.0 diff --git a/recipes/bioconductor-barley1cdf/meta.yaml b/recipes/bioconductor-barley1cdf/meta.yaml new file mode 100644 index 0000000000000..4c9d633ece424 --- /dev/null +++ b/recipes/bioconductor-barley1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "barley1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 16a2ca83f550518756d9fa3273672157 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Barley1.CDF file.' + diff --git a/recipes/bioconductor-barley1cdf/post-link.sh b/recipes/bioconductor-barley1cdf/post-link.sh new file mode 100644 index 0000000000000..e8b400df14186 --- /dev/null +++ b/recipes/bioconductor-barley1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="barley1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/barley1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/barley1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-barley1cdf/bioconductor-barley1cdf_2.18.0_src_all.tar.gz" +) +MD5="16a2ca83f550518756d9fa3273672157" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-barley1cdf/pre-unlink.sh b/recipes/bioconductor-barley1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..d812ccfc9a13a --- /dev/null +++ b/recipes/bioconductor-barley1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ barley1cdf diff --git a/recipes/bioconductor-barley1probe/meta.yaml b/recipes/bioconductor-barley1probe/meta.yaml new file mode 100644 index 0000000000000..926d7db678b32 --- /dev/null +++ b/recipes/bioconductor-barley1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "barley1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 80595d8ecf83ba83ea84a722a24ab474 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Barley1\_probe\_tab.' + diff --git a/recipes/bioconductor-barley1probe/post-link.sh b/recipes/bioconductor-barley1probe/post-link.sh new file mode 100644 index 0000000000000..8738af1967302 --- /dev/null +++ b/recipes/bioconductor-barley1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="barley1probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/barley1probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/barley1probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-barley1probe/bioconductor-barley1probe_2.18.0_src_all.tar.gz" +) +MD5="80595d8ecf83ba83ea84a722a24ab474" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-barley1probe/pre-unlink.sh b/recipes/bioconductor-barley1probe/pre-unlink.sh new file mode 100644 index 0000000000000..10a91d8267743 --- /dev/null +++ b/recipes/bioconductor-barley1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ barley1probe diff --git a/recipes/bioconductor-basecallqc/build.sh b/recipes/bioconductor-basecallqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-basecallqc/build.sh +++ b/recipes/bioconductor-basecallqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-basecallqc/meta.yaml b/recipes/bioconductor-basecallqc/meta.yaml index 8be86eb5b4bc4..db2ff1fa77fa9 100644 --- a/recipes/bioconductor-basecallqc/meta.yaml +++ b/recipes/bioconductor-basecallqc/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "basecallQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 015a2b6bc9c89997550ba38f500df87350728eafd7d8d44e37631a2daa0c21fd + md5: 88e03b7e9ba40099f69694c3b228bbe5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle +# SystemRequirements: bcl2Fastq (versions >= 2.1.7) requirements: host: - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-data.table - r-dplyr @@ -35,7 +38,7 @@ requirements: - r-xml - r-yaml run: - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-data.table - r-dplyr @@ -55,10 +58,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The basecallQC package provides tools to work with Illumina bcl2Fastq (versions >= 2.1.7) software.Prior to basecalling and demultiplexing using the bcl2Fastq software, basecallQC functions allow the user to update Illumina sample sheets from versions <= 1.8.9 to >= 2.1.7 standards, clean sample sheets of common problems such as invalid sample names and IDs, create read and index basemasks and the bcl2Fastq command. Following the generation of basecalled and demultiplexed data, the basecallQC packages allows the user to generate HTML tables, plots and a self contained report of summary metrics from Illumina XML output files.' extra: notes: | 'This package relies on bcl2fastq being available in the system PATH. Due to licensing restrictions Bioconda does not provide this package.' + parent_recipe: + name: bioconductor-basecallqc + path: recipes/bioconductor-basecallqc + version: 1.4.0 + diff --git a/recipes/bioconductor-basespacer/build.sh b/recipes/bioconductor-basespacer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-basespacer/build.sh +++ b/recipes/bioconductor-basespacer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-basespacer/meta.yaml b/recipes/bioconductor-basespacer/meta.yaml index 06123e4e21467..dbaaa393c796a 100644 --- a/recipes/bioconductor-basespacer/meta.yaml +++ b/recipes/bioconductor-basespacer/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BaseSpaceR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 89e78f2f80d6b18f261ff7ad4c69acb91f437f2c26a7c7c53e50de71c35487ce + md5: 25da31488eb0751ca13b4c24ef1d27f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, IRanges, Rsamtools requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'A rich R interface to Illumina''s BaseSpace cloud computing environment, enabling the fast development of data analysis and visualisation tools.' extra: identifiers: - biotools:basespacer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-basespacer + path: recipes/bioconductor-basespacer + version: 1.24.0 + diff --git a/recipes/bioconductor-basic4cseq/build.sh b/recipes/bioconductor-basic4cseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-basic4cseq/build.sh +++ b/recipes/bioconductor-basic4cseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-basic4cseq/meta.yaml b/recipes/bioconductor-basic4cseq/meta.yaml index 0a82fcef3e521..370460b60cf8d 100644 --- a/recipes/bioconductor-basic4cseq/meta.yaml +++ b/recipes/bioconductor-basic4cseq/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Basic4Cseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7a6003173cb26bb7d531b53c6cab9b83f332bc7f782e5187cd3357c325228f21 + md5: 2be7b773728e3e0f11702a26a7891b3f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.1000,<1.5.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-catools - r-rcircos run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.1000,<1.5.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.ecoli.ncbi.20080805 >=1.3.0,<1.4.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-catools - r-rcircos @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Basic4Cseq is an R/Bioconductor package for basic filtering, analysis and subsequent visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment''s viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.' extra: identifiers: - biotools:basic4cseq - doi:10.1093/bioinformatics/btu497 + parent_recipe: + name: bioconductor-basic4cseq + path: recipes/bioconductor-basic4cseq + version: 1.16.0 + diff --git a/recipes/bioconductor-basics/build.sh b/recipes/bioconductor-basics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-basics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-basics/meta.yaml b/recipes/bioconductor-basics/meta.yaml new file mode 100644 index 0000000000000..7771c6f918ee1 --- /dev/null +++ b/recipes/bioconductor-basics/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.4.0" %} +{% set name = "BASiCS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e695dfb2ea1fd76c8674873beb4eb3a4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scran >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coda + - r-data.table + - r-ggplot2 + - r-kernsmooth + - r-mass + - r-matrixstats + - 'r-rcpp >=0.11.3' + - r-rcpparmadillo + - r-testthat + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scran >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coda + - r-data.table + - r-ggplot2 + - r-kernsmooth + - r-mass + - r-matrixstats + - 'r-rcpp >=0.11.3' + - r-rcpparmadillo + - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Single-cell mRNA sequencing can uncover novel cell-to-cell heterogeneity in gene expression levels in seemingly homogeneous populations of cells. However, these experiments are prone to high levels of technical noise, creating new challenges for identifying genes that show genuine heterogeneous expression within the population of cells under study. BASiCS (Bayesian Analysis of Single-Cell Sequencing data) is an integrated Bayesian hierarchical model to perform statistical analyses of single-cell RNA sequencing datasets in the context of supervised experiments (where the groups of cells of interest are known a priori, e.g. experimental conditions or cell types). BASiCS performs built-in data normalisation (global scaling) and technical noise quantification (based on spike-in genes). BASiCS provides an intuitive detection criterion for highly (or lowly) variable genes within a single group of cells. Additionally, BASiCS can compare gene expression patterns between two or more pre-specified groups of cells. Unlike traditional differential expression tools, BASiCS quantifies changes in expression that lie beyond comparisons of means, also allowing the study of changes in cell-to-cell heterogeneity. The latter can be quantified via a biological over-dispersion parameter that measures the excess of variability that is observed with respect to Poisson sampling noise, after normalisation and technical noise removal. Due to the strong mean/over-dispersion confounding that is typically observed for scRNA-seq datasets, BASiCS also tests for changes in residual over-dispersion, defined by residual values with respect to a global mean/over-dispersion trend.' + diff --git a/recipes/bioconductor-basicstarrseq/build.sh b/recipes/bioconductor-basicstarrseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-basicstarrseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-basicstarrseq/meta.yaml b/recipes/bioconductor-basicstarrseq/meta.yaml new file mode 100644 index 0000000000000..004bbcf168dfc --- /dev/null +++ b/recipes/bioconductor-basicstarrseq/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.10.0" %} +{% set name = "BasicSTARRseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6ef49c32242bce2db8d44a695ed756a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'Basic peak calling on STARR-seq data based on a method introduced in "Genome-Wide Quantitative Enhancer Activity Maps Identified by STARR-seq" Arnold et al. Science. 2013 Mar 1;339(6123):1074-7. doi: 10.1126/science. 1232542. Epub 2013 Jan 17.' + diff --git a/recipes/bioconductor-batchqc/build.sh b/recipes/bioconductor-batchqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-batchqc/build.sh +++ b/recipes/bioconductor-batchqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-batchqc/meta.yaml b/recipes/bioconductor-batchqc/meta.yaml index f6a7410402b87..2eb38476eead9 100644 --- a/recipes/bioconductor-batchqc/meta.yaml +++ b/recipes/bioconductor-batchqc/meta.yaml @@ -1,25 +1,28 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.1" %} {% set name = "BatchQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3d3eb2a68c018066506b2ff4d2c4a94cbca5ebcfac35d68e322cd642893044a0 + md5: 5011c3bec69aa680c0d3e6130b483dcd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat +# SystemRequirements: pandoc (http://pandoc.org/installing.html) for generating reports from markdown files. requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-corpcor - r-d3heatmap @@ -35,8 +38,8 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-corpcor - r-d3heatmap @@ -55,9 +58,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Sequencing and microarray samples often are collected or processed in multiple batches or at different times. This often produces technical biases that can lead to incorrect results in the downstream analysis. BatchQC is a software tool that streamlines batch preprocessing and evaluation by providing interactive diagnostics, visualizations, and statistical analyses to explore the extent to which batch variation impacts the data. BatchQC diagnostics help determine whether batch adjustment needs to be done, and how correction should be applied before proceeding with a downstream analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches to the data, and the user can quickly see the benefits of each method. BatchQC is developed as a Shiny App. The output is organized into multiple tabs, and each tab features an important part of the batch effect analysis and visualization of the data. The BatchQC interface has the following analysis groups: Summary, Differential Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape, ComBat and SVA.' extra: identifiers: - biotools:batchqc + parent_recipe: + name: bioconductor-batchqc + path: recipes/bioconductor-batchqc + version: 1.8.1 + diff --git a/recipes/bioconductor-bayesknockdown/build.sh b/recipes/bioconductor-bayesknockdown/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bayesknockdown/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bayesknockdown/meta.yaml b/recipes/bioconductor-bayesknockdown/meta.yaml new file mode 100644 index 0000000000000..ee3f63c5655d2 --- /dev/null +++ b/recipes/bioconductor-bayesknockdown/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.8.0" %} +{% set name = "BayesKnockdown" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 75b7426ec5da2b1e3513f9f78c739412 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A simple, fast Bayesian method for computing posterior probabilities for relationships between a single predictor variable and multiple potential outcome variables, incorporating prior probabilities of relationships. In the context of knockdown experiments, the predictor variable is the knocked-down gene, while the other genes are potential targets. Can also be used for differential expression/2-class data.' + diff --git a/recipes/bioconductor-bayespeak/build.sh b/recipes/bioconductor-bayespeak/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bayespeak/build.sh +++ b/recipes/bioconductor-bayespeak/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bayespeak/meta.yaml b/recipes/bioconductor-bayespeak/meta.yaml index 19bb10b2bc9a5..458867be9198c 100644 --- a/recipes/bioconductor-bayespeak/meta.yaml +++ b/recipes/bioconductor-bayespeak/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "BayesPeak" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 42592e5fb0dd4629b705679f963b23780ff04f9a8d4500559943bca7eb61ac17 + md5: e92c2c9940b0329142b613fe625eba15 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, parallel requirements: host: - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base build: - {{ compiler('c') }} @@ -30,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data.' extra: identifiers: - biotools:bayespeak + parent_recipe: + name: bioconductor-bayespeak + path: recipes/bioconductor-bayespeak + version: 1.32.0 + diff --git a/recipes/bioconductor-baynorm/build.sh b/recipes/bioconductor-baynorm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-baynorm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-baynorm/meta.yaml b/recipes/bioconductor-baynorm/meta.yaml new file mode 100644 index 0000000000000..ebf34e5b26271 --- /dev/null +++ b/recipes/bioconductor-baynorm/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.0.6" %} +{% set name = "bayNorm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b4f6f28c11a1448671eb4b01b8b09a07 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocStyle, devtools, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bb + - r-dosnow + - r-fitdistrplus + - r-foreach + - r-iterators + - r-locfit + - r-mass + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-rcppprogress + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bb + - r-dosnow + - r-fitdistrplus + - r-foreach + - r-iterators + - r-locfit + - r-mass + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-rcppprogress + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'bayNorm is used for normalizing single-cell RNA-seq data.' + diff --git a/recipes/bioconductor-bayseq/build.sh b/recipes/bioconductor-bayseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bayseq/build.sh +++ b/recipes/bioconductor-bayseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bayseq/meta.yaml b/recipes/bioconductor-bayseq/meta.yaml index 4782fde701c81..4e8cea35b8f55 100644 --- a/recipes/bioconductor-bayseq/meta.yaml +++ b/recipes/bioconductor-bayseq/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "baySeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8fcee22b032a24ce2fac943bfbace3597d0ee6b5b3af9a54562b52a402a87541 + md5: 640b6b622f46258525fecc4304ffbac5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-abind - r-base run: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-abind - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package identifies differential expression in high-throughput ''count'' data, such as that derived from next-generation sequencing machines, calculating estimated posterior likelihoods of differential expression (or more complex hypotheses) via empirical Bayesian methods.' extra: identifiers: - biotools:bayseq - doi:10.1186/1471-2105-11-422 + parent_recipe: + name: bioconductor-bayseq + path: recipes/bioconductor-bayseq + version: 2.14.0 + diff --git a/recipes/bioconductor-bbcanalyzer/build.sh b/recipes/bioconductor-bbcanalyzer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bbcanalyzer/build.sh +++ b/recipes/bioconductor-bbcanalyzer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bbcanalyzer/meta.yaml b/recipes/bioconductor-bbcanalyzer/meta.yaml index 315e37200c9e0..48e176fca2799 100644 --- a/recipes/bioconductor-bbcanalyzer/meta.yaml +++ b/recipes/bioconductor-bbcanalyzer/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "BBCAnalyzer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0a1dfb72e58e6371d8120df49c3d79a8e1fa94e8fe7531413be03828ec257e5e + md5: a43ebce794b431b5600923809bbd81f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'BBCAnalyzer is a package for visualizing the relative or absolute number of bases, deletions and insertions at defined positions in sequence alignment data available as bam files in comparison to the reference bases. Markers for the relative base frequencies, the mean quality of the detected bases, known mutations or polymorphisms and variants called in the data may additionally be included in the plots.' extra: identifiers: - biotools:bbcanalyzer - doi:10.1186/s12859-017-1549-4 + parent_recipe: + name: bioconductor-bbcanalyzer + path: recipes/bioconductor-bbcanalyzer + version: 1.10.0 + diff --git a/recipes/bioconductor-bcellviper/meta.yaml b/recipes/bioconductor-bcellviper/meta.yaml new file mode 100644 index 0000000000000..ed110e74888a6 --- /dev/null +++ b/recipes/bioconductor-bcellviper/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "bcellViper" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9fb04cd65ec9c1bd6673bf0e53878c28 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package provides a human B-cell context-specific transcriptional regulatory network and a human normal B-cells dataset for the examples in package viper.' + diff --git a/recipes/bioconductor-bcellviper/post-link.sh b/recipes/bioconductor-bcellviper/post-link.sh new file mode 100644 index 0000000000000..0041861654664 --- /dev/null +++ b/recipes/bioconductor-bcellviper/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bcellViper_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bcellViper_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bcellViper_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bcellviper/bioconductor-bcellviper_1.18.0_src_all.tar.gz" +) +MD5="9fb04cd65ec9c1bd6673bf0e53878c28" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bcellviper/pre-unlink.sh b/recipes/bioconductor-bcellviper/pre-unlink.sh new file mode 100644 index 0000000000000..d96b05f2df444 --- /dev/null +++ b/recipes/bioconductor-bcellviper/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bcellViper diff --git a/recipes/bioconductor-bcrank/build.sh b/recipes/bioconductor-bcrank/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bcrank/build.sh +++ b/recipes/bioconductor-bcrank/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bcrank/meta.yaml b/recipes/bioconductor-bcrank/meta.yaml index 39f4f0fe83af9..66fd7f0898de2 100644 --- a/recipes/bioconductor-bcrank/meta.yaml +++ b/recipes/bioconductor-bcrank/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "BCRANK" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 98196790877a23218038419beb4f8fc6b977f04ff58ca311998b528349810247 + md5: 69400b8a8212a30ece13daec99343f3d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: seqLogo requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions and classes for de novo prediction of transcription factor binding consensus by heuristic search' extra: identifiers: - biotools:bcrank - doi:10.1093/nar/gkp381 + parent_recipe: + name: bioconductor-bcrank + path: recipes/bioconductor-bcrank + version: 1.42.0 + diff --git a/recipes/bioconductor-bcseq/build.sh b/recipes/bioconductor-bcseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bcseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bcseq/meta.yaml b/recipes/bioconductor-bcseq/meta.yaml new file mode 100644 index 0000000000000..bbee61677cacb --- /dev/null +++ b/recipes/bioconductor-bcseq/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.4.0" %} +{% set name = "bcSeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 045854c6264a3f8f1f80931333d0b477 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-matrix + - 'r-rcpp >=0.12.12' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-matrix + - 'r-rcpp >=0.12.12' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This Rcpp-based package implements a highly efficient data structure and algorithm for performing alignment of short reads from CRISPR or shRNA screens to reference barcode library. Sequencing error are considered and matching qualities are evaluated based on Phred scores. A Bayes'' classifier is employed to predict the originating barcode of a read. The package supports provision of user-defined probability models for evaluating matching qualities. The package also supports multi-threading.' + diff --git a/recipes/bioconductor-bdmmacorrect/build.sh b/recipes/bioconductor-bdmmacorrect/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bdmmacorrect/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bdmmacorrect/meta.yaml b/recipes/bioconductor-bdmmacorrect/meta.yaml new file mode 100644 index 0000000000000..5f685a1b8bd7b --- /dev/null +++ b/recipes/bioconductor-bdmmacorrect/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.0.0" %} +{% set name = "BDMMAcorrect" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4a778faf834a0328b8493cbd3f3dd198 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocGenerics +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-ellipse + - r-ggplot2 + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-rcppeigen + - r-vegan + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-ellipse + - r-ggplot2 + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-rcppeigen + - r-vegan + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Metagenomic sequencing techniques enable quantitative analyses of the microbiome. However, combining the microbial data from these experiments is challenging due to the variations between experiments. The existing methods for correcting batch effects do not consider the interactions between variables—microbial taxa in microbial studies—and the overdispersion of the microbiome data. Therefore, they are not applicable to microbiome data. We develop a new method, Bayesian Dirichlet-multinomial regression meta-analysis (BDMMA), to simultaneously model the batch effects and detect the microbial taxa associated with phenotypes. BDMMA automatically models the dependence among microbial taxa and is robust to the high dimensionality of the microbiome and their association sparsity.' + diff --git a/recipes/bioconductor-beachmat/build.sh b/recipes/bioconductor-beachmat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beachmat/build.sh +++ b/recipes/bioconductor-beachmat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beachmat/conda_build_config.yaml b/recipes/bioconductor-beachmat/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-beachmat/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-beachmat/meta.yaml b/recipes/bioconductor-beachmat/meta.yaml index 4060272cc7a27..527c077e4fd32 100644 --- a/recipes/bioconductor-beachmat/meta.yaml +++ b/recipes/bioconductor-beachmat/meta.yaml @@ -1,34 +1,38 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "beachmat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 26a5233331710cbc57a05586926111718bdfc09ceda5d47f77f9fdd025d820f1 + md5: 41e56c5e6b9366f13fca35053c15fced build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, BiocStyle, knitr, rmarkdown, Matrix, devtools +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - r-base - 'r-rcpp >=0.12.14' run: - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - r-base - 'r-rcpp >=0.12.14' build: @@ -39,8 +43,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides a consistent C++ class interface for a variety of commonly used matrix types, including sparse and HDF5-backed matrices.' - +extra: + parent_recipe: + name: bioconductor-beachmat + path: recipes/bioconductor-beachmat + version: 1.2.1 diff --git a/recipes/bioconductor-beadarray/build.sh b/recipes/bioconductor-beadarray/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beadarray/build.sh +++ b/recipes/bioconductor-beadarray/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beadarray/meta.yaml b/recipes/bioconductor-beadarray/meta.yaml index accffbdc82565..11b11e169407a 100644 --- a/recipes/bioconductor-beadarray/meta.yaml +++ b/recipes/bioconductor-beadarray/meta.yaml @@ -1,43 +1,44 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "beadarray" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b62f7771a1a0ae050f5bd983182d57b857428e40c6076d67e6848855a7cbefe5 + md5: 3a4e97e6601c7dd23ecc9581624fe74e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: lumi, vsn, affy, hwriter, beadarrayExampleData, illuminaHumanv3.db, gridExtra, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, ggbio, Nozzle.R1, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-beaddatapackr >=1.32.0,<1.34.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-beaddatapackr >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-beaddatapackr >=1.32.0,<1.34.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-beaddatapackr >=1.34.0,<1.35.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 - r-reshape2 @@ -48,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is able to read bead-level data (raw TIFFs and text files) output by BeadScan as well as bead-summary data from BeadStudio. Methods for quality assessment and low-level analysis are provided.' extra: identifiers: - biotools:beadarray + parent_recipe: + name: bioconductor-beadarray + path: recipes/bioconductor-beadarray + version: 2.30.0 + diff --git a/recipes/bioconductor-beadarrayexampledata/meta.yaml b/recipes/bioconductor-beadarrayexampledata/meta.yaml new file mode 100644 index 0000000000000..182c2f952bc11 --- /dev/null +++ b/recipes/bioconductor-beadarrayexampledata/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "beadarrayExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 256c9a9bb54f750aba53708c59e3c132 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'An small dataset that can be used to run examples from the beadarray vignette and examples' + diff --git a/recipes/bioconductor-beadarrayexampledata/post-link.sh b/recipes/bioconductor-beadarrayexampledata/post-link.sh new file mode 100644 index 0000000000000..eff5b62b36d65 --- /dev/null +++ b/recipes/bioconductor-beadarrayexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="beadarrayExampleData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/beadarrayExampleData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/beadarrayExampleData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beadarrayexampledata/bioconductor-beadarrayexampledata_1.20.0_src_all.tar.gz" +) +MD5="256c9a9bb54f750aba53708c59e3c132" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-beadarrayexampledata/pre-unlink.sh b/recipes/bioconductor-beadarrayexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..ee8a52f30a6d1 --- /dev/null +++ b/recipes/bioconductor-beadarrayexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ beadarrayExampleData diff --git a/recipes/bioconductor-beadarraysnp/build.sh b/recipes/bioconductor-beadarraysnp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beadarraysnp/build.sh +++ b/recipes/bioconductor-beadarraysnp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beadarraysnp/meta.yaml b/recipes/bioconductor-beadarraysnp/meta.yaml index 66e4cb0473639..5b058e50cb783 100644 --- a/recipes/bioconductor-beadarraysnp/meta.yaml +++ b/recipes/bioconductor-beadarraysnp/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "beadarraySNP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ee552cb355c5eb34a594c5193ca954e955f934225a1f8ec56fa0479dfcd0e522 + md5: 6022599758a0d8487f62868a6b0895ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: aCGH, affy, limma, snapCGH, beadarray, DNAcopy requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Importing data from Illumina SNP experiments and performing copy number calculations and reports.' extra: identifiers: - biotools:beadarraysnp - doi:10.1093/bioinformatics/btm311 + parent_recipe: + name: bioconductor-beadarraysnp + path: recipes/bioconductor-beadarraysnp + version: 1.46.0 + diff --git a/recipes/bioconductor-beadarrayusecases/meta.yaml b/recipes/bioconductor-beadarrayusecases/meta.yaml new file mode 100644 index 0000000000000..a9d42c154e973 --- /dev/null +++ b/recipes/bioconductor-beadarrayusecases/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.20.0" %} +{% set name = "BeadArrayUseCases" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aa5309f7583a03c59235ce459a749cd6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, GenomicRanges, illuminaHumanv1.db, illuminaHumanv2.db, illuminaHumanv3.db +requirements: + host: + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + run: + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Example data files and use cases for processing Illumina BeadArray expression data using Bioconductor' + diff --git a/recipes/bioconductor-beadarrayusecases/post-link.sh b/recipes/bioconductor-beadarrayusecases/post-link.sh new file mode 100644 index 0000000000000..c20ea3b397810 --- /dev/null +++ b/recipes/bioconductor-beadarrayusecases/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BeadArrayUseCases_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/BeadArrayUseCases_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/BeadArrayUseCases_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beadarrayusecases/bioconductor-beadarrayusecases_1.20.0_src_all.tar.gz" +) +MD5="aa5309f7583a03c59235ce459a749cd6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-beadarrayusecases/pre-unlink.sh b/recipes/bioconductor-beadarrayusecases/pre-unlink.sh new file mode 100644 index 0000000000000..ac7f4f4f264c3 --- /dev/null +++ b/recipes/bioconductor-beadarrayusecases/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BeadArrayUseCases diff --git a/recipes/bioconductor-beaddatapackr/build.sh b/recipes/bioconductor-beaddatapackr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beaddatapackr/build.sh +++ b/recipes/bioconductor-beaddatapackr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beaddatapackr/meta.yaml b/recipes/bioconductor-beaddatapackr/meta.yaml index 48bd14c7d71c2..9c19af64948bc 100644 --- a/recipes/bioconductor-beaddatapackr/meta.yaml +++ b/recipes/bioconductor-beaddatapackr/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "BeadDataPackR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8247bcb91a803b6cf95d9595fac032a68c761cf78e6cdc9a949bbd1d9137d7bf + md5: 0e53726240d897ac98a7fc3044bc198e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr requirements: host: - r-base @@ -28,9 +29,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Provides functionality for the compression and decompression of raw bead-level data from the Illumina BeadArray platform.' extra: identifiers: - biotools:beaddatapackr + parent_recipe: + name: bioconductor-beaddatapackr + path: recipes/bioconductor-beaddatapackr + version: 1.32.0 + diff --git a/recipes/bioconductor-bearscc/build.sh b/recipes/bioconductor-bearscc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bearscc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bearscc/meta.yaml b/recipes/bioconductor-bearscc/meta.yaml new file mode 100644 index 0000000000000..1b25ad37e2bea --- /dev/null +++ b/recipes/bioconductor-bearscc/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.2.0" %} +{% set name = "BEARscc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fbc3fa284b714e75f62395ac202b9ac3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, cowplot, knitr, rmarkdown, BiocStyle, NMF +requirements: + host: + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-ggplot2 + run: + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'BEARscc is a noise estimation and injection tool that is designed to assess putative single-cell RNA-seq clusters in the context of experimental noise estimated by ERCC spike-in controls.' + diff --git a/recipes/bioconductor-beat/build.sh b/recipes/bioconductor-beat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beat/build.sh +++ b/recipes/bioconductor-beat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beat/meta.yaml b/recipes/bioconductor-beat/meta.yaml index 56022fba6d895..9f47f27ff9d66 100644 --- a/recipes/bioconductor-beat/meta.yaml +++ b/recipes/bioconductor-beat/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "BEAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 687556436e352a09f1c1b944d5e783bf30da8ed2badbae4d0401534844e6199d + md5: ab5e4b148aaa23bd59a5c28bf5939877 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3.0)' summary: 'Model-based analysis of single-cell methylation data' extra: identifiers: - biotools:beat - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-beat + path: recipes/bioconductor-beat + version: 1.18.0 + diff --git a/recipes/bioconductor-beclear/build.sh b/recipes/bioconductor-beclear/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-beclear/build.sh +++ b/recipes/bioconductor-beclear/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-beclear/meta.yaml b/recipes/bioconductor-beclear/meta.yaml index 567aadbbce56d..f6074d3950770 100644 --- a/recipes/bioconductor-beclear/meta.yaml +++ b/recipes/bioconductor-beclear/meta.yaml @@ -1,38 +1,51 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "BEclear" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aa88a47163ae33af1760be2c82200ba2a9419ab956ac6ba9ce33640a22ad81e9 + md5: f7d173d8b8e409c822746bced7049a1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat requirements: host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base + - 'r-data.table >=1.11.8' + - r-futile.logger - r-matrix - - r-snowfall + - r-rdpack run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base + - 'r-data.table >=1.11.8' + - r-futile.logger - r-matrix - - r-snowfall + - r-rdpack test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'Provides some functions to detect and correct for batch effects in DNA methylation data. The core function "BEclear" is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' + summary: 'Provides some functions to detect and correct for batch effects in DNA methylation data. The core function is based on latent factor models and can also be used to predict missing values in any other matrix containing real numbers.' extra: identifiers: - biotools:beclear - doi:10.1371/journal.pone.0159921 + parent_recipe: + name: bioconductor-beclear + path: recipes/bioconductor-beclear + version: 1.12.1 + diff --git a/recipes/bioconductor-beta7/meta.yaml b/recipes/bioconductor-beta7/meta.yaml new file mode 100644 index 0000000000000..bc5042f88e095 --- /dev/null +++ b/recipes/bioconductor-beta7/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "beta7" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 135330c43b9aa93aedc4559f15e83c76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Data from 6 gpr files aims to identify differential expressed genes between the beta 7+ and beta 7- memory T helper cells.' + diff --git a/recipes/bioconductor-beta7/post-link.sh b/recipes/bioconductor-beta7/post-link.sh new file mode 100644 index 0000000000000..92587f096045c --- /dev/null +++ b/recipes/bioconductor-beta7/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="beta7_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/beta7_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/beta7_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-beta7/bioconductor-beta7_1.20.0_src_all.tar.gz" +) +MD5="135330c43b9aa93aedc4559f15e83c76" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-beta7/pre-unlink.sh b/recipes/bioconductor-beta7/pre-unlink.sh new file mode 100644 index 0000000000000..6a597d624cbfa --- /dev/null +++ b/recipes/bioconductor-beta7/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ beta7 diff --git a/recipes/bioconductor-bgafun/build.sh b/recipes/bioconductor-bgafun/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bgafun/build.sh +++ b/recipes/bioconductor-bgafun/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bgafun/meta.yaml b/recipes/bioconductor-bgafun/meta.yaml index 1ec910c309f3d..098b8dd39cb5b 100644 --- a/recipes/bioconductor-bgafun/meta.yaml +++ b/recipes/bioconductor-bgafun/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "bgafun" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2edd5d30b472fb64a65b635a28b2a704b1c642693515814f7743bb2a18d43f6b + md5: 592bfaec5b579e3e9b2cd37afb26e9d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-made4 >=1.54.0,<1.56.0' + - 'bioconductor-made4 >=1.56.0,<1.57.0' - r-ade4 - r-base - r-seqinr run: - - 'bioconductor-made4 >=1.54.0,<1.56.0' + - 'bioconductor-made4 >=1.56.0,<1.57.0' - r-ade4 - r-base - r-seqinr @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A method to identify specifity determining residues in protein families using Between Group Analysis' extra: identifiers: - biotools:bgafun - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bgafun + path: recipes/bioconductor-bgafun + version: 1.42.0 + diff --git a/recipes/bioconductor-bgeedb/build.sh b/recipes/bioconductor-bgeedb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bgeedb/build.sh +++ b/recipes/bioconductor-bgeedb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bgeedb/meta.yaml b/recipes/bioconductor-bgeedb/meta.yaml index 58641fa86905c..515facb9d1023 100644 --- a/recipes/bioconductor-bgeedb/meta.yaml +++ b/recipes/bioconductor-bgeedb/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "2.6.2" %} +{% set version = "2.8.0" %} {% set name = "BgeeDB" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cc65796afb8b77a2b3b88fb80a7b5e9973b00af90321bd790d754f212ed7262e + md5: 124a63f929213a6fc1b30f964cf3e1b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest @@ -28,9 +30,9 @@ requirements: - r-rcurl - r-tidyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-data.table - r-digest @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A package for the annotation and gene expression data download from Bgee database, and TopAnat analysis: GO-like enrichment of anatomical terms, mapped to genes by expression patterns.' extra: identifiers: - biotools:bgeedb - doi:10.12688/f1000research.9973.1 + parent_recipe: + name: bioconductor-bgeedb + path: recipes/bioconductor-bgeedb + version: 2.6.2 + diff --git a/recipes/bioconductor-bgmix/build.sh b/recipes/bioconductor-bgmix/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bgmix/build.sh +++ b/recipes/bioconductor-bgmix/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bgmix/meta.yaml b/recipes/bioconductor-bgmix/meta.yaml index 09f5188b3f08f..f85866820e5b6 100644 --- a/recipes/bioconductor-bgmix/meta.yaml +++ b/recipes/bioconductor-bgmix/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BGmix" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1b6e97e8efb812e25f02e7a7894220229b459c0ad35681f130a3ea9be53a7f6d + md5: 0fe9456585e4fa7c1ef2e87e2c93fd26 build: number: 0 rpaths: @@ -32,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Fully Bayesian mixture models for differential gene expression' extra: identifiers: - biotools:bgmix - doi:10.2202/1544-6115.1314 + parent_recipe: + name: bioconductor-bgmix + path: recipes/bioconductor-bgmix + version: 1.40.0 + diff --git a/recipes/bioconductor-bgx/build.sh b/recipes/bioconductor-bgx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bgx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bgx/meta.yaml b/recipes/bioconductor-bgx/meta.yaml new file mode 100644 index 0000000000000..d8fbcef88d5f8 --- /dev/null +++ b/recipes/bioconductor-bgx/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.48.1" %} +{% set name = "bgx" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 16b83dd458322f39c457d82c63b37602 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: affydata, hgu95av2cdf +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - r-base + - 'r-rcpp >=0.11.0' + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - r-base + - 'r-rcpp >=0.11.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Bayesian integrated analysis of Affymetrix GeneChips' + diff --git a/recipes/bioconductor-bhc/build.sh b/recipes/bioconductor-bhc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bhc/build.sh +++ b/recipes/bioconductor-bhc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bhc/meta.yaml b/recipes/bioconductor-bhc/meta.yaml index 296d82a111e03..c5e47b1b9c089 100644 --- a/recipes/bioconductor-bhc/meta.yaml +++ b/recipes/bioconductor-bhc/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "BHC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 99668cb1cc2d3caf7609de429c754003d8bb82819861fe4cec2e20741f932c07 + md5: 7779188efbd83088fc32df257617e208 build: number: 0 rpaths: @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The method performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data. This version also includes a randomised algorithm which is more efficient for larger data sets.' extra: identifiers: - biotools:bhc - doi:10.1186/1471-2105-10-242 + parent_recipe: + name: bioconductor-bhc + path: recipes/bioconductor-bhc + version: 1.32.0 + diff --git a/recipes/bioconductor-bicare/build.sh b/recipes/bioconductor-bicare/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bicare/build.sh +++ b/recipes/bioconductor-bicare/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bicare/meta.yaml b/recipes/bioconductor-bicare/meta.yaml index 9599a3119a9d8..f485716d8c4da 100644 --- a/recipes/bioconductor-bicare/meta.yaml +++ b/recipes/bioconductor-bicare/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "BicARE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b9fb578fa611f3cbc4fe26995fd7ffa0d82d2873cc65a895507320179e34863a + md5: 90878d870f7ec218fc9eea9fe9b5d839 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base build: - {{ compiler('c') }} @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Biclustering Analysis and Results Exploration' extra: identifiers: - biotools:bicare - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bicare + path: recipes/bioconductor-bicare + version: 1.38.0 + diff --git a/recipes/bioconductor-bifet/build.sh b/recipes/bioconductor-bifet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bifet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bifet/meta.yaml b/recipes/bioconductor-bifet/meta.yaml new file mode 100644 index 0000000000000..eb7ec3eea3dd1 --- /dev/null +++ b/recipes/bioconductor-bifet/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "BiFET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a4fb307fab64ae9ffcf38919bb865d72 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - r-poibin + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - r-poibin +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'BiFET identifies TFs whose footprints are over-represented in target regions compared to background regions after correcting for the bias arising from the imbalance in read counts and GC contents between the target and background regions. For a given TF k, BiFET tests the null hypothesis that the target regions have the same probability of having footprints for the TF k as the background regions while correcting for the read count and GC content bias. For this, we use the number of target regions with footprints for TF k, t_k as a test statistic and calculate the p-value as the probability of observing t_k or more target regions with footprints under the null hypothesis.' + diff --git a/recipes/bioconductor-biggr/build.sh b/recipes/bioconductor-biggr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biggr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biggr/meta.yaml b/recipes/bioconductor-biggr/meta.yaml new file mode 100644 index 0000000000000..365e9d7b0972c --- /dev/null +++ b/recipes/bioconductor-biggr/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.18.0" %} +{% set name = "BiGGR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c0bbb2a19b06bc77e802c9f131b5bd0e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-hyperdraw >=1.34.0,<1.35.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rsbml >=2.40.0,<2.41.0' + - r-base + - r-lim + - r-limsolve + - r-stringr + run: + - 'bioconductor-hyperdraw >=1.34.0,<1.35.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rsbml >=2.40.0,<2.41.0' + - r-base + - r-lim + - r-limsolve + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package provides an interface to simulate metabolic reconstruction from the BiGG database(http://bigg.ucsd.edu/) and other metabolic reconstruction databases. The package facilitates flux balance analysis (FBA) and the sampling of feasible flux distributions. Metabolic networks and estimated fluxes can be visualized with hypergraphs.' + diff --git a/recipes/bioconductor-bigmelon/build.sh b/recipes/bioconductor-bigmelon/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bigmelon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bigmelon/meta.yaml b/recipes/bioconductor-bigmelon/meta.yaml new file mode 100644 index 0000000000000..6ad31c415ea85 --- /dev/null +++ b/recipes/bioconductor-bigmelon/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.8.0" %} +{% set name = "bigmelon" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3b7456161c012f3441cffda28e3ce9ca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, minfiData, parallel, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, bumphunter +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods for working with Illumina arrays using gdsfmt.' + diff --git a/recipes/bioconductor-bigmemoryextras/build.sh b/recipes/bioconductor-bigmemoryextras/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bigmemoryextras/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bigmemoryextras/meta.yaml b/recipes/bioconductor-bigmemoryextras/meta.yaml new file mode 100644 index 0000000000000..c30746165c20e --- /dev/null +++ b/recipes/bioconductor-bigmemoryextras/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.30.0" %} +{% set name = "bigmemoryExtras" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fea9a5d5915ed5832554e56d06b8389a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocGenerics, BiocStyle, knitr +requirements: + host: + - r-base + - 'r-bigmemory >=4.5.31' + run: + - r-base + - 'r-bigmemory >=4.5.31' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package defines a "BigMatrix" ReferenceClass which adds safety and convenience features to the filebacked.big.matrix class from the bigmemory package. BigMatrix protects against segfaults by monitoring and gracefully restoring the connection to on-disk data and it also protects against accidental data modification with a filesystem-based permissions system. We provide utilities for using BigMatrix-derived classes as assayData matrices within the Biobase package''s eSet family of classes. BigMatrix provides some optimizations related to attaching to, and indexing into, file-backed matrices with dimnames. Additionally, the package provides a "BigMatrixFactor" class, a file-backed matrix with factor properties.' + diff --git a/recipes/bioconductor-bioassayr/build.sh b/recipes/bioconductor-bioassayr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioassayr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioassayr/meta.yaml b/recipes/bioconductor-bioassayr/meta.yaml new file mode 100644 index 0000000000000..88abd096f41af --- /dev/null +++ b/recipes/bioconductor-bioassayr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.20.0" %} +{% set name = "bioassayR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bbd5e77fd57be1603b1f5657fc222532 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, RCurl, biomaRt, cellHTS2, knitr, knitcitations, knitrBootstrap, testthat, ggplot2, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - 'r-dbi >=0.3.1' + - r-matrix + - r-rjson + - 'r-rsqlite >=1.0.0' + - r-xml + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - 'r-dbi >=0.3.1' + - r-matrix + - r-rjson + - 'r-rsqlite >=1.0.0' + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'bioassayR is a computational tool that enables simultaneous analysis of thousands of bioassay experiments performed over a diverse set of compounds and biological targets. Unique features include support for large-scale cross-target analyses of both public and custom bioassays, generation of high throughput screening fingerprints (HTSFPs), and an optional preloaded database that provides access to a substantial portion of publicly available bioactivity data.' + diff --git a/recipes/bioconductor-biobase/build.sh b/recipes/bioconductor-biobase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biobase/build.sh +++ b/recipes/bioconductor-biobase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biobase/meta.yaml b/recipes/bioconductor-biobase/meta.yaml index f1d21e6926c9e..46a0a99bb76a7 100644 --- a/recipes/bioconductor-biobase/meta.yaml +++ b/recipes/bioconductor-biobase/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "Biobase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5fa69ab2eac24911ef839055f5046766206b0fa3d6dfd5529849e45894d08dc7 + md5: a7137201a04682443ec0a418309e006b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: tools, tkWidgets, ALL, RUnit, golubEsets requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base build: - {{ compiler('c') }} @@ -30,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions that are needed by many other packages or which replace R functions.' extra: identifiers: - biotools:biobase + parent_recipe: + name: bioconductor-biobase + path: recipes/bioconductor-biobase + version: 2.40.0 + diff --git a/recipes/bioconductor-biobroom/build.sh b/recipes/bioconductor-biobroom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biobroom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biobroom/meta.yaml b/recipes/bioconductor-biobroom/meta.yaml new file mode 100644 index 0000000000000..dde88b982a020 --- /dev/null +++ b/recipes/bioconductor-biobroom/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.14.0" %} +{% set name = "biobroom" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8e8a35fc42f28c672f6f5b8b144cc2b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, DESeq2, airway, ggplot2, plyr, GenomicRanges, testthat, magrittr, edgeR, qvalue, knitr, data.table, MSnbase, SummarizedExperiment +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-broom + - r-dplyr + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-broom + - r-dplyr + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This package contains methods for converting standard objects constructed by bioinformatics packages, especially those in Bioconductor, and converting them to tidy data. It thus serves as a complement to the broom package, and follows the same the tidy, augment, glance division of tidying methods. Tidying data makes it easy to recombine, reshape and visualize bioinformatics analyses.' + diff --git a/recipes/bioconductor-biocancer/build.sh b/recipes/bioconductor-biocancer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocancer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocancer/meta.yaml b/recipes/bioconductor-biocancer/meta.yaml new file mode 100644 index 0000000000000..6cb7c1cb4add0 --- /dev/null +++ b/recipes/bioconductor-biocancer/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.10.0" %} +{% set name = "bioCancer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9365942b5cc542b374bb471501a93e49 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr, testthat (>= 0.10.0) +requirements: + host: + - 'bioconductor-annotationfuncs >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'r-algdesign >=1.1.7.3' + - r-base + - 'r-cgdsr >=1.2.6' + - 'r-diagrammer >=0.7' + - 'r-dplyr >=0.7.2' + - 'r-dt >=0.3' + - r-htmlwidgets + - 'r-import >=1.1.0' + - r-plyr + - 'r-radiant.data >=0.9.1' + - 'r-shiny >=1.0.5' + - r-shinythemes + - r-tibble + - r-visnetwork + - 'r-xml >=3.98' + run: + - 'bioconductor-annotationfuncs >=1.32.0,<1.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'r-algdesign >=1.1.7.3' + - r-base + - 'r-cgdsr >=1.2.6' + - 'r-diagrammer >=0.7' + - 'r-dplyr >=0.7.2' + - 'r-dt >=0.3' + - r-htmlwidgets + - 'r-import >=1.1.0' + - r-plyr + - 'r-radiant.data >=0.9.1' + - 'r-shiny >=1.0.5' + - r-shinythemes + - r-tibble + - r-visnetwork + - 'r-xml >=3.98' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'AGPL-3 | file LICENSE' + summary: 'bioCancer is a Shiny App to visualize and analyse interactively Multi-Assays of Cancer Genomic Data.' + diff --git a/recipes/bioconductor-bioccasestudies/build.sh b/recipes/bioconductor-bioccasestudies/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioccasestudies/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioccasestudies/meta.yaml b/recipes/bioconductor-bioccasestudies/meta.yaml new file mode 100644 index 0000000000000..100947b70a203 --- /dev/null +++ b/recipes/bioconductor-bioccasestudies/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.44.0" %} +{% set name = "BiocCaseStudies" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b42e2a90273bbc029e3163dddc35656c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: affy (>= 1.17.3), affyPLM (>= 1.15.1), affyQCReport (>= 1.17.0), ALL (>= 1.4.3), annaffy (>= 1.11.1), annotate (>= 1.17.3), AnnotationDbi (>= 1.1.6), apComplex (>= 2.5.0), Biobase (>= 1.17.5), bioDist (>= 1.11.3), biocGraph (>= 1.1.1), biomaRt (>= 1.13.5), CCl4 (>= 1.0.6), CLL (>= 1.2.4), Category (>= 2.5.0), class (>= 7.2-38), cluster (>= 1.11.9), convert (>= 1.15.0), gcrma (>= 2.11.1), genefilter (>= 1.17.6), geneplotter (>= 1.17.2), GO.db (>= 2.0.2), GOstats (>= 2.5.0), graph (>= 1.17.4), GSEABase (>= 1.1.13), hgu133a.db (>= 2.0.2), hgu95av2.db, hgu95av2cdf (>= 2.0.0), hgu95av2probe (>= 2.0.0), hopach (>= 1.13.0), KEGG.db (>= 2.0.2), kohonen (>= 2.0.2), lattice (>= 0.17.2), latticeExtra (>= 0.3-1), limma (>= 2.13.1), MASS (>= 7.2-38), MLInterfaces (>= 1.13.17), multtest (>= 1.19.0), org.Hs.eg.db (>= 2.0.2), ppiStats (>= 1.5.4), randomForest (>= 4.5-20), RBGL (>= 1.15.6), RColorBrewer (>= 1.0-2), Rgraphviz (>= 1.17.11), vsn (>= 3.4.0), weaver (>= 1.5.0), xtable (>= 1.5-2), yeastExpData (>= 0.9.11) +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Software and data to support the case studies.' + diff --git a/recipes/bioconductor-bioccheck/build.sh b/recipes/bioconductor-bioccheck/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioccheck/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioccheck/meta.yaml b/recipes/bioconductor-bioccheck/meta.yaml new file mode 100644 index 0000000000000..7990c51e330f5 --- /dev/null +++ b/recipes/bioconductor-bioccheck/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.18.0" %} +{% set name = "BiocCheck" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89d98a97234600db83aa55aa628bbeef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, Biobase, RJSONIO, rmarkdown, devtools (>= 1.4.1) +requirements: + host: + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-biocmanager + - r-codetools + - r-httr + - r-knitr + - r-optparse + - r-stringdist + run: + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-biocmanager + - r-codetools + - r-httr + - r-knitr + - r-optparse + - r-stringdist +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Executes Bioconductor-specific package checks.' + diff --git a/recipes/bioconductor-biocfilecache/build.sh b/recipes/bioconductor-biocfilecache/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocfilecache/build.sh +++ b/recipes/bioconductor-biocfilecache/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocfilecache/meta.yaml b/recipes/bioconductor-biocfilecache/meta.yaml index 24bb0a0c4583b..fb47a6f0e0689 100644 --- a/recipes/bioconductor-biocfilecache/meta.yaml +++ b/recipes/bioconductor-biocfilecache/meta.yaml @@ -1,24 +1,27 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "BiocFileCache" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0e8d1f6571795b67d68defdd5501a4983f36c341ee1978c26f8b66b0858aff74 + md5: c5b4282a6191a520567d03508bf46652 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, BiocStyle, rmarkdown, rtracklayer requirements: host: - r-base + - r-curl - r-dbi - 'r-dbplyr >=1.0.0' - r-dplyr @@ -27,6 +30,7 @@ requirements: - r-rsqlite run: - r-base + - r-curl - r-dbi - 'r-dbplyr >=1.0.0' - r-dplyr @@ -37,8 +41,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package creates a persistent on-disk cache of files that the user can add, update, and retrieve. It is useful for managing resources (such as custom Txdb objects) that are costly or difficult to create, web resources, and data files used across sessions.' - +extra: + parent_recipe: + name: bioconductor-biocfilecache + path: recipes/bioconductor-biocfilecache + version: 1.4.0 diff --git a/recipes/bioconductor-biocgenerics/build.sh b/recipes/bioconductor-biocgenerics/build.sh index 4a709afbd7ab4..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocgenerics/build.sh +++ b/recipes/bioconductor-biocgenerics/build.sh @@ -1,11 +1,11 @@ - #!/bin/bash - mv DESCRIPTION DESCRIPTION.old - grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - mkdir -p ~/.R - echo -e "CC=$CC +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC FC=$FC -$CXX=$CXX +CXX=$CXX CXX98=$CXX CXX11=$CXX CXX14=$CXX" > ~/.R/Makevars - $R CMD INSTALL --build . \ No newline at end of file +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocgraph/build.sh b/recipes/bioconductor-biocgraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocgraph/build.sh +++ b/recipes/bioconductor-biocgraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocgraph/meta.yaml b/recipes/bioconductor-biocgraph/meta.yaml index 869b70e51a793..90fe3917e0c36 100644 --- a/recipes/bioconductor-biocgraph/meta.yaml +++ b/recipes/bioconductor-biocgraph/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "biocGraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 28b1e9cacd61f633c51c1b48a017e6a3caaa21d9efe660d6fe75cb5e9ea2f902 + md5: eca6aee70c90d6a42c92bcada35490eb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: fibroEset, geneplotter, hgu95av2.db requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides examples and code that make use of the different graph related packages produced by Bioconductor.' extra: identifiers: - biotools:biocgraph - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocgraph + path: recipes/bioconductor-biocgraph + version: 1.42.0 + diff --git a/recipes/bioconductor-biocinstaller/build.sh b/recipes/bioconductor-biocinstaller/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocinstaller/build.sh +++ b/recipes/bioconductor-biocinstaller/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocinstaller/conda_build_config.yaml b/recipes/bioconductor-biocinstaller/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-biocinstaller/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-biocinstaller/meta.yaml b/recipes/bioconductor-biocinstaller/meta.yaml index d3fa05009189a..fd36c36939776 100644 --- a/recipes/bioconductor-biocinstaller/meta.yaml +++ b/recipes/bioconductor-biocinstaller/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.1" %} {% set name = "BiocInstaller" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e0395bb6b4d81f7629658730a350bf924d92ab7d414419cea56e1707437ce1f5 + md5: cc58048dad0325a2fca2a92680611c22 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: remotes, RUnit, BiocGenerics requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is used to install and update Bioconductor, CRAN, and (some) github packages.' extra: identifiers: - biotools:biocinstaller - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocinstaller + path: recipes/bioconductor-biocinstaller + version: 1.30.0 + diff --git a/recipes/bioconductor-biocneighbors/build.sh b/recipes/bioconductor-biocneighbors/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocneighbors/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocneighbors/meta.yaml b/recipes/bioconductor-biocneighbors/meta.yaml new file mode 100644 index 0000000000000..e7d97d0d48065 --- /dev/null +++ b/recipes/bioconductor-biocneighbors/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "BiocNeighbors" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 654e4deee2cadb9901f8137142719b16 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle, knitr, rmarkdown, FNN, RcppAnnoy +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-rcpp + - r-rcppannoy + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-rcpp + - r-rcppannoy + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Implements exact and approximate methods for nearest neighbor detection, in a framework that allows them to be easily switched within Bioconductor packages or workflows. The exact algorithm is implemented using pre-clustering with the k-means algorithm, as described by Wang (2012). This is faster than conventional kd-trees for neighbor searching in higher (> 20) dimensional data. The approximate method uses the Annoy algorithm. Functions are also provided to search for all neighbors within a given distance. Parallelization is achieved for all methods using the BiocParallel framework.' + diff --git a/recipes/bioconductor-bioconcotk/build.sh b/recipes/bioconductor-bioconcotk/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioconcotk/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioconcotk/meta.yaml b/recipes/bioconductor-bioconcotk/meta.yaml new file mode 100644 index 0000000000000..d6897fbc276ab --- /dev/null +++ b/recipes/bioconductor-bioconcotk/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.2.0" %} +{% set name = "BiocOncoTK" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 26a8f3e8a0262f795f4e1ebba65f7022 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, dbplyr, DBI, org.Hs.eg.db, MultiAssayExperiment, BiocStyle, ontoProc, ontologyPlot, pogos, GenomeInfoDb, restfulSE (>= 1.3.7), BiocFileCache, TxDb.Hsapiens.UCSC.hg19.knownGene, Biobase, TxDb.Hsapiens.UCSC.hg18.knownGene, reshape2, testthat, AnnotationDbi, FDb.InfiniumMethylation.hg19, EnsDb.Hsapiens.v75 +requirements: + host: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bigrquery + - r-dbi + - r-dplyr + - r-dt + - r-ggplot2 + - r-httr + - r-magrittr + - r-rjson + - r-shiny + run: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bigrquery + - r-dbi + - r-dplyr + - r-dt + - r-ggplot2 + - r-httr + - r-magrittr + - r-rjson + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provide a central interface to various tools for genome-scale analysis of cancer studies.' + diff --git a/recipes/bioconductor-biocor/build.sh b/recipes/bioconductor-biocor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocor/meta.yaml b/recipes/bioconductor-biocor/meta.yaml new file mode 100644 index 0000000000000..0cafbf55eaec4 --- /dev/null +++ b/recipes/bioconductor-biocor/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.6.0" %} +{% set name = "BioCor" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b242a547b800e76229cb0e0e2af8acee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: reactome.db, org.Hs.eg.db, WGCNA, methods, GOSemSim, testthat, knitr, rmarkdown, BiocStyle, airway, DESeq2, boot, targetscan.Hs.eg.db, Hmisc, spelling +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-matrix + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Calculates functional similarities based on the pathways described on KEGG and REACTOME or in gene sets. These similarities can be calculated for pathways or gene sets, genes, or clusters and combined with other similarities. They can be used to improve networks, gene selection, testing relationships...' + diff --git a/recipes/bioconductor-biocparallel/build.sh b/recipes/bioconductor-biocparallel/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocparallel/build.sh +++ b/recipes/bioconductor-biocparallel/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocparallel/meta.yaml b/recipes/bioconductor-biocparallel/meta.yaml index 6e35ffa466d0a..54ace42b445cd 100644 --- a/recipes/bioconductor-biocparallel/meta.yaml +++ b/recipes/bioconductor-biocparallel/meta.yaml @@ -1,24 +1,24 @@ -{% set version = "1.14.2" %} +{% set version = "1.16.2" %} {% set name = "BiocParallel" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d5c568362f06b36494d54f4134a7ac06b45fe2a10236fcdaed9e58288c2a8bd2 + md5: d1141e263ddb453d85dea17f1e89c2e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocGenerics, tools, foreach, BatchJobs, BBmisc, doParallel, Rmpi, GenomicRanges, RNAseqData.HNRNPC.bam.chr14, TxDb.Hsapiens.UCSC.hg19.knownGene, VariantAnnotation, Rsamtools, GenomicAlignments, ShortRead, codetools, RUnit, BiocStyle, knitr, batchtools, data.table +# SystemRequirements: C++11 requirements: - build: - - {{ compiler('fortran') }} host: - r-base - r-bh @@ -37,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | GPL-3' summary: 'This package provides modified versions and novel implementation of functions for parallel evaluation, tailored to use with Bioconductor objects.' extra: identifiers: - biotools:biocparallel - doi:10.1214/14-STS476 + parent_recipe: + name: bioconductor-biocparallel + path: recipes/bioconductor-biocparallel + version: 1.14.2 + diff --git a/recipes/bioconductor-biocpkgtools/build.sh b/recipes/bioconductor-biocpkgtools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocpkgtools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocpkgtools/meta.yaml b/recipes/bioconductor-biocpkgtools/meta.yaml new file mode 100644 index 0000000000000..a4d80d4b00c5c --- /dev/null +++ b/recipes/bioconductor-biocpkgtools/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.1" %} +{% set name = "BiocPkgTools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4cf893ac4c27e85b4fdd4f610abe7e3e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, tm, SnowballC, pdftools, visNetwork, biocViews +requirements: + host: + - r-base + - r-biocmanager + - r-dplyr + - r-dt + - r-htmltools + - r-htmlwidgets + - r-httr + - r-igraph + - r-jsonlite + - r-readr + - r-rex + - r-rvest + - r-stringr + - r-tibble + - r-tidyr + - r-xml2 + run: + - r-base + - r-biocmanager + - r-dplyr + - r-dt + - r-htmltools + - r-htmlwidgets + - r-httr + - r-igraph + - r-jsonlite + - r-readr + - r-rex + - r-rvest + - r-stringr + - r-tibble + - r-tidyr + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Bioconductor has a rich ecosystem of metadata around packages, usage, and build status. This package is a simple collection of functions to access that metadata from R. The goal is to expose metadata for data mining and value-added functionality such as package searching, text mining, and analytics on packages.' + diff --git a/recipes/bioconductor-biocsklearn/build.sh b/recipes/bioconductor-biocsklearn/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocsklearn/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocsklearn/meta.yaml b/recipes/bioconductor-biocsklearn/meta.yaml new file mode 100644 index 0000000000000..6c4f446a60ce5 --- /dev/null +++ b/recipes/bioconductor-biocsklearn/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.4.0" %} +{% set name = "BiocSklearn" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 789848b2d360055fa151d1d1724d9e37 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, restfulSE, HDF5Array +# SystemRequirements: python (>= 2.7), sklearn, numpy, pandas, h5py +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bbmisc + - r-knitr + - r-reticulate + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bbmisc + - r-knitr + - r-reticulate +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides interfaces to selected sklearn elements, and demonstrates fault tolerant use of python modules requiring extensive iteration.' + diff --git a/recipes/bioconductor-biocstyle/build.sh b/recipes/bioconductor-biocstyle/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocstyle/build.sh +++ b/recipes/bioconductor-biocstyle/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocstyle/meta.yaml b/recipes/bioconductor-biocstyle/meta.yaml index d2f39629136ec..7c9ab087a8816 100644 --- a/recipes/bioconductor-biocstyle/meta.yaml +++ b/recipes/bioconductor-biocstyle/meta.yaml @@ -1,30 +1,34 @@ -{% set version = "2.8.2" %} +{% set version = "2.10.0" %} {% set name = "BiocStyle" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5750903f26a961b874c66365936da83dfe523608c9156c870a1c804f7d00a99e + md5: 7f0128f86d5c39d959ad11312d343e1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit, htmltools requirements: host: - r-base + - r-biocmanager - r-bookdown - 'r-knitr >=1.12' - 'r-rmarkdown >=1.2' - r-yaml run: - r-base + - r-biocmanager - r-bookdown - 'r-knitr >=1.12' - 'r-rmarkdown >=1.2' @@ -33,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides standard formatting styles for Bioconductor PDF and HTML documents. Package vignettes illustrate use and functionality.' extra: identifiers: - biotools:biocstyle - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocstyle + path: recipes/bioconductor-biocstyle + version: 2.8.2 + diff --git a/recipes/bioconductor-biocversion/build.sh b/recipes/bioconductor-biocversion/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biocversion/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocversion/meta.yaml b/recipes/bioconductor-biocversion/meta.yaml new file mode 100644 index 0000000000000..3c0f8e8ee20fd --- /dev/null +++ b/recipes/bioconductor-biocversion/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "3.8.0" %} +{% set name = "BiocVersion" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7ebb61bfd78dcc1567b649a35dee075a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides repository information for the appropriate version of Bioconductor.' + diff --git a/recipes/bioconductor-biocviews/build.sh b/recipes/bioconductor-biocviews/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocviews/build.sh +++ b/recipes/bioconductor-biocviews/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocviews/meta.yaml b/recipes/bioconductor-biocviews/meta.yaml index 508ff8266c0e9..dc2e035c72ce2 100644 --- a/recipes/bioconductor-biocviews/meta.yaml +++ b/recipes/bioconductor-biocviews/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.48.3" %} +{% set version = "1.50.9" %} {% set name = "biocViews" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6582f5a443e33bc33ba584e7021d3564fcd791ff9a7ec5a4ec4fef8867e4bbe7 + md5: 4e7e0b4cb13c29161ecc38e0a7f8d0b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-rcurl - r-runit - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-rcurl - r-runit @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infrastructure to support Bioconductor ''views'' used to classify software packages. ''biocViews'' are directed acyclic graphs of terms from a controlled vocabulary. There are three major classifications, corresponding to ''software'', ''annotation'', and ''experiment data'' packages.' extra: identifiers: - biotools:biocviews - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biocviews + path: recipes/bioconductor-biocviews + version: 1.48.3 + diff --git a/recipes/bioconductor-biocworkflowtools/build.sh b/recipes/bioconductor-biocworkflowtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biocworkflowtools/build.sh +++ b/recipes/bioconductor-biocworkflowtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biocworkflowtools/meta.yaml b/recipes/bioconductor-biocworkflowtools/meta.yaml index 1fd21e9ffcd68..cd39744d2304a 100644 --- a/recipes/bioconductor-biocworkflowtools/meta.yaml +++ b/recipes/bioconductor-biocworkflowtools/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "BiocWorkflowTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c617c971066c904c48c3cdb3b4aedcd991abbf6d9188f418d562c0329b7c9076 + md5: 6c344c8e215be2318eca98bc8f579a67 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - r-base - r-bookdown - r-devtools @@ -29,7 +30,7 @@ requirements: - r-rstudioapi - r-stringr run: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - r-base - r-bookdown - r-devtools @@ -43,9 +44,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Provides functions to ease the transition between Rmarkdown and LaTeX documents when authoring a Bioconductor Workflow.' extra: identifiers: - biotools:BiocWorkflowTools + parent_recipe: + name: bioconductor-biocworkflowtools + path: recipes/bioconductor-biocworkflowtools + version: 1.6.2 + diff --git a/recipes/bioconductor-biodist/build.sh b/recipes/bioconductor-biodist/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biodist/build.sh +++ b/recipes/bioconductor-biodist/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biodist/meta.yaml b/recipes/bioconductor-biodist/meta.yaml index d42dd03291571..402f7738896de 100644 --- a/recipes/bioconductor-biodist/meta.yaml +++ b/recipes/bioconductor-biodist/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "bioDist" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5cae25551992991abfdbab65d72e71155e74fefa5b269caa4d2e549a125684c1 + md5: fed70af697577a8e3f3f7065be6b790b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: locfit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-kernsmooth run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-kernsmooth test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of software tools for calculating distance measures.' extra: identifiers: - biotools:biodist - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biodist + path: recipes/bioconductor-biodist + version: 1.52.0 + diff --git a/recipes/bioconductor-biomart/build.sh b/recipes/bioconductor-biomart/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biomart/build.sh +++ b/recipes/bioconductor-biomart/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomart/meta.yaml b/recipes/bioconductor-biomart/meta.yaml index 221067c0faacf..b4df06623c7a8 100644 --- a/recipes/bioconductor-biomart/meta.yaml +++ b/recipes/bioconductor-biomart/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "2.36.1" %} +{% set version = "2.38.0" %} {% set name = "biomaRt" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 94c6abf38f5953f8d4914e56f9ce6afda7fcd5958395dfc726873907cad0e02c + md5: 4a9185e87108865494abcd7340cab002 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: annotate, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-httr - r-progress @@ -26,7 +28,7 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-httr - r-progress @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. Examples of BioMart databases are Ensembl, COSMIC, Uniprot, HGNC, Gramene, Wormbase and dbSNP mapped to Ensembl. These major databases give biomaRt users direct access to a diverse set of data and enable a wide range of powerful online queries from gene annotation to database mining.' + summary: 'In recent years a wealth of biological data has become available in public data repositories. Easy access to these valuable data resources and firm integration with data analysis is needed for comprehensive bioinformatics data analysis. biomaRt provides an interface to a growing collection of databases implementing the BioMart software suite (http://www.biomart.org). The package enables retrieval of large amounts of data in a uniform way without the need to know the underlying database schemas or write complex SQL queries. The most prominent examples of BioMart databases are Ensembl, which provides biomaRt users direct access to a diverse set of data and enables a wide range of powerful online queries from gene annotation to database mining.' extra: identifiers: - biotools:biomaRt - doi:10.1038/nprot.2009.97 + parent_recipe: + name: bioconductor-biomart + path: recipes/bioconductor-biomart + version: 2.36.1 + diff --git a/recipes/bioconductor-biomformat/build.sh b/recipes/bioconductor-biomformat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biomformat/build.sh +++ b/recipes/bioconductor-biomformat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomformat/meta.yaml b/recipes/bioconductor-biomformat/meta.yaml index 7026f64d24cd1..d833e57a94f5b 100644 --- a/recipes/bioconductor-biomformat/meta.yaml +++ b/recipes/bioconductor-biomformat/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "biomformat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9cdc0620e70e96b232d12cbb233e2ddcb728ff9469c1ac01960b9cd43f45375b + md5: 05c08763cf5c899648c492e2e63771bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat (>= 0.10), knitr (>= 1.10), BiocStyle (>= 1.6), rmarkdown (>= 0.7) requirements: host: - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' - 'r-plyr >=1.8' run: - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - r-base - 'r-jsonlite >=0.9.16' - 'r-matrix >=1.2' @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This is an R package for interfacing with the BIOM format. This package includes basic tools for reading biom-format files, accessing and subsetting data tables from a biom object (which is more complex than a single table), as well as limited support for writing a biom-object back to a biom-format file. The design of this API is intended to match the python API and other tools included with the biom-format project, but with a decidedly "R flavor" that should be familiar to R users. This includes S4 classes and methods, as well as extensions of common core functions/methods.' extra: identifiers: - biotools:biomformat - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biomformat + path: recipes/bioconductor-biomformat + version: 1.8.0 + diff --git a/recipes/bioconductor-biomvcclass/build.sh b/recipes/bioconductor-biomvcclass/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biomvcclass/build.sh +++ b/recipes/bioconductor-biomvcclass/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomvcclass/meta.yaml b/recipes/bioconductor-biomvcclass/meta.yaml index bdd9d8609b700..f620842beb20f 100644 --- a/recipes/bioconductor-biomvcclass/meta.yaml +++ b/recipes/bioconductor-biomvcclass/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "BioMVCClass" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0fc37d1bb8c04530f42a99d925e9dc4c23bbc877466947b4f1eecc8481f9d9c4 + md5: a37c816ced8ff46c22e7493f9e10997f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-mvcclass >=1.54.0,<1.56.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-mvcclass >=1.56.0,<1.57.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-mvcclass >=1.54.0,<1.56.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-mvcclass >=1.56.0,<1.57.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Creates classes used in model-view-controller (MVC) design' extra: identifiers: - biotools:biomvcclass - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biomvcclass + path: recipes/bioconductor-biomvcclass + version: 1.48.0 + diff --git a/recipes/bioconductor-biomvrcns/build.sh b/recipes/bioconductor-biomvrcns/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biomvrcns/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biomvrcns/meta.yaml b/recipes/bioconductor-biomvrcns/meta.yaml new file mode 100644 index 0000000000000..e257e5f12e0c1 --- /dev/null +++ b/recipes/bioconductor-biomvrcns/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.22.0" %} +{% set name = "biomvRCNS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 43649cec95f927eace8290ffe12e756d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: cluster, parallel, GenomicFeatures, dynamicTreeCut, Rsamtools, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-mvtnorm + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-mvtnorm + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'In this package, a Hidden Semi Markov Model (HSMM) and one homogeneous segmentation model are designed and implemented for segmentation genomic data, with the aim of assisting in transcripts detection using high throughput technology like RNA-seq or tiling array, and copy number analysis using aCGH or sequencing.' + diff --git a/recipes/bioconductor-bionet/build.sh b/recipes/bioconductor-bionet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bionet/build.sh +++ b/recipes/bioconductor-bionet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bionet/meta.yaml b/recipes/bioconductor-bionet/meta.yaml index baca54696a37d..d0c3a172034e5 100644 --- a/recipes/bioconductor-bionet/meta.yaml +++ b/recipes/bioconductor-bionet/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "BioNet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6aa91986c4dd4d77f9920e7600c66a1951343e648c4e1f8d31ca48b993d259ab + md5: c87b42a860906cd6ec25b02150e4b763 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: rgl, impute, DLBCL, genefilter, xtable, ALL, limma, hgu95av2.db, XML requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - 'r-igraph >=1.0.1' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - 'r-igraph >=1.0.1' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides functions for the integrated analysis of protein-protein interaction networks and the detection of functional modules. Different datasets can be integrated into the network by assigning p-values of statistical tests to the nodes of the network. E.g. p-values obtained from the differential expression of the genes from an Affymetrix array are assigned to the nodes of the network. By fitting a beta-uniform mixture model and calculating scores from the p-values, overall scores of network regions can be calculated and an integer linear programming algorithm identifies the maximum scoring subnetwork.' extra: identifiers: - biotools:bionet + parent_recipe: + name: bioconductor-bionet + path: recipes/bioconductor-bionet + version: 1.40.0 + diff --git a/recipes/bioconductor-bionetstat/build.sh b/recipes/bioconductor-bionetstat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bionetstat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bionetstat/meta.yaml b/recipes/bioconductor-bionetstat/meta.yaml new file mode 100644 index 0000000000000..b995e11123ce1 --- /dev/null +++ b/recipes/bioconductor-bionetstat/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.2.0" %} +{% set name = "BioNetStat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 094c9aa37860763275b7117819e9ef01 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - r-base + - r-ggplot2 + - r-hmisc + - r-igraph + - r-knitr + - r-pheatmap + - r-plyr + - r-psych + - r-rcolorbrewer + - r-rjsonio + - r-shiny + - r-shinybs + - r-whisker + - r-yaml + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - r-base + - r-ggplot2 + - r-hmisc + - r-igraph + - r-knitr + - r-pheatmap + - r-plyr + - r-psych + - r-rcolorbrewer + - r-rjsonio + - r-shiny + - r-shinybs + - r-whisker + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'A package to perform differential network analysis, differential node analysis (differential coexpression analysis), network and metabolic pathways view.' + diff --git a/recipes/bioconductor-bioqc/build.sh b/recipes/bioconductor-bioqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bioqc/build.sh +++ b/recipes/bioconductor-bioqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioqc/meta.yaml b/recipes/bioconductor-bioqc/meta.yaml index c9e4e9a393fa9..4d120ef1c597a 100644 --- a/recipes/bioconductor-bioqc/meta.yaml +++ b/recipes/bioconductor-bioqc/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "BioQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ef22544a0fb005c332a14edd802772146cc346a03e229a46b09592423bb2a0ee + md5: 47b14e1b9485410002bb96d5346fb525 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, lattice, latticeExtra, rbenchmark, gplots, gridExtra, hgu133plus2.db, ineq requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcpp run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcpp build: @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'BioQC performs quality control of high-throughput expression data based on tissue gene signatures. It can detect tissue heterogeneity in gene expression data. The core algorithm is a Wilcoxon-Mann-Whitney test that is optimised for high performance.' extra: identifiers: - biotools:bioqc - doi:10.1186/s12864-017-3661-2 + parent_recipe: + name: bioconductor-bioqc + path: recipes/bioconductor-bioqc + version: 1.8.0 + diff --git a/recipes/bioconductor-bioseqclass/build.sh b/recipes/bioconductor-bioseqclass/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bioseqclass/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bioseqclass/meta.yaml b/recipes/bioconductor-bioseqclass/meta.yaml new file mode 100644 index 0000000000000..738ec4695c788 --- /dev/null +++ b/recipes/bioconductor-bioseqclass/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.40.0" %} +{% set name = "BioSeqClass" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9bb1fbea1848a6ffe2e020deaa1f3777 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: scatterplot3d +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-class + - r-e1071 + - r-foreign + - r-ipred + - r-klar + - r-nnet + - r-party + - r-randomforest + - r-rpart + - r-scatterplot3d + - r-tree + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-class + - r-e1071 + - r-foreign + - r-ipred + - r-klar + - r-nnet + - r-party + - r-randomforest + - r-rpart + - r-scatterplot3d + - r-tree +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'Extracting Features from Biological Sequences and Building Classification Model' + diff --git a/recipes/bioconductor-biosigner/build.sh b/recipes/bioconductor-biosigner/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biosigner/build.sh +++ b/recipes/bioconductor-biosigner/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biosigner/meta.yaml b/recipes/bioconductor-biosigner/meta.yaml index 41fecfe9c5a0e..173a47f5d06fb 100644 --- a/recipes/bioconductor-biosigner/meta.yaml +++ b/recipes/bioconductor-biosigner/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "biosigner" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9a06b5b98dd98afe127a170415815dfa3aabf65561f7ee01f67c103f2ab632df + md5: 5a7f57cd3552ed1c2cf21cf18f33da77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BioMark, RUnit, BiocGenerics, BiocStyle, golubEsets, hu6800.db, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ropls >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' - r-base - r-e1071 - r-randomforest run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ropls >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' - r-base - r-e1071 - r-randomforest @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Feature selection is critical in omics data analysis to extract restricted and meaningful molecular signatures from complex and high-dimension data, and to build robust classifiers. This package implements a new method to assess the relevance of the variables for the prediction performances of the classifier. The approach can be run in parallel with the PLS-DA, Random Forest, and SVM binary classifiers. The signatures and the corresponding ''restricted'' models are returned, enabling future predictions on new datasets. A Galaxy implementation of the package is available within the Workflow4metabolomics.org online infrastructure for computational metabolomics.' extra: identifiers: - biotools:biosigner - doi:10.3389/fmolb.2016.00026 + parent_recipe: + name: bioconductor-biosigner + path: recipes/bioconductor-biosigner + version: 1.8.0 + diff --git a/recipes/bioconductor-biostrings/build.sh b/recipes/bioconductor-biostrings/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biostrings/build.sh +++ b/recipes/bioconductor-biostrings/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biostrings/meta.yaml b/recipes/bioconductor-biostrings/meta.yaml index 8d95d5a78488c..06df5c73056ac 100644 --- a/recipes/bioconductor-biostrings/meta.yaml +++ b/recipes/bioconductor-biostrings/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.1" %} {% set name = "Biostrings" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d244dd2dbe1fdaff293b07d6a9009f7fea49742dc252535f6cfea02941220b85 + md5: a61189641d25f5a7bb17738198885ce4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome (>= 1.13.14), BSgenome.Celegans.UCSC.ce2 (>= 1.3.11), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.11), BSgenome.Hsapiens.UCSC.hg18, drosophila2probe, hgu95av2probe, hgu133aprobe, GenomicFeatures (>= 1.3.14), hgu95av2cdf, affy (>= 1.41.3), affydata (>= 1.11.5), RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Memory efficient string containers, string matching algorithms, and other utilities, for fast manipulation of large biological sequences or sets of sequences.' extra: identifiers: - biotools:biostrings - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biostrings + path: recipes/bioconductor-biostrings + version: 2.48.0 + diff --git a/recipes/bioconductor-biosvd/build.sh b/recipes/bioconductor-biosvd/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biosvd/build.sh +++ b/recipes/bioconductor-biosvd/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biosvd/meta.yaml b/recipes/bioconductor-biosvd/meta.yaml index 0ed265a9622c9..906c728864411 100644 --- a/recipes/bioconductor-biosvd/meta.yaml +++ b/recipes/bioconductor-biosvd/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "biosvd" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 203134745fde2bde03a835516459261f87bd52bddc055be15b7d6609a488b507 + md5: aeb5728b6822575a2e87140073a2de84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-nmf run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-nmf test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The biosvd package contains functions to reduce the input data set from the feature x assay space to the reduced diagonalized eigenfeature x eigenassay space, with the eigenfeatures and eigenassays unique orthonormal superpositions of the features and assays, respectively. Results of SVD applied to the data can subsequently be inspected based on generated graphs, such as a heatmap of the eigenfeature x assay matrix and a bar plot with the eigenexpression fractions of all eigenfeatures. These graphs aid in deciding which eigenfeatures and eigenassays to filter out (i.e., eigenfeatures representing steady state, noise, or experimental artifacts; or when applied to the variance in the data, eigenfeatures representing steady-scale variance). After possible removal of steady state expression, steady-scale variance, noise and experimental artifacts, and after re-applying SVD to the normalized data, a summary html report of the eigensystem is generated, containing among others polar plots of the assays and features, a table with the list of features sortable according to their coordinates, radius and phase in the polar plot, and a visualization of the data sorted according to the two selected eigenfeatures and eigenassays with colored feature/assay annotation information when provided. This gives a global picture of the dynamics of expression/intensity levels, in which individual features and assays are classified in groups of similar regulation and function or similar cellular state and biological phenotype.' extra: identifiers: - biotools:biosvd - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biosvd + path: recipes/bioconductor-biosvd + version: 2.16.0 + diff --git a/recipes/bioconductor-biotmle/build.sh b/recipes/bioconductor-biotmle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-biotmle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biotmle/meta.yaml b/recipes/bioconductor-biotmle/meta.yaml new file mode 100644 index 0000000000000..78b9b5de9386e --- /dev/null +++ b/recipes/bioconductor-biotmle/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.6.0" %} +{% set name = "biotmle" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 19b83e8aa5038a0a939357fa63638a44 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, Matrix, DBI, biotmleData (>= 1.1.1) +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dofuture + - r-dplyr + - r-future + - r-ggplot2 + - r-ggsci + - r-superheat + - r-tmle + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dofuture + - r-dplyr + - r-future + - r-ggplot2 + - r-ggsci + - r-superheat + - r-tmle +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package facilitates the discovery of biomarkers from biological sequencing data (e.g., microarrays, RNA-seq) based on the associations of potential biomarkers with exposure and outcome variables by implementing an estimation procedure that combines a generalization of moderated statistics with targeted minimum loss-based estimates (TMLE) of parameters defined via causal inference (e.g., Average Treatment Effect) whose estimators admit asymptotically linear representations.' + diff --git a/recipes/bioconductor-biotmledata/meta.yaml b/recipes/bioconductor-biotmledata/meta.yaml new file mode 100644 index 0000000000000..32c9a28a71506 --- /dev/null +++ b/recipes/bioconductor-biotmledata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.6.0" %} +{% set name = "biotmleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 14d22102df0583c9d12c3bc003a4c544 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, SummarizedExperiment +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Microarray data (from the Illumina Ref-8 BeadChips platform) and phenotype-level data from an epidemiological investigation of benzene exposure, packaged using "SummarizedExperiemnt", for use as an example with the "biotmle" R package.' + diff --git a/recipes/bioconductor-biotmledata/post-link.sh b/recipes/bioconductor-biotmledata/post-link.sh new file mode 100644 index 0000000000000..66ace8661c31e --- /dev/null +++ b/recipes/bioconductor-biotmledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="biotmleData_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/biotmleData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/biotmleData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-biotmledata/bioconductor-biotmledata_1.6.0_src_all.tar.gz" +) +MD5="14d22102df0583c9d12c3bc003a4c544" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-biotmledata/pre-unlink.sh b/recipes/bioconductor-biotmledata/pre-unlink.sh new file mode 100644 index 0000000000000..3c9efddb76881 --- /dev/null +++ b/recipes/bioconductor-biotmledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ biotmleData diff --git a/recipes/bioconductor-biovizbase/build.sh b/recipes/bioconductor-biovizbase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biovizbase/build.sh +++ b/recipes/bioconductor-biovizbase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biovizbase/meta.yaml b/recipes/bioconductor-biovizbase/meta.yaml index e68fc8be366e4..57d93c5ada305 100644 --- a/recipes/bioconductor-biovizbase/meta.yaml +++ b/recipes/bioconductor-biovizbase/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.28.2" %} +{% set version = "1.30.0" %} {% set name = "biovizBase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f82137f3f5c985f567ae65ecc6e65cbfa385ec90b2cfb90889015807872c8471 + md5: d4ca948ad432870df1899d43083b6f64 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome, rtracklayer, EnsDb.Hsapiens.v75, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-dichromat - r-hmisc @@ -39,20 +40,20 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-dichromat - r-hmisc @@ -66,10 +67,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The biovizBase package is designed to provide a set of utilities, color schemes and conventions for genomic data. It serves as the base for various high-level packages for biological data visualization. This saves development effort and encourages consistency.' extra: identifiers: - biotools:biovizbase - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-biovizbase + path: recipes/bioconductor-biovizbase + version: 1.28.2 + diff --git a/recipes/bioconductor-birewire/build.sh b/recipes/bioconductor-birewire/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-birewire/build.sh +++ b/recipes/bioconductor-birewire/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-birewire/meta.yaml b/recipes/bioconductor-birewire/meta.yaml index 2d2946cc97c6f..7f61935190187 100644 --- a/recipes/bioconductor-birewire/meta.yaml +++ b/recipes/bioconductor-birewire/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "3.12.0" %} +{% set version = "3.14.0" %} {% set name = "BiRewire" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 05c9329d86695b52a6a550762b5d56529113a48d5fde9b6579340f78bb0dc4b8 + md5: dfa755b6535050e3c39865feedb53c55 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -36,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Fast functions for bipartite network rewiring through N consecutive switching steps (See References) and for the computation of the minimal number of switching steps to be performed in order to maximise the dissimilarity with respect to the original network. Includes functions for the analysis of the introduced randomness across the switching steps and several other routines to analyse the resulting networks and their natural projections. Extension to undirected networks and directed signed networks is also provided. Starting from version 1.9.7 a more precise bound (especially for small network) has been implemented. Starting from version 2.2.0 the analysis routine is more complete and a visual montioring of the underlying Markov Chain has been implemented. Starting from 3.6.0 the library can handle also matrices with NA (not for the directed signed graphs).' extra: identifiers: - biotools:birewire + parent_recipe: + name: bioconductor-birewire + path: recipes/bioconductor-birewire + version: 3.12.0 + diff --git a/recipes/bioconductor-birta/build.sh b/recipes/bioconductor-birta/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-birta/build.sh +++ b/recipes/bioconductor-birta/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-birta/meta.yaml b/recipes/bioconductor-birta/meta.yaml index 34856df322513..783f517362b43 100644 --- a/recipes/bioconductor-birta/meta.yaml +++ b/recipes/bioconductor-birta/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "birta" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7bb2ddab319fc6d155912eb285acb1258f7842d030965ee2267b2937546cdcc0 + md5: 16a30ffecfc786f5ba64e8796f4a8266 build: number: 0 rpaths: @@ -18,13 +18,13 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-mass build: @@ -35,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. birta (Bayesian Inference of Regulation of Transcriptional Activity) uses the regulatory networks of TFs and miRNAs together with mRNA and miRNA expression data to predict switches in regulatory activity between two conditions. A Bayesian network is used to model the regulatory structure and Markov-Chain-Monte-Carlo is applied to sample the activity states.' extra: identifiers: - biotools:birta - doi:10.1093/bioinformatics/bts257 + parent_recipe: + name: bioconductor-birta + path: recipes/bioconductor-birta + version: 1.24.0 + diff --git a/recipes/bioconductor-birte/build.sh b/recipes/bioconductor-birte/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-birte/build.sh +++ b/recipes/bioconductor-birte/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-birte/meta.yaml b/recipes/bioconductor-birte/meta.yaml index ab032f5eae665..c4998faa7e1ec 100644 --- a/recipes/bioconductor-birte/meta.yaml +++ b/recipes/bioconductor-birte/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "birte" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 55af4ce33820be43a9f42fbffca1955321d6ae3af521400b45cf001a990a4bdc + md5: b36a82163e94932b5fc3c7bf23b0fa3f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr +# SystemRequirements: BLAS, LAPACK requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' - r-base - r-glmnet - r-mass - r-rcpp - 'r-rcpparmadillo >=0.3.6.1' - - openblas run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' - r-base - r-glmnet - r-mass - r-rcpp - 'r-rcpparmadillo >=0.3.6.1' - - openblas + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Expression levels of mRNA molecules are regulated by different processes, comprising inhibition or activation by transcription factors and post-transcriptional degradation by microRNAs. biRte uses regulatory networks of TFs, miRNAs and possibly other factors, together with mRNA, miRNA and other available expression data to predict the relative influence of a regulator on the expression of its target genes. Inference is done in a Bayesian modeling framework using Markov-Chain-Monte-Carlo. A special feature is the possibility for follow-up network reverse engineering between active regulators.' extra: identifiers: - biotools:birte - doi:10.1093/bioinformatics/btv379 + parent_recipe: + name: bioconductor-birte + path: recipes/bioconductor-birte + version: 1.16.0 + diff --git a/recipes/bioconductor-biseq/build.sh b/recipes/bioconductor-biseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-biseq/build.sh +++ b/recipes/bioconductor-biseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-biseq/meta.yaml b/recipes/bioconductor-biseq/meta.yaml index 64da5cbc8f06c..2a25a7b39bc31 100644 --- a/recipes/bioconductor-biseq/meta.yaml +++ b/recipes/bioconductor-biseq/meta.yaml @@ -1,46 +1,47 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "BiSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b2c2794e56066315ef680cdc513797def0e92651cc1c722af9f6a8b884ca8de0 + md5: 2a92d9e431dba31d85eb4b55a7239214 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-betareg - r-formula - r-lokern run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-betareg - r-formula @@ -49,10 +50,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The BiSeq package provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data. In particular, it implements an algorithm to detect differentially methylated regions (DMRs). The package takes already aligned BS data from one or multiple samples.' extra: identifiers: - biotools:biseq - doi:10.1093/bib/bbv095 + parent_recipe: + name: bioconductor-biseq + path: recipes/bioconductor-biseq + version: 1.20.0 + diff --git a/recipes/bioconductor-bitseq/build.sh b/recipes/bioconductor-bitseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bitseq/build.sh +++ b/recipes/bioconductor-bitseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bitseq/meta.yaml b/recipes/bioconductor-bitseq/meta.yaml index 1c64a36820da9..83286885dbed2 100644 --- a/recipes/bioconductor-bitseq/meta.yaml +++ b/recipes/bioconductor-bitseq/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BitSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 073667c05fbec52c3eea932a3da68393240ae94fe069a46841b6bc5862060491 + md5: 563db99a022384f3bb02354a18ca1397 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: edgeR, DESeq, BiocStyle requirements: host: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'The BitSeq package is targeted for transcript expression analysis and differential expression analysis of RNA-seq data in two stage process. In the first stage it uses Bayesian inference methodology to infer expression of individual transcripts from individual RNA-seq experiments. The second stage of BitSeq embraces the differential expression analysis of transcript expression. Providing expression estimates from replicates of multiple conditions, Log-Normal model of the estimates is used for inferring the condition mean transcript expression and ranking the transcripts based on the likelihood of differential expression.' extra: identifiers: - biotools:bitseq + parent_recipe: + name: bioconductor-bitseq + path: recipes/bioconductor-bitseq + version: 1.24.0 + diff --git a/recipes/bioconductor-bladderbatch/meta.yaml b/recipes/bioconductor-bladderbatch/meta.yaml index a8b10fa28b62d..35443e01d4fb6 100644 --- a/recipes/bioconductor-bladderbatch/meta.yaml +++ b/recipes/bioconductor-bladderbatch/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "bladderbatch" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecf44aaa06317c9ae9cad015718c889510f7f9b9fb6eb4d46ef23f0150ab0005 + md5: 27cf90b928cffce1c1ae3e0b3a99e687 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package contains microarray gene expression data on 57 bladder samples from 5 batches. The data are used as an illustrative example for the sva package.' - +extra: + parent_recipe: + name: bioconductor-bladderbatch + path: recipes/bioconductor-bladderbatch + version: 1.18.0 diff --git a/recipes/bioconductor-bladderbatch/post-link.sh b/recipes/bioconductor-bladderbatch/post-link.sh index c1c628daf295c..e5a7808b57944 100644 --- a/recipes/bioconductor-bladderbatch/post-link.sh +++ b/recipes/bioconductor-bladderbatch/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="bladderbatch_1.18.0.tar.gz" +FN="bladderbatch_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/bladderbatch_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/bladderbatch_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bladderbatch_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/bladderbatch_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bladderbatch/bioconductor-bladderbatch_1.20.0_src_all.tar.gz" ) -MD5="c9baea96a9d50fadbbdfcf319c76b717" +MD5="27cf90b928cffce1c1ae3e0b3a99e687" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-blima/build.sh b/recipes/bioconductor-blima/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-blima/build.sh +++ b/recipes/bioconductor-blima/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-blima/meta.yaml b/recipes/bioconductor-blima/meta.yaml index c14ed977ef371..853a126673e1b 100644 --- a/recipes/bioconductor-blima/meta.yaml +++ b/recipes/bioconductor-blima/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "blima" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9548736beec21598bc8496f0d56fbeee88ad9d8fecf16c38c47950d629163935 + md5: a12b89fa5b76052797843be0affdd48c build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: xtable, blimaTestingData, BiocStyle, illuminaHumanv4.db, lumi, knitr requirements: host: - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - 'r-rcpp >=0.12.8' run: - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - 'r-rcpp >=0.12.8' build: @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Package blima includes several algorithms for the preprocessing of Illumina microarray data. It focuses to the bead level analysis and provides novel approach to the quantile normalization of the vectors of unequal lengths. It provides variety of the methods for background correction including background subtraction, RMA like convolution and background outlier removal. It also implements variance stabilizing transformation on the bead level. There are also implemented methods for data summarization. It also provides the methods for performing T-tests on the detector (bead) level and on the probe level for differential expression testing.' extra: identifiers: - biotools:blima - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-blima + path: recipes/bioconductor-blima + version: 1.14.0 + diff --git a/recipes/bioconductor-blimatestingdata/meta.yaml b/recipes/bioconductor-blimatestingdata/meta.yaml new file mode 100644 index 0000000000000..216db70d0daee --- /dev/null +++ b/recipes/bioconductor-blimatestingdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "blimaTestingData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7e41a94448ab84c270161d5e9cb5a623 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: blima, beadarray, illuminaHumanv4.db, BiocStyle +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Experiment data package. The set were prepared using microarray images of human mesenchymal cells treated with various supplements. This package is intended to provide example data to test functionality provided by blima.' + diff --git a/recipes/bioconductor-blimatestingdata/post-link.sh b/recipes/bioconductor-blimatestingdata/post-link.sh new file mode 100644 index 0000000000000..e2b36c5324549 --- /dev/null +++ b/recipes/bioconductor-blimatestingdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="blimaTestingData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/blimaTestingData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/blimaTestingData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-blimatestingdata/bioconductor-blimatestingdata_1.2.0_src_all.tar.gz" +) +MD5="7e41a94448ab84c270161d5e9cb5a623" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-blimatestingdata/pre-unlink.sh b/recipes/bioconductor-blimatestingdata/pre-unlink.sh new file mode 100644 index 0000000000000..72c41f86ef0a0 --- /dev/null +++ b/recipes/bioconductor-blimatestingdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ blimaTestingData diff --git a/recipes/bioconductor-blma/build.sh b/recipes/bioconductor-blma/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-blma/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-blma/meta.yaml b/recipes/bioconductor-blma/meta.yaml new file mode 100644 index 0000000000000..3d424c5bde083 --- /dev/null +++ b/recipes/bioconductor-blma/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "BLMA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 42b39994812056f775ef77969f32ccdc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-padog >=1.24.0,<1.25.0' + - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - r-base + - r-gsa + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-padog >=1.24.0,<1.25.0' + - 'bioconductor-rontotools >=2.10.0,<2.11.0' + - r-base + - r-gsa +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Suit of tools for bi-level meta-analysis. The package can be used in a wide range of applications, including general hypothesis testings, differential expression analysis, functional analysis, and pathway analysis.' + diff --git a/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml new file mode 100644 index 0000000000000..213fd155cb387 --- /dev/null +++ b/recipes/bioconductor-bloodcancermultiomics2017/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.2.0" %} +{% set name = "BloodCancerMultiOmics2017" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 15b928a89d53d59a59901c520a2368f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, tidyverse, xtable +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-beeswarm + - r-devtools + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-glmnet + - r-gtable + - r-ipflasso + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-survival + - r-tibble + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-beeswarm + - r-devtools + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-glmnet + - r-gtable + - r-ipflasso + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-survival + - r-tibble + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 3)' + summary: 'The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.' + diff --git a/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh new file mode 100644 index 0000000000000..09dd5f367bc23 --- /dev/null +++ b/recipes/bioconductor-bloodcancermultiomics2017/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BloodCancerMultiOmics2017_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/BloodCancerMultiOmics2017_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/BloodCancerMultiOmics2017_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bloodcancermultiomics2017/bioconductor-bloodcancermultiomics2017_1.2.0_src_all.tar.gz" +) +MD5="15b928a89d53d59a59901c520a2368f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bloodcancermultiomics2017/pre-unlink.sh b/recipes/bioconductor-bloodcancermultiomics2017/pre-unlink.sh new file mode 100644 index 0000000000000..1b248285144aa --- /dev/null +++ b/recipes/bioconductor-bloodcancermultiomics2017/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BloodCancerMultiOmics2017 diff --git a/recipes/bioconductor-bnbc/build.sh b/recipes/bioconductor-bnbc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bnbc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bnbc/meta.yaml b/recipes/bioconductor-bnbc/meta.yaml new file mode 100644 index 0000000000000..36cfe9b3ea8bc --- /dev/null +++ b/recipes/bioconductor-bnbc/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.4.0" %} +{% set name = "bnbc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5aa07b96e10124cc3d9ce6f1b30aa935 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, RUnit +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-matrixstats + - 'r-rcpp >=0.12.12' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-matrixstats + - 'r-rcpp >=0.12.12' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools to normalize (several) Hi-C data from replicates.' + diff --git a/recipes/bioconductor-bovine.db/meta.yaml b/recipes/bioconductor-bovine.db/meta.yaml new file mode 100644 index 0000000000000..2d74db4665b52 --- /dev/null +++ b/recipes/bioconductor-bovine.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "bovine.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0006dd79279fa1bf69a275e0586f2197 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.bt.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.bt.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix bovine annotation data (chip bovine) assembled using data from public repositories' + diff --git a/recipes/bioconductor-bovine.db/post-link.sh b/recipes/bioconductor-bovine.db/post-link.sh new file mode 100644 index 0000000000000..fa327eb20d587 --- /dev/null +++ b/recipes/bioconductor-bovine.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bovine.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovine.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/bovine.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovine.db/bioconductor-bovine.db_3.2.3_src_all.tar.gz" +) +MD5="0006dd79279fa1bf69a275e0586f2197" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bovine.db/pre-unlink.sh b/recipes/bioconductor-bovine.db/pre-unlink.sh new file mode 100644 index 0000000000000..253aafa30b39f --- /dev/null +++ b/recipes/bioconductor-bovine.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bovine.db diff --git a/recipes/bioconductor-bovine.db0/meta.yaml b/recipes/bioconductor-bovine.db0/meta.yaml new file mode 100644 index 0000000000000..a70955401d4fd --- /dev/null +++ b/recipes/bioconductor-bovine.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "bovine.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 26ad273e690096d02697afa70888c38c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for bovine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-bovine.db0/post-link.sh b/recipes/bioconductor-bovine.db0/post-link.sh new file mode 100644 index 0000000000000..3249cd9c9462c --- /dev/null +++ b/recipes/bioconductor-bovine.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bovine.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovine.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/bovine.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovine.db0/bioconductor-bovine.db0_3.7.1_src_all.tar.gz" +) +MD5="26ad273e690096d02697afa70888c38c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bovine.db0/pre-unlink.sh b/recipes/bioconductor-bovine.db0/pre-unlink.sh new file mode 100644 index 0000000000000..dc2b7ae080fb9 --- /dev/null +++ b/recipes/bioconductor-bovine.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bovine.db0 diff --git a/recipes/bioconductor-bovinecdf/meta.yaml b/recipes/bioconductor-bovinecdf/meta.yaml new file mode 100644 index 0000000000000..5967e371f11df --- /dev/null +++ b/recipes/bioconductor-bovinecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "bovinecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e155fc7d5f84ee420d9b250a639af305 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Bovine.cdf file.' + diff --git a/recipes/bioconductor-bovinecdf/post-link.sh b/recipes/bioconductor-bovinecdf/post-link.sh new file mode 100644 index 0000000000000..959cc29725a63 --- /dev/null +++ b/recipes/bioconductor-bovinecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bovinecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovinecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bovinecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovinecdf/bioconductor-bovinecdf_2.18.0_src_all.tar.gz" +) +MD5="e155fc7d5f84ee420d9b250a639af305" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bovinecdf/pre-unlink.sh b/recipes/bioconductor-bovinecdf/pre-unlink.sh new file mode 100644 index 0000000000000..5fd857278ac52 --- /dev/null +++ b/recipes/bioconductor-bovinecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bovinecdf diff --git a/recipes/bioconductor-bovineprobe/meta.yaml b/recipes/bioconductor-bovineprobe/meta.yaml new file mode 100644 index 0000000000000..66f0294de4222 --- /dev/null +++ b/recipes/bioconductor-bovineprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "bovineprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9f9e25fc8c7a76acf541745b7c09748b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bovine\_probe\_tab.' + diff --git a/recipes/bioconductor-bovineprobe/post-link.sh b/recipes/bioconductor-bovineprobe/post-link.sh new file mode 100644 index 0000000000000..4a7e958e3ae3f --- /dev/null +++ b/recipes/bioconductor-bovineprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bovineprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bovineprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bovineprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bovineprobe/bioconductor-bovineprobe_2.18.0_src_all.tar.gz" +) +MD5="9f9e25fc8c7a76acf541745b7c09748b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bovineprobe/pre-unlink.sh b/recipes/bioconductor-bovineprobe/pre-unlink.sh new file mode 100644 index 0000000000000..754672fc0a421 --- /dev/null +++ b/recipes/bioconductor-bovineprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bovineprobe diff --git a/recipes/bioconductor-bprmeth/build.sh b/recipes/bioconductor-bprmeth/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bprmeth/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bprmeth/meta.yaml b/recipes/bioconductor-bprmeth/meta.yaml new file mode 100644 index 0000000000000..c13a191da64d7 --- /dev/null +++ b/recipes/bioconductor-bprmeth/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.8.0" %} +{% set name = "BPRMeth" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e65845c1ae3c23ab6094e7461b80fa7a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-assertthat + - r-base + - r-cowplot + - r-data.table + - r-doparallel + - r-e1071 + - r-earth + - r-foreach + - r-ggplot2 + - r-kernlab + - r-magrittr + - r-mass + - r-matrixcalc + - r-mvtnorm + - r-randomforest + - 'r-rcpp >=0.12.14' + - r-rcpparmadillo + - r-truncnorm + run: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-assertthat + - r-base + - r-cowplot + - r-data.table + - r-doparallel + - r-e1071 + - r-earth + - r-foreach + - r-ggplot2 + - r-kernlab + - r-magrittr + - r-mass + - r-matrixcalc + - r-mvtnorm + - r-randomforest + - 'r-rcpp >=0.12.14' + - r-rcpparmadillo + - r-truncnorm + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The BPRMeth package is a probabilistic method to quantify explicit features of methylation profiles, in a way that would make it easier to formally use such profiles in downstream modelling efforts, such as predicting gene expression levels or clustering genomic regions or cells according to their methylation profiles.' + diff --git a/recipes/bioconductor-brain/build.sh b/recipes/bioconductor-brain/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-brain/build.sh +++ b/recipes/bioconductor-brain/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-brain/meta.yaml b/recipes/bioconductor-brain/meta.yaml index 2fd2a9d8c0cb6..ee78ff869b55f 100644 --- a/recipes/bioconductor-brain/meta.yaml +++ b/recipes/bioconductor-brain/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "BRAIN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bf56e42ac4f497e66c020436a80fc24768b8f733b63ab8bef3e3ee8cbc0a40a6 + md5: 06078b007f8aa959113d885ba24e1667 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-lattice - r-polynomf run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-lattice - r-polynomf @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Package for calculating aggregated isotopic distribution and exact center-masses for chemical substances (in this version composed of C, H, N, O and S). This is an implementation of the BRAIN algorithm described in the paper by J. Claesen, P. Dittwald, T. Burzykowski and D. Valkenborg.' extra: identifiers: - biotools:brain - doi:10.1021/ac303439m + parent_recipe: + name: bioconductor-brain + path: recipes/bioconductor-brain + version: 1.26.0 + diff --git a/recipes/bioconductor-brainimager/build.sh b/recipes/bioconductor-brainimager/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-brainimager/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-brainimager/meta.yaml b/recipes/bioconductor-brainimager/meta.yaml new file mode 100644 index 0000000000000..01dc3279c8bcd --- /dev/null +++ b/recipes/bioconductor-brainimager/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "brainImageR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c77706bbf26dc837b806693cba2728d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-randomforest + - r-rcolorbrewer + - r-testthat + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-randomforest + - r-rcolorbrewer + - r-testthat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY-SA 4.0' + summary: 'BrainImageR is a package that provides the user with information of where in the human brain their gene set corresponds to. This is provided both as a continuous variable and as a easily-interpretable image. BrainImageR has additional functionality of identifying approximately when in developmental time that a gene expression dataset corresponds to. Both the spatial gene set enrichment and the developmental time point prediction are assessed in comparison to the Allen Brain Atlas reference data.' + diff --git a/recipes/bioconductor-brainimagerdata/meta.yaml b/recipes/bioconductor-brainimagerdata/meta.yaml new file mode 100644 index 0000000000000..a7615c52d92f0 --- /dev/null +++ b/recipes/bioconductor-brainimagerdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "brainImageRdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87e676b7cde0a2abb781670ade0e68d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'CC BY-SA 4.0' + summary: 'brainImageRdata contains image masks for the developing human and the adult human brain. These masks can be used in conjunction with the gene expression data to generate spatial gene set enrichment plots. It also contains the expression data for the 15 pcw human brain, the adult human brain, and the developing human brain.' + diff --git a/recipes/bioconductor-brainimagerdata/post-link.sh b/recipes/bioconductor-brainimagerdata/post-link.sh new file mode 100644 index 0000000000000..ceb99527cac88 --- /dev/null +++ b/recipes/bioconductor-brainimagerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="brainImageRdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/brainImageRdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/brainImageRdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-brainimagerdata/bioconductor-brainimagerdata_1.0.0_src_all.tar.gz" +) +MD5="87e676b7cde0a2abb781670ade0e68d9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-brainimagerdata/pre-unlink.sh b/recipes/bioconductor-brainimagerdata/pre-unlink.sh new file mode 100644 index 0000000000000..6038bfadb08b6 --- /dev/null +++ b/recipes/bioconductor-brainimagerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ brainImageRdata diff --git a/recipes/bioconductor-brainstars/build.sh b/recipes/bioconductor-brainstars/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-brainstars/build.sh +++ b/recipes/bioconductor-brainstars/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-brainstars/meta.yaml b/recipes/bioconductor-brainstars/meta.yaml index 47e34564b4a36..9484ef8d76f14 100644 --- a/recipes/bioconductor-brainstars/meta.yaml +++ b/recipes/bioconductor-brainstars/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "BrainStars" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b54f910a8fd645a46cfafe218f2f0c9e005d5b14cc168b4024dc32443c464a70 + md5: 163e6ff00d0a1c573ddbcc5631fb1c1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcurl - r-rjsonio run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcurl - r-rjsonio @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can search and get gene expression data and plots from BrainStars (B*). BrainStars is a quantitative expression database of the adult mouse brain. The database has genome-wide expression profile at 51 adult mouse CNS regions.' extra: identifiers: - biotools:brainstars - doi:10.1097/HTR.0b013e3181a7ecb0 + parent_recipe: + name: bioconductor-brainstars + path: recipes/bioconductor-brainstars + version: 1.24.0 + diff --git a/recipes/bioconductor-branchpointer/build.sh b/recipes/bioconductor-branchpointer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-branchpointer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-branchpointer/meta.yaml b/recipes/bioconductor-branchpointer/meta.yaml new file mode 100644 index 0000000000000..7bdfff05dfcd0 --- /dev/null +++ b/recipes/bioconductor-branchpointer/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.8.0" %} +{% set name = "branchpointer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6632b483e3c0cbcf604ec23b145ce82a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-caret + - r-cowplot + - r-data.table + - r-gbm + - r-ggplot2 + - r-kernlab + - r-plyr + - r-stringr + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-caret + - r-cowplot + - r-data.table + - r-gbm + - r-ggplot2 + - r-kernlab + - r-plyr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'Predicts branchpoint probability for sites in intronic branchpoint windows. Queries can be supplied as intronic regions; or to evaluate the effects of mutations, SNPs.' + diff --git a/recipes/bioconductor-breakpointr/build.sh b/recipes/bioconductor-breakpointr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-breakpointr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-breakpointr/meta.yaml b/recipes/bioconductor-breakpointr/meta.yaml new file mode 100644 index 0000000000000..8661ddc85c731 --- /dev/null +++ b/recipes/bioconductor-breakpointr/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "breakpointR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a9e609669b8ffbc8116345d14dc59e42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-breakpointrdata >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-cowplot + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gtools + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-breakpointrdata >=1.0.0,<1.1.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-cowplot + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package implements functions for finding breakpoints, plotting and export of Strand-seq data.' + diff --git a/recipes/bioconductor-breakpointrdata/meta.yaml b/recipes/bioconductor-breakpointrdata/meta.yaml new file mode 100644 index 0000000000000..6f39f0351b27e --- /dev/null +++ b/recipes/bioconductor-breakpointrdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "breakpointRdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6484ead0a5a57fe29f9bd0edba517f10 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Strand-seq data to demonstrate functionalities of breakpointR package.' + diff --git a/recipes/bioconductor-breakpointrdata/post-link.sh b/recipes/bioconductor-breakpointrdata/post-link.sh new file mode 100644 index 0000000000000..8e36317a9d93a --- /dev/null +++ b/recipes/bioconductor-breakpointrdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breakpointRdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breakpointRdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/breakpointRdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breakpointrdata/bioconductor-breakpointrdata_1.0.0_src_all.tar.gz" +) +MD5="6484ead0a5a57fe29f9bd0edba517f10" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breakpointrdata/pre-unlink.sh b/recipes/bioconductor-breakpointrdata/pre-unlink.sh new file mode 100644 index 0000000000000..9d8e87f4e3885 --- /dev/null +++ b/recipes/bioconductor-breakpointrdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breakpointRdata diff --git a/recipes/bioconductor-breastcancermainz/meta.yaml b/recipes/bioconductor-breastcancermainz/meta.yaml new file mode 100644 index 0000000000000..006ee5e7ecd49 --- /dev/null +++ b/recipes/bioconductor-breastcancermainz/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerMAINZ" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d3c2b64b8798cb80b9f214fcb4958dfd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from the breast cancer study published by Schmidt et al. in 2008, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancermainz/post-link.sh b/recipes/bioconductor-breastcancermainz/post-link.sh new file mode 100644 index 0000000000000..358ea9380b52c --- /dev/null +++ b/recipes/bioconductor-breastcancermainz/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerMAINZ_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerMAINZ_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerMAINZ_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancermainz/bioconductor-breastcancermainz_1.20.0_src_all.tar.gz" +) +MD5="d3c2b64b8798cb80b9f214fcb4958dfd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancermainz/pre-unlink.sh b/recipes/bioconductor-breastcancermainz/pre-unlink.sh new file mode 100644 index 0000000000000..2402ddf6edfe5 --- /dev/null +++ b/recipes/bioconductor-breastcancermainz/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerMAINZ diff --git a/recipes/bioconductor-breastcancernki/meta.yaml b/recipes/bioconductor-breastcancernki/meta.yaml new file mode 100644 index 0000000000000..33eb5847d7ead --- /dev/null +++ b/recipes/bioconductor-breastcancernki/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerNKI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2f70179c1ded047824519512d9eed41b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genexpression data from a breast cancer study published by van''t Veer et al. in 2002 and van de Vijver et al. in 2002, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancernki/post-link.sh b/recipes/bioconductor-breastcancernki/post-link.sh new file mode 100644 index 0000000000000..6c7748940f8e8 --- /dev/null +++ b/recipes/bioconductor-breastcancernki/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerNKI_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerNKI_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerNKI_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancernki/bioconductor-breastcancernki_1.20.0_src_all.tar.gz" +) +MD5="2f70179c1ded047824519512d9eed41b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancernki/pre-unlink.sh b/recipes/bioconductor-breastcancernki/pre-unlink.sh new file mode 100644 index 0000000000000..c539f5a05e7a1 --- /dev/null +++ b/recipes/bioconductor-breastcancernki/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerNKI diff --git a/recipes/bioconductor-breastcancertransbig/meta.yaml b/recipes/bioconductor-breastcancertransbig/meta.yaml new file mode 100644 index 0000000000000..5a9727b80c727 --- /dev/null +++ b/recipes/bioconductor-breastcancertransbig/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerTRANSBIG" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c3fe59c8cf826647a2f11320f6b7a3bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from a breast cancer study published by Desmedt et al. in 2007, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancertransbig/post-link.sh b/recipes/bioconductor-breastcancertransbig/post-link.sh new file mode 100644 index 0000000000000..3545bfadb41ac --- /dev/null +++ b/recipes/bioconductor-breastcancertransbig/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerTRANSBIG_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerTRANSBIG_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerTRANSBIG_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancertransbig/bioconductor-breastcancertransbig_1.20.0_src_all.tar.gz" +) +MD5="c3fe59c8cf826647a2f11320f6b7a3bd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancertransbig/pre-unlink.sh b/recipes/bioconductor-breastcancertransbig/pre-unlink.sh new file mode 100644 index 0000000000000..6b4289ed3482e --- /dev/null +++ b/recipes/bioconductor-breastcancertransbig/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerTRANSBIG diff --git a/recipes/bioconductor-breastcancerunt/meta.yaml b/recipes/bioconductor-breastcancerunt/meta.yaml new file mode 100644 index 0000000000000..496ce28ada225 --- /dev/null +++ b/recipes/bioconductor-breastcancerunt/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerUNT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f70937326bfeab71ab497ce4ea46ff76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from a breast cancer study published by Sotiriou et al. in 2007, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancerunt/post-link.sh b/recipes/bioconductor-breastcancerunt/post-link.sh new file mode 100644 index 0000000000000..ba326183a48fc --- /dev/null +++ b/recipes/bioconductor-breastcancerunt/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerUNT_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerUNT_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerUNT_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancerunt/bioconductor-breastcancerunt_1.20.0_src_all.tar.gz" +) +MD5="f70937326bfeab71ab497ce4ea46ff76" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancerunt/pre-unlink.sh b/recipes/bioconductor-breastcancerunt/pre-unlink.sh new file mode 100644 index 0000000000000..2ca7bec78bf74 --- /dev/null +++ b/recipes/bioconductor-breastcancerunt/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerUNT diff --git a/recipes/bioconductor-breastcancerupp/meta.yaml b/recipes/bioconductor-breastcancerupp/meta.yaml new file mode 100644 index 0000000000000..db2cbf669c63c --- /dev/null +++ b/recipes/bioconductor-breastcancerupp/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerUPP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8a54948ea0e0328b3035e3f4d4551960 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from a breast cancer study published by Miller et al. in 2005, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancerupp/post-link.sh b/recipes/bioconductor-breastcancerupp/post-link.sh new file mode 100644 index 0000000000000..827a9c2b33a30 --- /dev/null +++ b/recipes/bioconductor-breastcancerupp/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerUPP_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerUPP_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerUPP_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancerupp/bioconductor-breastcancerupp_1.20.0_src_all.tar.gz" +) +MD5="8a54948ea0e0328b3035e3f4d4551960" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancerupp/pre-unlink.sh b/recipes/bioconductor-breastcancerupp/pre-unlink.sh new file mode 100644 index 0000000000000..e8e091456faa0 --- /dev/null +++ b/recipes/bioconductor-breastcancerupp/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerUPP diff --git a/recipes/bioconductor-breastcancervdx/meta.yaml b/recipes/bioconductor-breastcancervdx/meta.yaml new file mode 100644 index 0000000000000..571d409e31527 --- /dev/null +++ b/recipes/bioconductor-breastcancervdx/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "breastCancerVDX" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4b05a31ca8f4a0a069137dfc614039e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survcomp, genefu, Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from a breast cancer study published by Wang et al. in 2005 and Minn et al. in 2007, provided as an eSet.' + diff --git a/recipes/bioconductor-breastcancervdx/post-link.sh b/recipes/bioconductor-breastcancervdx/post-link.sh new file mode 100644 index 0000000000000..be586e50bc278 --- /dev/null +++ b/recipes/bioconductor-breastcancervdx/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="breastCancerVDX_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/breastCancerVDX_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/breastCancerVDX_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-breastcancervdx/bioconductor-breastcancervdx_1.20.0_src_all.tar.gz" +) +MD5="4b05a31ca8f4a0a069137dfc614039e8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-breastcancervdx/pre-unlink.sh b/recipes/bioconductor-breastcancervdx/pre-unlink.sh new file mode 100644 index 0000000000000..e1e59a26b2c76 --- /dev/null +++ b/recipes/bioconductor-breastcancervdx/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ breastCancerVDX diff --git a/recipes/bioconductor-brgedata/meta.yaml b/recipes/bioconductor-brgedata/meta.yaml new file mode 100644 index 0000000000000..3efe817c4f260 --- /dev/null +++ b/recipes/bioconductor-brgedata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.4.0" %} +{% set name = "brgedata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d2ad8ac2f818311243fa6afe0907e93c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: minfi, MultiAssayExperiment, knitr, rexposome +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package contains several sets of omics data including Gene Expression (ExpressionSet), Methylation (GenomicRatioSet), Proteome and Exposome (ExposomeSet). This data is used in vignettes and exaples at MEAL, MultiDataSet and omicRexposome.' + diff --git a/recipes/bioconductor-brgedata/post-link.sh b/recipes/bioconductor-brgedata/post-link.sh new file mode 100644 index 0000000000000..e80ec005b06bc --- /dev/null +++ b/recipes/bioconductor-brgedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="brgedata_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/brgedata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/brgedata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-brgedata/bioconductor-brgedata_1.4.0_src_all.tar.gz" +) +MD5="d2ad8ac2f818311243fa6afe0907e93c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-brgedata/pre-unlink.sh b/recipes/bioconductor-brgedata/pre-unlink.sh new file mode 100644 index 0000000000000..8857d43466e74 --- /dev/null +++ b/recipes/bioconductor-brgedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ brgedata diff --git a/recipes/bioconductor-bridge/build.sh b/recipes/bioconductor-bridge/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bridge/build.sh +++ b/recipes/bioconductor-bridge/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bridge/meta.yaml b/recipes/bioconductor-bridge/meta.yaml index 83a437aea9c0a..14205ddcf7298 100644 --- a/recipes/bioconductor-bridge/meta.yaml +++ b/recipes/bioconductor-bridge/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "bridge" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 69562d8824201c4ac2c6874e78665a9fa35b04b9dd8dcd86a324f09d5558ffaf + md5: 6c1d00b6b26a2ba3ae999dac684e71eb build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-rama >=1.54.0,<1.56.0' + - 'bioconductor-rama >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-rama >=1.54.0,<1.56.0' + - 'bioconductor-rama >=1.56.0,<1.57.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Test for differentially expressed genes with microarray data. This package can be used with both cDNA microarrays or Affymetrix chip. The packge fits a robust Bayesian hierarchical model for testing for differential expression. Outliers are modeled explicitly using a $t$-distribution. The model includes an exchangeable prior for the variances which allow different variances for the genes but still shrink extreme empirical variances. Our model can be used for testing for differentially expressed genes among multiple samples, and can distinguish between the different possible patterns of differential expression when there are three or more samples. Parameter estimation is carried out using a novel version of Markov Chain Monte Carlo that is appropriate when the model puts mass on subspaces of the full parameter space.' extra: identifiers: - biotools:bridge - doi:10.1111/j.1541-0420.2005.00397.x + parent_recipe: + name: bioconductor-bridge + path: recipes/bioconductor-bridge + version: 1.44.0 + diff --git a/recipes/bioconductor-bridgedbr/build.sh b/recipes/bioconductor-bridgedbr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bridgedbr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bridgedbr/meta.yaml b/recipes/bioconductor-bridgedbr/meta.yaml new file mode 100644 index 0000000000000..a324a55206be9 --- /dev/null +++ b/recipes/bioconductor-bridgedbr/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.16.0" %} +{% set name = "BridgeDbR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a80605ad22266b9ca9e7d1c062dc9ec8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - r-base + - r-rcurl + - r-rjava + run: + - r-base + - r-rcurl + - r-rjava +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Use BridgeDb functions and load identifier mapping databases in R.' + diff --git a/recipes/bioconductor-bronchialil13/meta.yaml b/recipes/bioconductor-bronchialil13/meta.yaml new file mode 100644 index 0000000000000..ac81a1c84014c --- /dev/null +++ b/recipes/bioconductor-bronchialil13/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "bronchialIL13" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 985ae91a81f525c68653969a59631523 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'derived from CNMC (pepr.cnmcresearch.org) http://pepr.cnmcresearch.org/browse.do?action=list_prj_exp&projectId=95 Human Bronchial Cell line A549' + diff --git a/recipes/bioconductor-bronchialil13/post-link.sh b/recipes/bioconductor-bronchialil13/post-link.sh new file mode 100644 index 0000000000000..9b5b7148554c9 --- /dev/null +++ b/recipes/bioconductor-bronchialil13/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bronchialIL13_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bronchialIL13_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/bronchialIL13_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bronchialil13/bioconductor-bronchialil13_1.20.0_src_all.tar.gz" +) +MD5="985ae91a81f525c68653969a59631523" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bronchialil13/pre-unlink.sh b/recipes/bioconductor-bronchialil13/pre-unlink.sh new file mode 100644 index 0000000000000..22ebd1033d0e0 --- /dev/null +++ b/recipes/bioconductor-bronchialil13/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bronchialIL13 diff --git a/recipes/bioconductor-browserviz/build.sh b/recipes/bioconductor-browserviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-browserviz/build.sh +++ b/recipes/bioconductor-browserviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-browserviz/meta.yaml b/recipes/bioconductor-browserviz/meta.yaml index 88bf9e6d4bba0..96f8e6f217d2e 100644 --- a/recipes/bioconductor-browserviz/meta.yaml +++ b/recipes/bioconductor-browserviz/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "BrowserViz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d84c9f4238491950ab72087e14981819e0c08654deddad5f7b6e0e793bde178e + md5: bb0a3c4799dfc95dc9b9467437ccb23c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - 'r-httpuv >=1.4.0' - 'r-jsonlite >=1.5' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - 'r-httpuv >=1.4.0' - 'r-jsonlite >=1.5' @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Interactvive graphics in a web browser from R, using websockets and JSON.' extra: identifiers: - biotools:browserviz - doi:10.1007/978-1-4302-4426-4_17 + parent_recipe: + name: bioconductor-browserviz + path: recipes/bioconductor-browserviz + version: 2.2.0 + diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml new file mode 100644 index 0000000000000..69798a5b573da --- /dev/null +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.0.0" %} +{% set name = "BSgenome.Alyrata.JGI.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2119e78ebb1957fd55ab186b167e0995 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Arabidopsis lyrata 8x Release [project ID 4002920] as provided by JGI ( snapshot from March 24, 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh new file mode 100644 index 0000000000000..5420f308f28d7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Alyrata.JGI.v1_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.alyrata.jgi.v1/bioconductor-bsgenome.alyrata.jgi.v1_1.0.0_src_all.tar.gz" +) +MD5="2119e78ebb1957fd55ab186b167e0995" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.alyrata.jgi.v1/pre-unlink.sh b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/pre-unlink.sh new file mode 100644 index 0000000000000..d1eb520a50b64 --- /dev/null +++ b/recipes/bioconductor-bsgenome.alyrata.jgi.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Alyrata.JGI.v1 diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml new file mode 100644 index 0000000000000..05707dede695a --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Amellifera.BeeBase.assembly4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 77495ee5eba48fe52902c9cc4f9ba7cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iFull genome sequences for Apis mellifera (Honey Bee) as provided by BeeBase (assembly4, Feb. 2008) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh new file mode 100644 index 0000000000000..2543f1b66c387 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.BeeBase.assembly4_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.beebase.assembly4/bioconductor-bsgenome.amellifera.beebase.assembly4_1.4.0_src_all.tar.gz" +) +MD5="77495ee5eba48fe52902c9cc4f9ba7cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/pre-unlink.sh b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/pre-unlink.sh new file mode 100644 index 0000000000000..0b88a5f5f54e8 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.beebase.assembly4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Amellifera.BeeBase.assembly4 diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml new file mode 100644 index 0000000000000..3f258398320f9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Amellifera.UCSC.apiMel2.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e7a7ff8cfce8e239b22116855456f23d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.amellifera.ucsc.apimel2 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Amellifera.UCSC.apiMel2, except that each of them has the 3 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), and (3) the mask of repeats from RepeatMasker (RM mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh new file mode 100644 index 0000000000000..da1e7b022c374 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked_1.3.99_src_all.tar.gz" +) +MD5="e7a7ff8cfce8e239b22116855456f23d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/pre-unlink.sh new file mode 100644 index 0000000000000..f283213bd60a5 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Amellifera.UCSC.apiMel2.masked diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml new file mode 100644 index 0000000000000..e4dd223a046ac --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Amellifera.UCSC.apiMel2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 436ddf54868906e7d1135369d41a2ffe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Apis mellifera (Honey Bee) as provided by UCSC (apiMel2, Jan. 2005) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh new file mode 100644 index 0000000000000..bc09999c3772a --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Amellifera.UCSC.apiMel2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.amellifera.ucsc.apimel2/bioconductor-bsgenome.amellifera.ucsc.apimel2_1.4.0_src_all.tar.gz" +) +MD5="436ddf54868906e7d1135369d41a2ffe" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/pre-unlink.sh b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/pre-unlink.sh new file mode 100644 index 0000000000000..3aaff81b6d5c6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.amellifera.ucsc.apimel2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Amellifera.UCSC.apiMel2 diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml new file mode 100644 index 0000000000000..ea2665a8a77da --- /dev/null +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.0.0" %} +{% set name = "BSgenome.Aofficinalis.NCBI.V1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3f8fd13e74eee63895a5ef528004b60b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-3 + summary: 'Full genome sequences for Asparagus officinalis (Garden asparagus) as provided by NCBI (Aspof.V1, Feb. 2017) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh new file mode 100644 index 0000000000000..7212469ff8c77 --- /dev/null +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Aofficinalis.NCBI.V1_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.aofficinalis.ncbi.v1/bioconductor-bsgenome.aofficinalis.ncbi.v1_1.0.0_src_all.tar.gz" +) +MD5="3f8fd13e74eee63895a5ef528004b60b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/pre-unlink.sh b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/pre-unlink.sh new file mode 100644 index 0000000000000..b481e64acd8c4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.aofficinalis.ncbi.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Aofficinalis.NCBI.V1 diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml new file mode 100644 index 0000000000000..491027f18c476 --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.3.1000" %} +{% set name = "BSgenome.Athaliana.TAIR.04232008" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6b8a31a228dbcf4468974f5ec1d98467 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Arabidopsis thaliana as provided by TAIR (snapshot from April 23, 2008) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh new file mode 100644 index 0000000000000..c7c73a235c134 --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.04232008_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.04232008/bioconductor-bsgenome.athaliana.tair.04232008_1.3.1000_src_all.tar.gz" +) +MD5="6b8a31a228dbcf4468974f5ec1d98467" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.04232008/pre-unlink.sh b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/pre-unlink.sh new file mode 100644 index 0000000000000..44c2a8fbca8a9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.04232008/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Athaliana.TAIR.04232008 diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml new file mode 100644 index 0000000000000..1333fdbe54030 --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.3.1000" %} +{% set name = "BSgenome.Athaliana.TAIR.TAIR9" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8c6709a5f544616d59f4d39aac5787a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Arabidopsis thaliana as provided by TAIR (TAIR9 Genome Release) and stored in Biostrings objects. Note that TAIR10 is an "annotation release" based on the same genome assembly as TAIR9.' + diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh new file mode 100644 index 0000000000000..1569f3e1d69e0 --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Athaliana.TAIR.TAIR9_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.athaliana.tair.tair9/bioconductor-bsgenome.athaliana.tair.tair9_1.3.1000_src_all.tar.gz" +) +MD5="8c6709a5f544616d59f4d39aac5787a7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.athaliana.tair.tair9/pre-unlink.sh b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/pre-unlink.sh new file mode 100644 index 0000000000000..e9af101b6c37f --- /dev/null +++ b/recipes/bioconductor-bsgenome.athaliana.tair.tair9/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Athaliana.TAIR.TAIR9 diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml new file mode 100644 index 0000000000000..5567929dd890a --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 50f7da5907cbe0d08183dc7161a8ca56 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh new file mode 100644 index 0000000000000..496a53e8d3fa7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked_1.3.99_src_all.tar.gz" +) +MD5="50f7da5907cbe0d08183dc7161a8ca56" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..91fa35324fd02 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau3.masked diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml new file mode 100644 index 0000000000000..06c2ce1632fe6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fe6c4d5853f91c3db3e716ddbc773580 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau3, Aug. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh new file mode 100644 index 0000000000000..4bd7c65209a53 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau3/bioconductor-bsgenome.btaurus.ucsc.bostau3_1.4.0_src_all.tar.gz" +) +MD5="fe6c4d5853f91c3db3e716ddbc773580" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/pre-unlink.sh new file mode 100644 index 0000000000000..e7693649bc035 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau3 diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml new file mode 100644 index 0000000000000..95f877065a86e --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau4.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7c5294349c7061adfb3948bc5659afeb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau4 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh new file mode 100644 index 0000000000000..c6099db4648a3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked_1.3.99_src_all.tar.gz" +) +MD5="7c5294349c7061adfb3948bc5659afeb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/pre-unlink.sh new file mode 100644 index 0000000000000..03f0ef0aea709 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau4.masked diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml new file mode 100644 index 0000000000000..0620b7907b08a --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 162cd253c719e347df5748ebb407a191 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau4, Oct. 2007) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh new file mode 100644 index 0000000000000..e6002c52b8c98 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau4_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau4/bioconductor-bsgenome.btaurus.ucsc.bostau4_1.4.0_src_all.tar.gz" +) +MD5="162cd253c719e347df5748ebb407a191" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/pre-unlink.sh new file mode 100644 index 0000000000000..d5b360d2c1346 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau4 diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml new file mode 100644 index 0000000000000..ff5d633929b16 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau6.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a176de6b1b91854d47e783b8249dbf58 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.btaurus.ucsc.bostau6 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Btaurus.UCSC.bosTau6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh new file mode 100644 index 0000000000000..dc0f359db335b --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked_1.3.99_src_all.tar.gz" +) +MD5="a176de6b1b91854d47e783b8249dbf58" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/pre-unlink.sh new file mode 100644 index 0000000000000..7869c2142557c --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau6.masked diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml new file mode 100644 index 0000000000000..44df585c1d99d --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b22391e0678fc3743daa4b77ecc55f66 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau6, Nov. 2009) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh new file mode 100644 index 0000000000000..6460206f50708 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau6_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau6/bioconductor-bsgenome.btaurus.ucsc.bostau6_1.4.0_src_all.tar.gz" +) +MD5="b22391e0678fc3743daa4b77ecc55f66" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/pre-unlink.sh new file mode 100644 index 0000000000000..397e134fceb70 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau6 diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml new file mode 100644 index 0000000000000..dc6ddd13aad19 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Btaurus.UCSC.bosTau8" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 61ababa7b2b5360fceeb06f0bf49b208 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Bos taurus (Cow) as provided by UCSC (bosTau8, Jun. 2014) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh new file mode 100644 index 0000000000000..5a0965df29b08 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Btaurus.UCSC.bosTau8_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.btaurus.ucsc.bostau8/bioconductor-bsgenome.btaurus.ucsc.bostau8_1.4.2_src_all.tar.gz" +) +MD5="61ababa7b2b5360fceeb06f0bf49b208" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/pre-unlink.sh b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/pre-unlink.sh new file mode 100644 index 0000000000000..3421f949b5526 --- /dev/null +++ b/recipes/bioconductor-bsgenome.btaurus.ucsc.bostau8/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Btaurus.UCSC.bosTau8 diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml new file mode 100644 index 0000000000000..e3af808a3a687 --- /dev/null +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.0.0" %} +{% set name = "BSgenome.Carietinum.NCBI.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eef018ecce6d32852aa18ac39cf377c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-3 + summary: 'Full genome sequences for Cicer arietinum (Chickpea) as provided by NCBI (ASM33114v1, Jan. 2013) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh new file mode 100644 index 0000000000000..b2f0d4b788064 --- /dev/null +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Carietinum.NCBI.v1_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.carietinum.ncbi.v1/bioconductor-bsgenome.carietinum.ncbi.v1_1.0.0_src_all.tar.gz" +) +MD5="eef018ecce6d32852aa18ac39cf377c6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/pre-unlink.sh b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/pre-unlink.sh new file mode 100644 index 0000000000000..7a12d7dfa31c1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.carietinum.ncbi.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Carietinum.NCBI.v1 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml index 1faba25a90d7e..d04271e0d65c2 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce10" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3337ffc0b59ee6d4f74e790cfd7aea9f54b8b3f87cbb48c2ecd792294faa5efd + md5: 98a8ca836d6db23e46674552669d7942 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce10, Oct. 2010) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.celegans.ucsc.ce10 + path: recipes/bioconductor-bsgenome.celegans.ucsc.ce10 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh index 3149d7232e3db..abbb8bfed82e0 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce10/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce10_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce10/bioconductor-bsgenome.celegans.ucsc.ce10_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml new file mode 100644 index 0000000000000..50fd52d697181 --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Celegans.UCSC.ce11" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b80e24149a0c6ed323d0c9a6d112ef52 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce11, Feb. 2013) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh new file mode 100644 index 0000000000000..71849f1a23522 --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce11_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce11/bioconductor-bsgenome.celegans.ucsc.ce11_1.4.2_src_all.tar.gz" +) +MD5="b80e24149a0c6ed323d0c9a6d112ef52" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/pre-unlink.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/pre-unlink.sh new file mode 100644 index 0000000000000..09ade85ffa883 --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce11/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Celegans.UCSC.ce11 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml new file mode 100644 index 0000000000000..32d3c283ca42c --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Celegans.UCSC.ce2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b2bf7eec2b07685cf9dcdf42840db208 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce2, Mar. 2004) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh new file mode 100644 index 0000000000000..b6088b50a7f2a --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce2/bioconductor-bsgenome.celegans.ucsc.ce2_1.4.0_src_all.tar.gz" +) +MD5="b2bf7eec2b07685cf9dcdf42840db208" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/pre-unlink.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/pre-unlink.sh new file mode 100644 index 0000000000000..3d65e99ca7ae3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Celegans.UCSC.ce2 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml index 2e0bb0533e53e..11a043d84d096 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Celegans.UCSC.ce6" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6997709c5f9eca77a1b7d3367bee676f765b672b61acb9471d4cec3eca581f57 + md5: cb86ff861d8f660c2abd8fc1907d84a6 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Celegans.UCSC.ce6.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Caenorhabditis elegans (Worm) as provided by UCSC (ce6, May 2008) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.celegans.ucsc.ce6 + path: recipes/bioconductor-bsgenome.celegans.ucsc.ce6 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh index a5a5ba9805914..496a98adabf50 100644 --- a/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh +++ b/recipes/bioconductor-bsgenome.celegans.ucsc.ce6/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Celegans.UCSC.ce6_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.celegans.ucsc.ce6/bioconductor-bsgenome.celegans.ucsc.ce6_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml new file mode 100644 index 0000000000000..390d645c0fd1e --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Cfamiliaris.UCSC.canFam2.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f921533bb83f83f43b8d227b00a48cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam2 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh new file mode 100644 index 0000000000000..66ec46c290d4b --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked_1.3.99_src_all.tar.gz" +) +MD5="6f921533bb83f83f43b8d227b00a48cb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/pre-unlink.sh new file mode 100644 index 0000000000000..9112e3c309c87 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Cfamiliaris.UCSC.canFam2.masked diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml new file mode 100644 index 0000000000000..c2b95b893c742 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Cfamiliaris.UCSC.canFam2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b98f5289ed5d362cd815db9352598634 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam2, May 2005) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh new file mode 100644 index 0000000000000..57f6fe216e81b --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2_1.4.0_src_all.tar.gz" +) +MD5="b98f5289ed5d362cd815db9352598634" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/pre-unlink.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/pre-unlink.sh new file mode 100644 index 0000000000000..6b9b9be5b67ef --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Cfamiliaris.UCSC.canFam2 diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml new file mode 100644 index 0000000000000..f3f4c3f8b21c8 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Cfamiliaris.UCSC.canFam3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8e2246f51fc967dc2ed748cf967a7649 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.cfamiliaris.ucsc.canfam3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Cfamiliaris.UCSC.canFam3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh new file mode 100644 index 0000000000000..fffe5785b22a2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked_1.3.99_src_all.tar.gz" +) +MD5="8e2246f51fc967dc2ed748cf967a7649" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..6cf9f8d8ed507 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Cfamiliaris.UCSC.canFam3.masked diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml new file mode 100644 index 0000000000000..77a7df8a7533a --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Cfamiliaris.UCSC.canFam3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: efcdc531042be86f99a734cd69c0688c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Canis lupus familiaris (Dog) as provided by UCSC (canFam3, Sep. 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh new file mode 100644 index 0000000000000..244d8b4e03a73 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Cfamiliaris.UCSC.canFam3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3_1.4.0_src_all.tar.gz" +) +MD5="efcdc531042be86f99a734cd69c0688c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/pre-unlink.sh b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/pre-unlink.sh new file mode 100644 index 0000000000000..0d71e61b58654 --- /dev/null +++ b/recipes/bioconductor-bsgenome.cfamiliaris.ucsc.canfam3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Cfamiliaris.UCSC.canFam3 diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml new file mode 100644 index 0000000000000..d5b5384b88a43 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Dmelanogaster.UCSC.dm2.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ae7ca3053e97a0d6bd20bc2b9635ecce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm2 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh new file mode 100644 index 0000000000000..f09e0ee4499ca --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked_1.3.99_src_all.tar.gz" +) +MD5="ae7ca3053e97a0d6bd20bc2b9635ecce" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/pre-unlink.sh new file mode 100644 index 0000000000000..d8aa0f93a2033 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Dmelanogaster.UCSC.dm2.masked diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml new file mode 100644 index 0000000000000..49b4ff4e39f91 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Dmelanogaster.UCSC.dm2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ebc88df5595fc7aad588b8f3f7de4784 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm2, Apr. 2004) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh new file mode 100644 index 0000000000000..966be3f58fe32 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/bioconductor-bsgenome.dmelanogaster.ucsc.dm2_1.4.0_src_all.tar.gz" +) +MD5="ebc88df5595fc7aad588b8f3f7de4784" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/pre-unlink.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/pre-unlink.sh new file mode 100644 index 0000000000000..07b2b265d150a --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Dmelanogaster.UCSC.dm2 diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml new file mode 100644 index 0000000000000..72cfc08f7343e --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Dmelanogaster.UCSC.dm3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 592e7ec451d126b2d314ab6c75d86830 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.dmelanogaster.ucsc.dm3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Dmelanogaster.UCSC.dm3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh new file mode 100644 index 0000000000000..03ddf17262cf7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked_1.3.99_src_all.tar.gz" +) +MD5="592e7ec451d126b2d314ab6c75d86830" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..bdecd5ffcca41 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Dmelanogaster.UCSC.dm3.masked diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml index 826cc2be08604..201b0742317be 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Dmelanogaster.UCSC.dm3" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 68ebdefa8c99330f320d1928673ac89601e842102990cbed1b4f4d08271d75a5 + md5: b7ceebf7bfee766596f602f9e808d069 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm3, Apr. 2006) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.dmelanogaster.ucsc.dm3 + path: recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh index 729fbf774928a..8850fce984937 100644 --- a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm3_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm3/bioconductor-bsgenome.dmelanogaster.ucsc.dm3_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml new file mode 100644 index 0000000000000..380242721ad2d --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.1" %} +{% set name = "BSgenome.Dmelanogaster.UCSC.dm6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f9d6e406b7893a17c08edd4521c2802f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Drosophila melanogaster (Fly) as provided by UCSC (dm6, Aug. 2014) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh new file mode 100644 index 0000000000000..7898ecb68f5dd --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Dmelanogaster.UCSC.dm6_1.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/bioconductor-bsgenome.dmelanogaster.ucsc.dm6_1.4.1_src_all.tar.gz" +) +MD5="f9d6e406b7893a17c08edd4521c2802f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/pre-unlink.sh b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/pre-unlink.sh new file mode 100644 index 0000000000000..db155a3adbe84 --- /dev/null +++ b/recipes/bioconductor-bsgenome.dmelanogaster.ucsc.dm6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Dmelanogaster.UCSC.dm6 diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml new file mode 100644 index 0000000000000..d4de3ba1bab5b --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Drerio.UCSC.danRer10" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8dbcc8a338a021ed35656b27b3dd4c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer10, Sep. 2014) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh new file mode 100644 index 0000000000000..ae87b8fc245aa --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer10_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer10/bioconductor-bsgenome.drerio.ucsc.danrer10_1.4.2_src_all.tar.gz" +) +MD5="b8dbcc8a338a021ed35656b27b3dd4c0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/pre-unlink.sh new file mode 100644 index 0000000000000..98e242d716364 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer10/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer10 diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml new file mode 100644 index 0000000000000..c98de599cb509 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Drerio.UCSC.danRer5.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8f0623bcbe1743754a56c55599b535f3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer5 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh new file mode 100644 index 0000000000000..56a947c85df3d --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/bioconductor-bsgenome.drerio.ucsc.danrer5.masked_1.3.99_src_all.tar.gz" +) +MD5="8f0623bcbe1743754a56c55599b535f3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/pre-unlink.sh new file mode 100644 index 0000000000000..fe5f358d66a97 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer5.masked diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml new file mode 100644 index 0000000000000..ad2802f3bff83 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Drerio.UCSC.danRer5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b1fee4bcc0d9cebb2bbdec5cb851f00d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer5, Jul. 2007) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh new file mode 100644 index 0000000000000..5fb6e5e771e4c --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer5_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer5/bioconductor-bsgenome.drerio.ucsc.danrer5_1.4.0_src_all.tar.gz" +) +MD5="b1fee4bcc0d9cebb2bbdec5cb851f00d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/pre-unlink.sh new file mode 100644 index 0000000000000..1fd00ea3d0e55 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer5 diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml new file mode 100644 index 0000000000000..f34b6c82ff70c --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Drerio.UCSC.danRer6.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 71c9b05c27b8d2e05735e6494a8f17ba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer6 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer6, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh new file mode 100644 index 0000000000000..7a41c8a32b18f --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/bioconductor-bsgenome.drerio.ucsc.danrer6.masked_1.3.99_src_all.tar.gz" +) +MD5="71c9b05c27b8d2e05735e6494a8f17ba" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/pre-unlink.sh new file mode 100644 index 0000000000000..42e406112fef3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer6.masked diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml new file mode 100644 index 0000000000000..747128e3dd1a9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Drerio.UCSC.danRer6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 537d37d29d97ae0c31d77decc67b25b0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer6, Dec. 2008) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh new file mode 100644 index 0000000000000..37d83f0728b41 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer6_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer6/bioconductor-bsgenome.drerio.ucsc.danrer6_1.4.0_src_all.tar.gz" +) +MD5="537d37d29d97ae0c31d77decc67b25b0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/pre-unlink.sh new file mode 100644 index 0000000000000..8f14676308b39 --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer6 diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml new file mode 100644 index 0000000000000..74d9528b4b17e --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Drerio.UCSC.danRer7.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5d68af24477d006ed22e7342ff97ac16 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Drerio.UCSC.danRer7, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh new file mode 100644 index 0000000000000..705dd689e88be --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/bioconductor-bsgenome.drerio.ucsc.danrer7.masked_1.3.99_src_all.tar.gz" +) +MD5="5d68af24477d006ed22e7342ff97ac16" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/pre-unlink.sh new file mode 100644 index 0000000000000..f31023e73127a --- /dev/null +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Drerio.UCSC.danRer7.masked diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml index 02b00c0b64861..40e81918d5664 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Drerio.UCSC.danRer7" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ef2e7e27508d7dbfc63e09ae36f96d2578590af1f12b82912fe029898084a39f + md5: 766b407a46f20d69a143eab0809eb10a build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GenomicFeatures requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Danio rerio (Zebrafish) as provided by UCSC (danRer7, Jul. 2010) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.drerio.ucsc.danrer7 + path: recipes/bioconductor-bsgenome.drerio.ucsc.danrer7 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh index b699f31ab28dc..be9038e829adc 100644 --- a/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh +++ b/recipes/bioconductor-bsgenome.drerio.ucsc.danrer7/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Drerio.UCSC.danRer7_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.drerio.ucsc.danrer7/bioconductor-bsgenome.drerio.ucsc.danrer7_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml index 77b37aa5e4963..84346d1fdfd65 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/meta.yaml @@ -1,35 +1,40 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Ecoli.NCBI.20080805" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4740ebd81b56e9a990e7bbf3eb799011346db8af4a2615572558cda0bd97f5d0 + md5: c653e9cbee3faeb6fd5759b7575f234d build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Escherichia coli full genomes for several strains as provided by NCBI on 2008/08/05 and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.ecoli.ncbi.20080805 + path: recipes/bioconductor-bsgenome.ecoli.ncbi.20080805 + version: 1.3.1000 diff --git a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh index 619361318f646..23826e14a44cb 100644 --- a/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh +++ b/recipes/bioconductor-bsgenome.ecoli.ncbi.20080805/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Ecoli.NCBI.20080805_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ecoli.ncbi.20080805/bioconductor-bsgenome.ecoli.ncbi.20080805_1.3.1000_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml new file mode 100644 index 0000000000000..b83f48f3cd9d1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9d9b9e70f4f4624ee4a2b09a59d44510 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.gaculeatus.ucsc.gasacu1 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Gaculeatus.UCSC.gasAcu1, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh new file mode 100644 index 0000000000000..79d771acd2b00 --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked_1.3.99_src_all.tar.gz" +) +MD5="9d9b9e70f4f4624ee4a2b09a59d44510" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/pre-unlink.sh new file mode 100644 index 0000000000000..dd29faac3a54f --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Gaculeatus.UCSC.gasAcu1.masked diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml new file mode 100644 index 0000000000000..c20b01d9c4f37 --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Gaculeatus.UCSC.gasAcu1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 412aa0570d9c556861b7bb9a5bbc2007 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gasterosteus aculeatus (Stickleback) as provided by UCSC (gasAcu1, Feb. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh new file mode 100644 index 0000000000000..3da9a1e5d4e48 --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Gaculeatus.UCSC.gasAcu1_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1_1.4.0_src_all.tar.gz" +) +MD5="412aa0570d9c556861b7bb9a5bbc2007" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/pre-unlink.sh b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/pre-unlink.sh new file mode 100644 index 0000000000000..8fcbe022388bf --- /dev/null +++ b/recipes/bioconductor-bsgenome.gaculeatus.ucsc.gasacu1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Gaculeatus.UCSC.gasAcu1 diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml new file mode 100644 index 0000000000000..4e7073699dced --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Ggallus.UCSC.galGal3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3224e3a2b15de379c068e61cedfefa6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ggallus.ucsc.galgal3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh new file mode 100644 index 0000000000000..4d37b1aead325 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked_1.3.99_src_all.tar.gz" +) +MD5="b3224e3a2b15de379c068e61cedfefa6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..ccf34baf852a9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ggallus.UCSC.galGal3.masked diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml new file mode 100644 index 0000000000000..48b392f7c0e8f --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Ggallus.UCSC.galGal3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a463e5ccfc8c6d2c62a6ade0da65dbc4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal3, May 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh new file mode 100644 index 0000000000000..ce402b4c5bc15 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal3/bioconductor-bsgenome.ggallus.ucsc.galgal3_1.4.0_src_all.tar.gz" +) +MD5="a463e5ccfc8c6d2c62a6ade0da65dbc4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/pre-unlink.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/pre-unlink.sh new file mode 100644 index 0000000000000..52041aab9152b --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ggallus.UCSC.galGal3 diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml new file mode 100644 index 0000000000000..d09edbd37f782 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Ggallus.UCSC.galGal4.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0166121ebd8d0b6a4d24d67e175cfe81 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ggallus.ucsc.galgal4 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ggallus.UCSC.galGal4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh new file mode 100644 index 0000000000000..2a8b04474e125 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked_1.3.99_src_all.tar.gz" +) +MD5="0166121ebd8d0b6a4d24d67e175cfe81" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/pre-unlink.sh new file mode 100644 index 0000000000000..4451aae93a1d9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ggallus.UCSC.galGal4.masked diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml new file mode 100644 index 0000000000000..3f792dcdc54cc --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Ggallus.UCSC.galGal4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c2cb4bfc39db93c060e78d8d12542c11 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal4, Nov. 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh new file mode 100644 index 0000000000000..b27f923b428b5 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal4_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal4/bioconductor-bsgenome.ggallus.ucsc.galgal4_1.4.0_src_all.tar.gz" +) +MD5="c2cb4bfc39db93c060e78d8d12542c11" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/pre-unlink.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/pre-unlink.sh new file mode 100644 index 0000000000000..5f15c8f325166 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ggallus.UCSC.galGal4 diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml new file mode 100644 index 0000000000000..adabefa429ef9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Ggallus.UCSC.galGal5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 93b42354404edd848b21ea6781ca135c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Gallus gallus (Chicken) as provided by UCSC (galGal5, Dec. 2015) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh new file mode 100644 index 0000000000000..9d7aa568c94f4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ggallus.UCSC.galGal5_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ggallus.ucsc.galgal5/bioconductor-bsgenome.ggallus.ucsc.galgal5_1.4.2_src_all.tar.gz" +) +MD5="93b42354404edd848b21ea6781ca135c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/pre-unlink.sh b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/pre-unlink.sh new file mode 100644 index 0000000000000..16123f94f461e --- /dev/null +++ b/recipes/bioconductor-bsgenome.ggallus.ucsc.galgal5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ggallus.UCSC.galGal5 diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml new file mode 100644 index 0000000000000..550b21f3e379d --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.99.1" %} +{% set name = "BSgenome.Hsapiens.1000genomes.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 164e1692d38fefa499c2c8ac5fc22793 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: '1000genomes Phase2 Reference Genome Sequence (hs37d5), based on NCBI GRCh37.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh new file mode 100644 index 0000000000000..bfc3daabdeaba --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.1000genomes.hs37d5_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5_0.99.1_src_all.tar.gz" +) +MD5="164e1692d38fefa499c2c8ac5fc22793" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..915c266de9a3f --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.1000genomes.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.1000genomes.hs37d5 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml new file mode 100644 index 0000000000000..ff2edbc51d6de --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.3.1000" %} +{% set name = "BSgenome.Hsapiens.NCBI.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 733d324b34d34d7da8c4bf38459f4fae +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by NCBI (GRCh38, 2013-12-17) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh new file mode 100644 index 0000000000000..ff702951a6d4b --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ncbi.grch38/bioconductor-bsgenome.hsapiens.ncbi.grch38_1.3.1000_src_all.tar.gz" +) +MD5="733d324b34d34d7da8c4bf38459f4fae" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..38bafc2565de2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ncbi.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.NCBI.GRCh38 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml new file mode 100644 index 0000000000000..0a480d04bbe19 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg17.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff6ee5196f234c5a2a3bcdd052c3c08e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg17 >=1.3.0,<1.4.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg17, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh new file mode 100644 index 0000000000000..b02348d8a0cc2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked_1.3.99_src_all.tar.gz" +) +MD5="ff6ee5196f234c5a2a3bcdd052c3c08e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/pre-unlink.sh new file mode 100644 index 0000000000000..8dd1a5801c2b9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg17.masked diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml new file mode 100644 index 0000000000000..2f445de455c1b --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.3.1000" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg17" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cbea3029c3d3125a88e6c061c3d3abde +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg17, May 2004) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh new file mode 100644 index 0000000000000..881150aec75fe --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg17_1.3.1000.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg17/bioconductor-bsgenome.hsapiens.ucsc.hg17_1.3.1000_src_all.tar.gz" +) +MD5="cbea3029c3d3125a88e6c061c3d3abde" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/pre-unlink.sh new file mode 100644 index 0000000000000..fd005d17adc69 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg17/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg17 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml new file mode 100644 index 0000000000000..a93051e22acac --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg18.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e6a31e3cba34ce5e0eb6f76d2c19870c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg18, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh new file mode 100644 index 0000000000000..9611a772b601e --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked_1.3.99_src_all.tar.gz" +) +MD5="e6a31e3cba34ce5e0eb6f76d2c19870c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/pre-unlink.sh new file mode 100644 index 0000000000000..d44dbbeed240c --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg18.masked diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml index c6e28bb8804f0..1ffe6b5aa9014 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.3.1000" %} {% set name = "BSgenome.Hsapiens.UCSC.hg18" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 26fa81bfdb16269d76299aae1f352ddd3c56bec30da7259785fe3e3d8985a7ad + md5: 51bb2e1ed4009860bb21aaac32fffd9c build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg18.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg18, Mar. 2006) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg18 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18 + version: 1.3.1000 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh index e8f0251f9e41e..d2aebf5da7d09 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg18/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg18_1.3.1000.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg18/bioconductor-bsgenome.hsapiens.ucsc.hg18_1.3.1000_src_all.tar.gz" ) MD5="51bb2e1ed4009860bb21aaac32fffd9c" @@ -43,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml new file mode 100644 index 0000000000000..c1bdbf89c852b --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg19.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8abeb2afb811e1a38cf822d1bc0cb50a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg19, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh new file mode 100644 index 0000000000000..27847b9725eb3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked_1.3.99_src_all.tar.gz" +) +MD5="8abeb2afb811e1a38cf822d1bc0cb50a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/pre-unlink.sh new file mode 100644 index 0000000000000..49b9dfa0799e3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg19.masked diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml index 573fe27c5f850..c0018e5414c7c 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Hsapiens.UCSC.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 88f515e5c27dd11d10654250e3a0a9389e4dfeb0b1c2d43419aa7086e6c516f8 + md5: 672a988b28d8602afb2bd5595db7303b build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg19, Feb. 2009) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg19 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh index 1fa4558fa5741..a4e6d31a11474 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg19_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg19/bioconductor-bsgenome.hsapiens.ucsc.hg19_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml new file mode 100644 index 0000000000000..8e8cf83f93edd --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Hsapiens.UCSC.hg38.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 50c9fc14be05113dc56651ea7a49beb1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects. The sequences are the same as in BSgenome.Hsapiens.UCSC.hg38, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh new file mode 100644 index 0000000000000..17f04c351ad20 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked_1.3.99_src_all.tar.gz" +) +MD5="50c9fc14be05113dc56651ea7a49beb1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/pre-unlink.sh new file mode 100644 index 0000000000000..7a0f807a67820 --- /dev/null +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Hsapiens.UCSC.hg38.masked diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml index 0eda5d3a25b9e..4ffda28b395ca 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.1" %} {% set name = "BSgenome.Hsapiens.UCSC.hg38" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 71d7e4557666e2ff76ffc6c637331bfab0c0b59f4963f2b6f5606f12f74580e2 + md5: 1b95bfdc9763351b04611666cd624b30 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Homo sapiens (Human) as provided by UCSC (hg38, Dec. 2013) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.hsapiens.ucsc.hg38 + path: recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38 + version: 1.4.1 diff --git a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh index 3cf524720b090..5620f9356e402 100644 --- a/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh +++ b/recipes/bioconductor-bsgenome.hsapiens.ucsc.hg38/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Hsapiens.UCSC.hg38_1.4.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.hsapiens.ucsc.hg38/bioconductor-bsgenome.hsapiens.ucsc.hg38_1.4.1_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml new file mode 100644 index 0000000000000..b6ed65d2c063a --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Mfascicularis.NCBI.5.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dba6ade39dc6b4f6d06f488141b5550b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca fascicularis (long-tailed macaque) as provided by NCBI (Macaca_fascicularis_5.0, 2013-06-12) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh new file mode 100644 index 0000000000000..af953c892d414 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mfascicularis.NCBI.5.0_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfascicularis.ncbi.5.0/bioconductor-bsgenome.mfascicularis.ncbi.5.0_1.4.2_src_all.tar.gz" +) +MD5="dba6ade39dc6b4f6d06f488141b5550b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/pre-unlink.sh b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/pre-unlink.sh new file mode 100644 index 0000000000000..47edaea3cf103 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfascicularis.ncbi.5.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mfascicularis.NCBI.5.0 diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml new file mode 100644 index 0000000000000..2bb2b9cda6784 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.1" %} +{% set name = "BSgenome.Mfuro.UCSC.musFur1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c33e71746ce551bcbcd22be1979aee63 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Mustela putorius furo (Ferret) as provided by UCSC (musFur1, Apr. 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh new file mode 100644 index 0000000000000..d64c1caf066fa --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mfuro.UCSC.musFur1_1.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mfuro.ucsc.musfur1/bioconductor-bsgenome.mfuro.ucsc.musfur1_1.4.1_src_all.tar.gz" +) +MD5="c33e71746ce551bcbcd22be1979aee63" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/pre-unlink.sh b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/pre-unlink.sh new file mode 100644 index 0000000000000..ecc14041d6d72 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mfuro.ucsc.musfur1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mfuro.UCSC.musFur1 diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml new file mode 100644 index 0000000000000..01fed394cff8b --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Mmulatta.UCSC.rheMac2.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7602d86b68df7e4c8d336fede4090a62 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac2 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default. NOTE: In most assemblies available at UCSC, Tandem Repeats Finder repeats were filtered to retain only the repeats with period <= 12. However, the filtering was omitted for this assembly, so the TRF masks contain all Tandem Repeats Finder results.' + diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh new file mode 100644 index 0000000000000..b67c79ab70cfb --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked_1.3.99_src_all.tar.gz" +) +MD5="7602d86b68df7e4c8d336fede4090a62" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/pre-unlink.sh new file mode 100644 index 0000000000000..af0b583832aac --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmulatta.UCSC.rheMac2.masked diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml new file mode 100644 index 0000000000000..56cae92713421 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Mmulatta.UCSC.rheMac2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 90c43e127e76dfd7cea90de9e1af9a50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac2, Jan. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh new file mode 100644 index 0000000000000..b30c078b8fbfd --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/bioconductor-bsgenome.mmulatta.ucsc.rhemac2_1.4.0_src_all.tar.gz" +) +MD5="90c43e127e76dfd7cea90de9e1af9a50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/pre-unlink.sh new file mode 100644 index 0000000000000..1e21ac6309499 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmulatta.UCSC.rheMac2 diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml new file mode 100644 index 0000000000000..f58f935695c36 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Mmulatta.UCSC.rheMac3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 94f8714865655d3144e14f6fc5c24e76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmulatta.ucsc.rhemac3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmulatta.UCSC.rheMac3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh new file mode 100644 index 0000000000000..2032568ccead0 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked_1.3.99_src_all.tar.gz" +) +MD5="94f8714865655d3144e14f6fc5c24e76" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..2fd0a48ef67f6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmulatta.UCSC.rheMac3.masked diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml new file mode 100644 index 0000000000000..17af3a9649e30 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Mmulatta.UCSC.rheMac3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dfa1ecb9d0bb7a5d9fa628092fb1c354 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac3, Oct. 2010) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh new file mode 100644 index 0000000000000..83a666bc84d52 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/bioconductor-bsgenome.mmulatta.ucsc.rhemac3_1.4.0_src_all.tar.gz" +) +MD5="dfa1ecb9d0bb7a5d9fa628092fb1c354" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/pre-unlink.sh new file mode 100644 index 0000000000000..1c9b257106c27 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmulatta.UCSC.rheMac3 diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml new file mode 100644 index 0000000000000..298a61b62ec93 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Mmulatta.UCSC.rheMac8" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e9ad1f70f652c62554e2c5af7638c015 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Macaca mulatta (Rhesus) as provided by UCSC (rheMac8, Nov. 2015) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh new file mode 100644 index 0000000000000..8881ddde3e188 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmulatta.UCSC.rheMac8_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/bioconductor-bsgenome.mmulatta.ucsc.rhemac8_1.4.2_src_all.tar.gz" +) +MD5="e9ad1f70f652c62554e2c5af7638c015" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/pre-unlink.sh new file mode 100644 index 0000000000000..4520ee466bf9d --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmulatta.ucsc.rhemac8/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmulatta.UCSC.rheMac8 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml new file mode 100644 index 0000000000000..627ac243ada86 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Mmusculus.UCSC.mm10.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c6a5365fa1a0d2a5ecb63752960eb3d7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, Dec. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm10, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask).' + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh new file mode 100644 index 0000000000000..c3896a6559802 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked_1.3.99_src_all.tar.gz" +) +MD5="c6a5365fa1a0d2a5ecb63752960eb3d7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/pre-unlink.sh new file mode 100644 index 0000000000000..01700b2906450 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm10.masked diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml index 95af0c8d1bfff..eafc6a150e051 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm10" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6e2eb3bce208cc7766f0e0ef1e14465289d5463b34d94c9a9279256545b5408b + md5: 929f8bd0ea9ad416ecc0c2c002500414 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Mmusculus.UCSC.mm10.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm10, Dec. 2011) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.mmusculus.ucsc.mm10 + path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh index 5ebb3f3980359..56bd4d6eddee8 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm10/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm10_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm10/bioconductor-bsgenome.mmusculus.ucsc.mm10_1.4.0_src_all.tar.gz" ) MD5="929f8bd0ea9ad416ecc0c2c002500414" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml new file mode 100644 index 0000000000000..12f4b224e9838 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Mmusculus.UCSC.mm8.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5809f925e0fe7c4b73b78a90c9a36fdd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm8 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm8, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh new file mode 100644 index 0000000000000..6ae61ca9fc4cb --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked_1.3.99_src_all.tar.gz" +) +MD5="5809f925e0fe7c4b73b78a90c9a36fdd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/pre-unlink.sh new file mode 100644 index 0000000000000..f24f323fa9e85 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm8.masked diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml new file mode 100644 index 0000000000000..ffcb9e70ba209 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Mmusculus.UCSC.mm8" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f6aa91cdce2607f30a34f6dd0d678aff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm8, Feb. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh new file mode 100644 index 0000000000000..7ff91773a76e3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm8_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm8/bioconductor-bsgenome.mmusculus.ucsc.mm8_1.4.0_src_all.tar.gz" +) +MD5="f6aa91cdce2607f30a34f6dd0d678aff" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/pre-unlink.sh new file mode 100644 index 0000000000000..e6877292ff26f --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm8/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm8 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml new file mode 100644 index 0000000000000..11a9983fe8ac0 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Mmusculus.UCSC.mm9.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a5dadab14e55cdfc39649ede7a8483d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects. The sequences are the same as in BSgenome.Mmusculus.UCSC.mm9, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh new file mode 100644 index 0000000000000..b8dbc797780d4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked_1.3.99_src_all.tar.gz" +) +MD5="a5dadab14e55cdfc39649ede7a8483d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/pre-unlink.sh new file mode 100644 index 0000000000000..758bfec6ef68d --- /dev/null +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Mmusculus.UCSC.mm9.masked diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml index 6d718bd04865a..7840558f80878 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.4.0" %} {% set name = "BSgenome.Mmusculus.UCSC.mm9" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3110745e93ae7c470b826921efc308fd5805efacdf497b7b8d5f890706c739ae + md5: 5a30ba2b4481a17e8e6979eb69eabf78 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Full genome sequences for Mus musculus (Mouse) as provided by UCSC (mm9, Jul. 2007) and stored in Biostrings objects.' - +extra: + parent_recipe: + name: bioconductor-bsgenome.mmusculus.ucsc.mm9 + path: recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9 + version: 1.4.0 diff --git a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh index 46e2c221f96b6..356ff7b3d7a3a 100644 --- a/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh +++ b/recipes/bioconductor-bsgenome.mmusculus.ucsc.mm9/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash -FN="bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" +FN="BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" "https://bioarchive.galaxyproject.org/BSgenome.Mmusculus.UCSC.mm9_1.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-bsgenome.mmusculus.ucsc.mm9/bioconductor-bsgenome.mmusculus.ucsc.mm9_1.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml new file mode 100644 index 0000000000000..ca58d27608d7e --- /dev/null +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.99.1" %} +{% set name = "BSgenome.Osativa.MSU.MSU7" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 459fe50be785d06ab680565aacca1c57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Oryza sativa full genome as provided by MSU (MSU7 Genome Release) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh b/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh new file mode 100644 index 0000000000000..0d94fc46a583c --- /dev/null +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Osativa.MSU.MSU7_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.osativa.msu.msu7/bioconductor-bsgenome.osativa.msu.msu7_0.99.1_src_all.tar.gz" +) +MD5="459fe50be785d06ab680565aacca1c57" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.osativa.msu.msu7/pre-unlink.sh b/recipes/bioconductor-bsgenome.osativa.msu.msu7/pre-unlink.sh new file mode 100644 index 0000000000000..6dcc76f67fcff --- /dev/null +++ b/recipes/bioconductor-bsgenome.osativa.msu.msu7/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Osativa.MSU.MSU7 diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml new file mode 100644 index 0000000000000..e40627060e3e5 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro2.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e6d069be23712b483b4e4c71554594cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro2 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro2, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh new file mode 100644 index 0000000000000..dd89722671c24 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked_1.3.99_src_all.tar.gz" +) +MD5="e6d069be23712b483b4e4c71554594cf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/pre-unlink.sh new file mode 100644 index 0000000000000..e8202c717f067 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro2.masked diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml new file mode 100644 index 0000000000000..66645a5a45d53 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 780200c315779ac75fcf0bdeb9a2eb8c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro2, Mar. 2006) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh new file mode 100644 index 0000000000000..beac98c21853b --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2_1.4.0_src_all.tar.gz" +) +MD5="780200c315779ac75fcf0bdeb9a2eb8c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/pre-unlink.sh new file mode 100644 index 0000000000000..38c55e19c2c3f --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro2 diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml new file mode 100644 index 0000000000000..c65123d76fb65 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89e96b3796d3b8e8793146597506e3f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.ptroglodytes.ucsc.pantro3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects. The sequences are the same as in BSgenome.Ptroglodytes.UCSC.panTro3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh new file mode 100644 index 0000000000000..68d2e4bd1010e --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked_1.3.99_src_all.tar.gz" +) +MD5="89e96b3796d3b8e8793146597506e3f5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..d77274fa39052 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro3.masked diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml new file mode 100644 index 0000000000000..8cf6705dd4895 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4677c75befd60742f3fc2a54c7f60666 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro3, Oct. 2010) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh new file mode 100644 index 0000000000000..8449ec40795e1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3_1.4.0_src_all.tar.gz" +) +MD5="4677c75befd60742f3fc2a54c7f60666" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/pre-unlink.sh new file mode 100644 index 0000000000000..b8993673634e7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro3 diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml new file mode 100644 index 0000000000000..b822523137cf2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5b88573dd9c3ef838699b65934f8abe3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro5, May 2016) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh new file mode 100644 index 0000000000000..147f9f9420711 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro5_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5_1.4.2_src_all.tar.gz" +) +MD5="5b88573dd9c3ef838699b65934f8abe3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/pre-unlink.sh new file mode 100644 index 0000000000000..df7b2766499da --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro5 diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml new file mode 100644 index 0000000000000..877b0b92e061a --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Ptroglodytes.UCSC.panTro6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1df05d985374e9edc1dd7c3df5118338 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Pan troglodytes (Chimp) as provided by UCSC (panTro6, Jan. 2018) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh new file mode 100644 index 0000000000000..2e297f45726d5 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Ptroglodytes.UCSC.panTro6_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6_1.4.2_src_all.tar.gz" +) +MD5="1df05d985374e9edc1dd7c3df5118338" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/pre-unlink.sh b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/pre-unlink.sh new file mode 100644 index 0000000000000..86891c8a09ef6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.ptroglodytes.ucsc.pantro6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Ptroglodytes.UCSC.panTro6 diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml new file mode 100644 index 0000000000000..625109cf69ef2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Rnorvegicus.UCSC.rn4.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7e2ea7df588b6b10515e07ea3868c568 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn4 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn4, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh new file mode 100644 index 0000000000000..aae11f1722ac9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked_1.3.99_src_all.tar.gz" +) +MD5="7e2ea7df588b6b10515e07ea3868c568" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/pre-unlink.sh new file mode 100644 index 0000000000000..ea1cf9722c008 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Rnorvegicus.UCSC.rn4.masked diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml new file mode 100644 index 0000000000000..b28a76eb79373 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Rnorvegicus.UCSC.rn4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3afe6729237781445d99ec38228ee1a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: TxDb.Rnorvegicus.UCSC.rn4.ensGene +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn4, Nov. 2004) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh new file mode 100644 index 0000000000000..7813879e0e7b8 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn4_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/bioconductor-bsgenome.rnorvegicus.ucsc.rn4_1.4.0_src_all.tar.gz" +) +MD5="3afe6729237781445d99ec38228ee1a8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/pre-unlink.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/pre-unlink.sh new file mode 100644 index 0000000000000..62c2105e8e9d2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Rnorvegicus.UCSC.rn4 diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml new file mode 100644 index 0000000000000..b19990b56d57a --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Rnorvegicus.UCSC.rn5.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 663233774b79012cb2cc08224ac275ed +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.rnorvegicus.ucsc.rn5 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects. The sequences are the same as in BSgenome.Rnorvegicus.UCSC.rn5, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh new file mode 100644 index 0000000000000..38418a2e57a23 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked_1.3.99_src_all.tar.gz" +) +MD5="663233774b79012cb2cc08224ac275ed" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/pre-unlink.sh new file mode 100644 index 0000000000000..03eca93cb8356 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Rnorvegicus.UCSC.rn5.masked diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml new file mode 100644 index 0000000000000..c36691b8dc09b --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Rnorvegicus.UCSC.rn5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 723b1f3ced395ef638b2d68053b05c86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: TxDb.Rnorvegicus.UCSC.rn5.refGene +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn5, Mar. 2012) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh new file mode 100644 index 0000000000000..bd3444c37264d --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn5_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/bioconductor-bsgenome.rnorvegicus.ucsc.rn5_1.4.0_src_all.tar.gz" +) +MD5="723b1f3ced395ef638b2d68053b05c86" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/pre-unlink.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/pre-unlink.sh new file mode 100644 index 0000000000000..b505fe33624ba --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Rnorvegicus.UCSC.rn5 diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml new file mode 100644 index 0000000000000..3d6047efb4d5d --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.1" %} +{% set name = "BSgenome.Rnorvegicus.UCSC.rn6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 60d3fb201e0b1475912aaf681927096d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Rattus norvegicus (Rat) as provided by UCSC (rn6, Jul. 2014) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh new file mode 100644 index 0000000000000..ff2dae830af46 --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Rnorvegicus.UCSC.rn6_1.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/bioconductor-bsgenome.rnorvegicus.ucsc.rn6_1.4.1_src_all.tar.gz" +) +MD5="60d3fb201e0b1475912aaf681927096d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/pre-unlink.sh b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/pre-unlink.sh new file mode 100644 index 0000000000000..12849272dd22b --- /dev/null +++ b/recipes/bioconductor-bsgenome.rnorvegicus.ucsc.rn6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Rnorvegicus.UCSC.rn6 diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml new file mode 100644 index 0000000000000..fb6e644b30bf2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Scerevisiae.UCSC.sacCer1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ad4c29c16a9635088bf13872b4a02ed4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer1, Oct. 2003) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh new file mode 100644 index 0000000000000..1367fdeeb5b10 --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer1_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/bioconductor-bsgenome.scerevisiae.ucsc.saccer1_1.4.0_src_all.tar.gz" +) +MD5="ad4c29c16a9635088bf13872b4a02ed4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/pre-unlink.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/pre-unlink.sh new file mode 100644 index 0000000000000..bf72b58b433ed --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Scerevisiae.UCSC.sacCer1 diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml new file mode 100644 index 0000000000000..b61f4f2e57edd --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Scerevisiae.UCSC.sacCer2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f1025b4d0fa7891dc46301550163753e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer2, June 2008) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh new file mode 100644 index 0000000000000..3a1cc98f61ebe --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer2_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/bioconductor-bsgenome.scerevisiae.ucsc.saccer2_1.4.0_src_all.tar.gz" +) +MD5="f1025b4d0fa7891dc46301550163753e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/pre-unlink.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/pre-unlink.sh new file mode 100644 index 0000000000000..16a94d7ef659d --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Scerevisiae.UCSC.sacCer2 diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml new file mode 100644 index 0000000000000..7ab884006c8f4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Scerevisiae.UCSC.sacCer3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7f2d8bba69c3dcebf426d9b19a6bed30 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Saccharomyces cerevisiae (Yeast) full genome as provided by UCSC (sacCer3, April 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh new file mode 100644 index 0000000000000..513cb0038e836 --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Scerevisiae.UCSC.sacCer3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/bioconductor-bsgenome.scerevisiae.ucsc.saccer3_1.4.0_src_all.tar.gz" +) +MD5="7f2d8bba69c3dcebf426d9b19a6bed30" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/pre-unlink.sh b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/pre-unlink.sh new file mode 100644 index 0000000000000..65e0f98b76cd2 --- /dev/null +++ b/recipes/bioconductor-bsgenome.scerevisiae.ucsc.saccer3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Scerevisiae.UCSC.sacCer3 diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml new file mode 100644 index 0000000000000..d74510e5c8916 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Sscrofa.UCSC.susScr11" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db22832229e31e1a629d107df522dff9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr11, Feb. 2017) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh new file mode 100644 index 0000000000000..647b6e12067c6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr11_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr11/bioconductor-bsgenome.sscrofa.ucsc.susscr11_1.4.2_src_all.tar.gz" +) +MD5="db22832229e31e1a629d107df522dff9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/pre-unlink.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/pre-unlink.sh new file mode 100644 index 0000000000000..b4e976df65c13 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr11/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Sscrofa.UCSC.susScr11 diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml new file mode 100644 index 0000000000000..76423854999b7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Sscrofa.UCSC.susScr3.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fd240651d22d169fd1e27a2b66e40dd7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.sscrofa.ucsc.susscr3 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects. The sequences are the same as in BSgenome.Sscrofa.UCSC.susScr3, except that each of them has the 4 following masks on top: (1) the mask of assembly gaps (AGAPS mask), (2) the mask of intra-contig ambiguities (AMB mask), (3) the mask of repeats from RepeatMasker (RM mask), and (4) the mask of repeats from Tandem Repeats Finder (TRF mask). Only the AGAPS and AMB masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh new file mode 100644 index 0000000000000..53232dfc7b96e --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked_1.3.99_src_all.tar.gz" +) +MD5="fd240651d22d169fd1e27a2b66e40dd7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/pre-unlink.sh new file mode 100644 index 0000000000000..7c9ce4a528eb1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Sscrofa.UCSC.susScr3.masked diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml new file mode 100644 index 0000000000000..78c985eb71dc7 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Sscrofa.UCSC.susScr3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0457ca52a81c9d7ceadad5830169e6cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Sus scrofa (Pig) as provided by UCSC (susScr3, Aug. 2011) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh new file mode 100644 index 0000000000000..c882a46e5c133 --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Sscrofa.UCSC.susScr3_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.sscrofa.ucsc.susscr3/bioconductor-bsgenome.sscrofa.ucsc.susscr3_1.4.0_src_all.tar.gz" +) +MD5="0457ca52a81c9d7ceadad5830169e6cf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/pre-unlink.sh b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/pre-unlink.sh new file mode 100644 index 0000000000000..c858fd9d4e84f --- /dev/null +++ b/recipes/bioconductor-bsgenome.sscrofa.ucsc.susscr3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Sscrofa.UCSC.susScr3 diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml new file mode 100644 index 0000000000000..ad1cccf276ab8 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.99.0" %} +{% set name = "BSgenome.Tgondii.ToxoDB.7.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8f204871f73f8d1c5194f3748e28878e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL 3' + summary: 'Toxoplasma gondii ME49 genome Release 7.0 available at http://www.toxodb.org' + diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh new file mode 100644 index 0000000000000..cf4201c036138 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Tgondii.ToxoDB.7.0_0.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tgondii.toxodb.7.0/bioconductor-bsgenome.tgondii.toxodb.7.0_0.99.0_src_all.tar.gz" +) +MD5="8f204871f73f8d1c5194f3748e28878e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/pre-unlink.sh b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/pre-unlink.sh new file mode 100644 index 0000000000000..317b52f95aad1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tgondii.toxodb.7.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Tgondii.ToxoDB.7.0 diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml new file mode 100644 index 0000000000000..a0dac90b902b0 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.3.99" %} +{% set name = "BSgenome.Tguttata.UCSC.taeGut1.masked" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 63684abb5b330bb54ff89fe78f2e6444 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.tguttata.ucsc.taegut1 >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects. The sequences are the same as in BSgenome.Tguttata.UCSC.taeGut1, except that each of them has the 2 following masks on top: (1) the mask of assembly gaps (AGAPS mask), and (2) the mask of intra-contig ambiguities (AMB mask). Both masks are "active" by default.' + diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh new file mode 100644 index 0000000000000..c2125b874c6c1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1.masked_1.3.99.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked_1.3.99_src_all.tar.gz" +) +MD5="63684abb5b330bb54ff89fe78f2e6444" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/pre-unlink.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/pre-unlink.sh new file mode 100644 index 0000000000000..9fb0cd5bc5573 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1.masked/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Tguttata.UCSC.taeGut1.masked diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml new file mode 100644 index 0000000000000..9cf3df48e63b4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "BSgenome.Tguttata.UCSC.taeGut1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9753d9568d2a866a627673a518a1dd8a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut1, Jul. 2008) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh new file mode 100644 index 0000000000000..c8e93e38b82d3 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut1_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut1/bioconductor-bsgenome.tguttata.ucsc.taegut1_1.4.0_src_all.tar.gz" +) +MD5="9753d9568d2a866a627673a518a1dd8a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/pre-unlink.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/pre-unlink.sh new file mode 100644 index 0000000000000..9b6c009162c37 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Tguttata.UCSC.taeGut1 diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml new file mode 100644 index 0000000000000..4b22b69d131f6 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.2" %} +{% set name = "BSgenome.Tguttata.UCSC.taeGut2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1d39678fb060e643f7e9c4ec25e828c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Full genome sequences for Taeniopygia guttata (Zebra finch) as provided by UCSC (taeGut2, Feb. 2013) and stored in Biostrings objects.' + diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh new file mode 100644 index 0000000000000..78dfd39087ec1 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Tguttata.UCSC.taeGut2_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.tguttata.ucsc.taegut2/bioconductor-bsgenome.tguttata.ucsc.taegut2_1.4.2_src_all.tar.gz" +) +MD5="1d39678fb060e643f7e9c4ec25e828c0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/pre-unlink.sh b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/pre-unlink.sh new file mode 100644 index 0000000000000..2e8c64aaffb02 --- /dev/null +++ b/recipes/bioconductor-bsgenome.tguttata.ucsc.taegut2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Tguttata.UCSC.taeGut2 diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml new file mode 100644 index 0000000000000..58d7463116fc4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1" %} +{% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3f791de6d699325a97080cd98be86d89 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: CC0 + summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv0) and available at the URGI (INRA)' + diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh new file mode 100644 index 0000000000000..384b6fd25186f --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv0_0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0_0.1_src_all.tar.gz" +) +MD5="3f791de6d699325a97080cd98be86d89" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/pre-unlink.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/pre-unlink.sh new file mode 100644 index 0000000000000..2e533e8a5a5e9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Vvinifera.URGI.IGGP12Xv0 diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml new file mode 100644 index 0000000000000..2ae3de04058a9 --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1" %} +{% set name = "BSgenome.Vvinifera.URGI.IGGP12Xv2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 95472e574ab46327c19e241c381b26a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: CC0 + summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 12Xv2) and available at the URGI (INRA)' + diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh new file mode 100644 index 0000000000000..39fd328f8f52c --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP12Xv2_0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2_0.1_src_all.tar.gz" +) +MD5="95472e574ab46327c19e241c381b26a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/pre-unlink.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/pre-unlink.sh new file mode 100644 index 0000000000000..e44e0c8acdc4d --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp12xv2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Vvinifera.URGI.IGGP12Xv2 diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml new file mode 100644 index 0000000000000..12b2376f59d8b --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.1" %} +{% set name = "BSgenome.Vvinifera.URGI.IGGP8X" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fccaf60e5c9352b9c454f7a8ecac2a20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: CC0 + summary: 'Full reference nuclear genome sequences for Vitis vinifera subsp. vinifera PN40024 (derived from Pinot Noir and close to homozygosity after 6-9 rounds of selfing) as assembled by the IGGP (version 8X) and available at the URGI (INRA). More details in Jaillon et al (Nature, 2007).' + diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh new file mode 100644 index 0000000000000..a1381a0ecae46 --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" + "https://bioarchive.galaxyproject.org/BSgenome.Vvinifera.URGI.IGGP8X_0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsgenome.vvinifera.urgi.iggp8x/bioconductor-bsgenome.vvinifera.urgi.iggp8x_0.1_src_all.tar.gz" +) +MD5="fccaf60e5c9352b9c454f7a8ecac2a20" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/pre-unlink.sh b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/pre-unlink.sh new file mode 100644 index 0000000000000..c6bb0fcb6d4b4 --- /dev/null +++ b/recipes/bioconductor-bsgenome.vvinifera.urgi.iggp8x/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ BSgenome.Vvinifera.URGI.IGGP8X diff --git a/recipes/bioconductor-bsgenome/build.sh b/recipes/bioconductor-bsgenome/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bsgenome/build.sh +++ b/recipes/bioconductor-bsgenome/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bsgenome/meta.yaml b/recipes/bioconductor-bsgenome/meta.yaml index a13a0c56f047b..ae0befa1ed030 100644 --- a/recipes/bioconductor-bsgenome/meta.yaml +++ b/recipes/bioconductor-bsgenome/meta.yaml @@ -1,52 +1,59 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "BSgenome" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e815eb2def62b70e9aade10094f0cee3d9d3c44179581a4a9bf7b68271bc62e6 + md5: f395bece508475220d86ec87f694436b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocManager, Biobase, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.UCSC.hg38, BSgenome.Hsapiens.UCSC.hg38.masked, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Rnorvegicus.UCSC.rn5, BSgenome.Scerevisiae.UCSC.sacCer1, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, XtraSNPlocs.Hsapiens.dbSNP144.GRCh38, hgu95av2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infrastructure shared by all the Biostrings-based genome data packages.' extra: identifiers: - biotools:bsgenome - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bsgenome + path: recipes/bioconductor-bsgenome + version: 1.48.0 + diff --git a/recipes/bioconductor-bsseq/build.sh b/recipes/bioconductor-bsseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bsseq/build.sh +++ b/recipes/bioconductor-bsseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bsseq/meta.yaml b/recipes/bioconductor-bsseq/meta.yaml index 90046ca92c9e6..55fc373a6d536 100644 --- a/recipes/bioconductor-bsseq/meta.yaml +++ b/recipes/bioconductor-bsseq/meta.yaml @@ -1,67 +1,92 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "bsseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a5463893c12ab9cf479ecc3d32113d2e436b657c02def951dcc56d748c1ab064 + md5: 27d165f57d1a2fdfd2fb2af640039d90 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, bsseqData, BiocStyle, rmarkdown, knitr, Matrix, doParallel, rtracklayer, BSgenome.Hsapiens.UCSC.hg38, beachmat +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-data.table + - 'r-data.table >=1.11.8' - r-gtools - r-locfit - r-permute - 'r-r.utils >=2.0.0' + - r-rcpp - r-scales run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-data.table + - 'r-data.table >=1.11.8' - r-gtools - r-locfit - r-permute - 'r-r.utils >=2.0.0' + - r-rcpp - r-scales + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of tools for analyzing and visualizing bisulfite sequencing data.' extra: identifiers: - biotools:bsseq + parent_recipe: + name: bioconductor-bsseq + path: recipes/bioconductor-bsseq + version: 1.16.1 + diff --git a/recipes/bioconductor-bsseqdata/meta.yaml b/recipes/bioconductor-bsseqdata/meta.yaml new file mode 100644 index 0000000000000..dd74f194bc515 --- /dev/null +++ b/recipes/bioconductor-bsseqdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.20.0" %} +{% set name = "bsseqData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb6e98b0545c71b6447d69747244036c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Example whole genome bisulfite data for the bsseq package' + diff --git a/recipes/bioconductor-bsseqdata/post-link.sh b/recipes/bioconductor-bsseqdata/post-link.sh new file mode 100644 index 0000000000000..2f8679f403870 --- /dev/null +++ b/recipes/bioconductor-bsseqdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bsseqData_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/bsseqData_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/bsseqData_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsseqdata/bioconductor-bsseqdata_0.20.0_src_all.tar.gz" +) +MD5="fb6e98b0545c71b6447d69747244036c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsseqdata/pre-unlink.sh b/recipes/bioconductor-bsseqdata/pre-unlink.sh new file mode 100644 index 0000000000000..be918bed85ee4 --- /dev/null +++ b/recipes/bioconductor-bsseqdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bsseqData diff --git a/recipes/bioconductor-bsubtiliscdf/meta.yaml b/recipes/bioconductor-bsubtiliscdf/meta.yaml new file mode 100644 index 0000000000000..eff2885d2ee36 --- /dev/null +++ b/recipes/bioconductor-bsubtiliscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "bsubtiliscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7d7893d28c601206805819ae0e49b31b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Bsubtilis.CDF file.' + diff --git a/recipes/bioconductor-bsubtiliscdf/post-link.sh b/recipes/bioconductor-bsubtiliscdf/post-link.sh new file mode 100644 index 0000000000000..54baf47f6e017 --- /dev/null +++ b/recipes/bioconductor-bsubtiliscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bsubtiliscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bsubtiliscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bsubtiliscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsubtiliscdf/bioconductor-bsubtiliscdf_2.18.0_src_all.tar.gz" +) +MD5="7d7893d28c601206805819ae0e49b31b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsubtiliscdf/pre-unlink.sh b/recipes/bioconductor-bsubtiliscdf/pre-unlink.sh new file mode 100644 index 0000000000000..5f8128ce560bb --- /dev/null +++ b/recipes/bioconductor-bsubtiliscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bsubtiliscdf diff --git a/recipes/bioconductor-bsubtilisprobe/meta.yaml b/recipes/bioconductor-bsubtilisprobe/meta.yaml new file mode 100644 index 0000000000000..f9891ca5b1ce5 --- /dev/null +++ b/recipes/bioconductor-bsubtilisprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "bsubtilisprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83568fcea2122350b7ce982e79b7ec53 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Bsubtilis\_probe\_tab.' + diff --git a/recipes/bioconductor-bsubtilisprobe/post-link.sh b/recipes/bioconductor-bsubtilisprobe/post-link.sh new file mode 100644 index 0000000000000..1d9c54028d7c0 --- /dev/null +++ b/recipes/bioconductor-bsubtilisprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="bsubtilisprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/bsubtilisprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/bsubtilisprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-bsubtilisprobe/bioconductor-bsubtilisprobe_2.18.0_src_all.tar.gz" +) +MD5="83568fcea2122350b7ce982e79b7ec53" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-bsubtilisprobe/pre-unlink.sh b/recipes/bioconductor-bsubtilisprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e9a465394427e --- /dev/null +++ b/recipes/bioconductor-bsubtilisprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ bsubtilisprobe diff --git a/recipes/bioconductor-bubbletree/build.sh b/recipes/bioconductor-bubbletree/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bubbletree/build.sh +++ b/recipes/bioconductor-bubbletree/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bubbletree/meta.yaml b/recipes/bioconductor-bubbletree/meta.yaml index 0ee695d98fbac..f437494d0bbb2 100644 --- a/recipes/bioconductor-bubbletree/meta.yaml +++ b/recipes/bioconductor-bubbletree/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "BubbleTree" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 966e8e59ae9ac9ae950faf6559eb395cd42d1853d12504bea1065308fffdd83c + md5: 7a76991a141f4d831fbea768e01d76bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-e1071 @@ -37,13 +39,13 @@ requirements: - r-rcolorbrewer - r-writexls run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-e1071 @@ -59,10 +61,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'CNV analysis in groups of tumor samples.' extra: identifiers: - biotools:bubbletree - doi:10.1093/nar/gkv1102 + parent_recipe: + name: bioconductor-bubbletree + path: recipes/bioconductor-bubbletree + version: 2.10.0 + diff --git a/recipes/bioconductor-bufferedmatrix/build.sh b/recipes/bioconductor-bufferedmatrix/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bufferedmatrix/build.sh +++ b/recipes/bioconductor-bufferedmatrix/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bufferedmatrix/meta.yaml b/recipes/bioconductor-bufferedmatrix/meta.yaml index 3639dca003a4e..9b99b7625774a 100644 --- a/recipes/bioconductor-bufferedmatrix/meta.yaml +++ b/recipes/bioconductor-bufferedmatrix/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BufferedMatrix" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f366c3b558e925f14d600bbedc23ac17afe7541d8b4e18d73fe3287b57db4036 + md5: ac35d5e400ae81406bd70ca1f631b593 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A tabular style data object where most data is stored outside main memory. A buffer is used to speed up access to data.' extra: identifiers: - biotools:bufferedmatrix - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bufferedmatrix + path: recipes/bioconductor-bufferedmatrix + version: 1.44.0 + diff --git a/recipes/bioconductor-bufferedmatrixmethods/build.sh b/recipes/bioconductor-bufferedmatrixmethods/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/build.sh +++ b/recipes/bioconductor-bufferedmatrixmethods/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml index d2f016af7a0fc..4937771b0c390 100644 --- a/recipes/bioconductor-bufferedmatrixmethods/meta.yaml +++ b/recipes/bioconductor-bufferedmatrixmethods/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "BufferedMatrixMethods" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b0824c8216f969d722c055ef0c38421f38533bd83c0f67c435f835de40a0a02b + md5: fd0c01ee09b195d76b9b4e76ccda07ca build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affyio, affy requirements: host: - - 'bioconductor-bufferedmatrix >=1.44.0,<1.46.0' + - 'bioconductor-bufferedmatrix >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-bufferedmatrix >=1.44.0,<1.46.0' + - 'bioconductor-bufferedmatrix >=1.46.0,<1.47.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Microarray analysis methods that use BufferedMatrix objects' extra: identifiers: - biotools:bufferedmatrixmethods - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bufferedmatrixmethods + path: recipes/bioconductor-bufferedmatrixmethods + version: 1.44.0 + diff --git a/recipes/bioconductor-bumhmm/build.sh b/recipes/bioconductor-bumhmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-bumhmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bumhmm/meta.yaml b/recipes/bioconductor-bumhmm/meta.yaml new file mode 100644 index 0000000000000..5842d6e9975f5 --- /dev/null +++ b/recipes/bioconductor-bumhmm/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "BUMHMM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1a6387144538ea8c29eb322172c268d6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, BiocStyle +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-devtools + - r-gtools + - r-stringi + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-devtools + - r-gtools + - r-stringi +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This is a probabilistic modelling pipeline for computing per- nucleotide posterior probabilities of modification from the data collected in structure probing experiments. The model supports multiple experimental replicates and empirically corrects coverage- and sequence-dependent biases. The model utilises the measure of a "drop-off rate" for each nucleotide, which is compared between replicates through a log-ratio (LDR). The LDRs between control replicates define a null distribution of variability in drop-off rate observed by chance and LDRs between treatment and control replicates gets compared to this distribution. Resulting empirical p-values (probability of being "drawn" from the null distribution) are used as observations in a Hidden Markov Model with a Beta-Uniform Mixture model used as an emission model. The resulting posterior probabilities indicate the probability of a nucleotide of having being modified in a structure probing experiment.' + diff --git a/recipes/bioconductor-bumphunter/build.sh b/recipes/bioconductor-bumphunter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bumphunter/build.sh +++ b/recipes/bioconductor-bumphunter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bumphunter/meta.yaml b/recipes/bioconductor-bumphunter/meta.yaml index 68ff1af08260b..816f0f9f17d07 100644 --- a/recipes/bioconductor-bumphunter/meta.yaml +++ b/recipes/bioconductor-bumphunter/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.5" %} {% set name = "bumphunter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bedff4dc62c5274ac835c877de825f959d1f40e0779d356d42117847efcd4b34 + md5: 7c38a75e34594b999dbe13f58de13d2d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, RUnit, doParallel, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dorng - r-foreach @@ -33,14 +35,14 @@ requirements: - r-locfit - r-matrixstats run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-dorng - r-foreach @@ -51,9 +53,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for finding bumps in genomic data' extra: identifiers: - biotools:bumphunter + parent_recipe: + name: bioconductor-bumphunter + path: recipes/bioconductor-bumphunter + version: 1.22.0 + diff --git a/recipes/bioconductor-bus/build.sh b/recipes/bioconductor-bus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-bus/build.sh +++ b/recipes/bioconductor-bus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-bus/meta.yaml b/recipes/bioconductor-bus/meta.yaml index b269e37a0d528..bfa1f473abafd 100644 --- a/recipes/bioconductor-bus/meta.yaml +++ b/recipes/bioconductor-bus/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "BUS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dc2262578a875ff3a5a17100c11dc110977847a742f96138ff6cfaec05dc85cf + md5: ebdfc2420596f5fdc284694c57183488 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-minet >=3.38.0,<3.40.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' - r-base - r-infotheo run: - - 'bioconductor-minet >=3.38.0,<3.40.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' - r-base - r-infotheo build: @@ -33,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package can be used to compute associations among genes (gene-networks) or between genes and some external traits (i.e. clinical).' extra: identifiers: - biotools:bus - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-bus + path: recipes/bioconductor-bus + version: 1.36.0 + diff --git a/recipes/bioconductor-buscorrect/build.sh b/recipes/bioconductor-buscorrect/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-buscorrect/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-buscorrect/meta.yaml b/recipes/bioconductor-buscorrect/meta.yaml new file mode 100644 index 0000000000000..19e95d5dd71cb --- /dev/null +++ b/recipes/bioconductor-buscorrect/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "BUScorrect" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aadd22d922c6821cf37445835612c4b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gplots + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gplots + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'High-throughput experimental data are accumulating exponentially in public databases. However, mining valid scientific discoveries from these abundant resources is hampered by technical artifacts and inherent biological heterogeneity. The former are usually termed "batch effects," and the latter is often modelled by "subtypes." The R package BUScorrect fits a Bayesian hierarchical model, the Batch-effects-correction-with-Unknown-Subtypes model (BUS), to correct batch effects in the presence of unknown subtypes. BUS is capable of (a) correcting batch effects explicitly, (b) grouping samples that share similar characteristics into subtypes, (c) identifying features that distinguish subtypes, and (d) enjoying a linear-order computation complexity.' + diff --git a/recipes/bioconductor-cafe/build.sh b/recipes/bioconductor-cafe/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cafe/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cafe/meta.yaml b/recipes/bioconductor-cafe/meta.yaml new file mode 100644 index 0000000000000..b5c66dafcffcf --- /dev/null +++ b/recipes/bioconductor-cafe/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.18.0" %} +{% set name = "CAFE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db87b028e56b69c3372cf9e8b0f04836 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-ggplot2 + - r-gridextra + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-ggplot2 + - r-gridextra +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Detection and visualizations of gross chromosomal aberrations using Affymetrix expression microarrays as input' + diff --git a/recipes/bioconductor-cagefightr/build.sh b/recipes/bioconductor-cagefightr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cagefightr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cagefightr/meta.yaml b/recipes/bioconductor-cagefightr/meta.yaml new file mode 100644 index 0000000000000..7a1ff29a15e6a --- /dev/null +++ b/recipes/bioconductor-cagefightr/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.2.0" %} +{% set name = "CAGEfightR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bed28d787f521b9fb0ee568b6188041f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm9.knownGene +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicinteractions >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'r-assertthat >=0.2.0' + - r-base + - 'r-grr >=0.9.5' + - 'r-matrix >=1.2-12' + - 'r-matrix.utils >=0.9.6' + - 'r-pryr >=0.1.3' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicinteractions >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'r-assertthat >=0.2.0' + - r-base + - 'r-grr >=0.9.5' + - 'r-matrix >=1.2-12' + - 'r-matrix.utils >=0.9.6' + - 'r-pryr >=0.1.3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'CAGE is a widely used high throughput assay for measuring transcription start site (TSS) activity. CAGEfightR is an R/Bioconductor package for performing a wide range of common data analysis tasks for CAGE and 5''-end data in general. Core functionality includes: import of CAGE TSSs (CTSSs), tag (or unidirectional) clustering for TSS identification, bidirectional clustering for enhancer identification, annotation with transcript and gene models, correlation of TSS and enhancer expression, calculation of TSS shapes, quantification of CAGE expression as expression matrices and genome brower visualization.' + diff --git a/recipes/bioconductor-cager/build.sh b/recipes/bioconductor-cager/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cager/build.sh +++ b/recipes/bioconductor-cager/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cager/conda_build_config.yaml b/recipes/bioconductor-cager/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-cager/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-cager/meta.yaml b/recipes/bioconductor-cager/meta.yaml index dc985ba8818b5..a13c3c74c52e4 100644 --- a/recipes/bioconductor-cager/meta.yaml +++ b/recipes/bioconductor-cager/meta.yaml @@ -1,39 +1,42 @@ -{% set version = "1.22.3" %} +{% set version = "1.24.0" %} {% set name = "CAGEr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c4651de70deada80715d6013a52f3818aa7fee025d558584edc416d1606a8d57 + md5: 9ecbf3e0bb2fb6d00e1de0a3652d845e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Drerio.UCSC.danRer7, DESeq2, FANTOM3and4CAGE, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-beanplot - r-data.table + - r-formula.tools - 'r-ggplot2 >=2.2.0' - r-gtools - r-kernsmooth @@ -46,22 +49,23 @@ requirements: - r-vegan - r-vgam run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-beanplot - r-data.table + - r-formula.tools - 'r-ggplot2 >=2.2.0' - r-gtools - r-kernsmooth @@ -77,9 +81,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Preprocessing of CAGE sequencing data, identification and normalization of transcription start sites and downstream analysis of transcription start sites clusters (promoters).' extra: identifiers: - biotools:cager + parent_recipe: + name: bioconductor-cager + path: recipes/bioconductor-cager + version: 1.22.3 + diff --git a/recipes/bioconductor-calib/build.sh b/recipes/bioconductor-calib/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-calib/build.sh +++ b/recipes/bioconductor-calib/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-calib/meta.yaml b/recipes/bioconductor-calib/meta.yaml index 48e9d343f46b0..6b6179dd13fbe 100644 --- a/recipes/bioconductor-calib/meta.yaml +++ b/recipes/bioconductor-calib/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "CALIB" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5cf0010419dda41f2ea4e5e04b9edee580d491275d709ff0476febb4e2d693e2 + md5: 1b50dd84b955b6ca81e18509167b4896 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base build: - {{ compiler('c') }} @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package contains functions for normalizing spotted microarray data, based on a physically motivated calibration model. The model parameters and error distributions are estimated from external control spikes.' extra: identifiers: - biotools:calib - doi:10.1093/bioinformatics/btm159 + parent_recipe: + name: bioconductor-calib + path: recipes/bioconductor-calib + version: 1.46.0 + diff --git a/recipes/bioconductor-camera/build.sh b/recipes/bioconductor-camera/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-camera/build.sh +++ b/recipes/bioconductor-camera/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-camera/meta.yaml b/recipes/bioconductor-camera/meta.yaml index bc0b25f3b60c6..c0e783f153423 100644 --- a/recipes/bioconductor-camera/meta.yaml +++ b/recipes/bioconductor-camera/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CAMERA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a009b4b5ba0e30ae9eed3962e7a81228eaaffc5e768355b3e4e68bfcb6c170ad + md5: 021aa21643dbc8c7fef321c6ad373443 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: faahKO, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-hmisc - r-igraph run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-hmisc - r-igraph @@ -40,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Annotation of peaklists generated by xcms, rule based annotation of isotopes and adducts, isotope validation, EIC correlation based tagging of unknown adducts and fragments' extra: identifiers: - biotools:camera + parent_recipe: + name: bioconductor-camera + path: recipes/bioconductor-camera + version: 1.36.0 + diff --git a/recipes/bioconductor-camthc/build.sh b/recipes/bioconductor-camthc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-camthc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-camthc/meta.yaml b/recipes/bioconductor-camthc/meta.yaml new file mode 100644 index 0000000000000..92309001dd6b7 --- /dev/null +++ b/recipes/bioconductor-camthc/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "CAMTHC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cb62c6d7934584f5d24869db7d927437 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat, GEOquery, rgl +# SystemRequirements: Java (>= 1.8) +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-apcluster + - r-base + - r-corpcor + - r-dmwr + - r-geometry + - r-nmf + - r-pcapp + - r-rjava + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-apcluster + - r-base + - r-corpcor + - r-dmwr + - r-geometry + - r-nmf + - r-pcapp + - r-rjava +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'An R package for tissue heterogeneity characterization by convex analysis of mixtures (CAM). It provides basic functions to perform unsupervised deconvolution on mixture expression profiles by CAM and some auxiliary functions to help understand the subpopulation-specific results. It also implements functions to perform supervised deconvolution based on prior knowledge of molecular markers, S matrix or A matrix. Combining molecular markers from CAM and from prior knowledge can achieve semi-supervised deconvolution of mixtures.' + diff --git a/recipes/bioconductor-cancer/build.sh b/recipes/bioconductor-cancer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cancer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancer/meta.yaml b/recipes/bioconductor-cancer/meta.yaml new file mode 100644 index 0000000000000..0c4f570b505ad --- /dev/null +++ b/recipes/bioconductor-cancer/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.16.0" %} +{% set name = "canceR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6194127d4d1248ea09dfcaa420cedb1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat (>= 0.10.0), R.rsp +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsealm >=1.42.0,<1.43.0' + - 'bioconductor-phenotest >=1.30.0,<1.31.0' + - r-base + - r-cgdsr + - r-circlize + - r-formula + - r-plyr + - r-rpart + - r-runit + - r-survival + - r-tcltk2 + - r-tkrplot + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genetclassifier >=1.22.0,<1.23.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsealm >=1.42.0,<1.43.0' + - 'bioconductor-phenotest >=1.30.0,<1.31.0' + - r-base + - r-cgdsr + - r-circlize + - r-formula + - r-plyr + - r-rpart + - r-runit + - r-survival + - r-tcltk2 + - r-tkrplot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package is user friendly interface based on the cgdsr and other modeling packages to explore, compare, and analyse all available Cancer Data (Clinical data, Gene Mutation, Gene Methylation, Gene Expression, Protein Phosphorylation, Copy Number Alteration) hosted by the Computational Biology Center at Memorial-Sloan-Kettering Cancer Center (MSKCC).' + diff --git a/recipes/bioconductor-cancerclass/build.sh b/recipes/bioconductor-cancerclass/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cancerclass/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancerclass/meta.yaml b/recipes/bioconductor-cancerclass/meta.yaml new file mode 100644 index 0000000000000..87a58892d74fe --- /dev/null +++ b/recipes/bioconductor-cancerclass/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.26.0" %} +{% set name = "cancerclass" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 046f83f4ae882a6cc05716c51e2cfee2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: cancerdata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-binom + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-binom + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL 3' + summary: 'The classification protocol starts with a feature selection step and continues with nearest-centroid classification. The accurarcy of the predictor can be evaluated using training and test set validation, leave-one-out cross-validation or in a multiple random validation protocol. Methods for calculation and visualization of continuous prediction scores allow to balance sensitivity and specificity and define a cutoff value according to clinical requirements.' + diff --git a/recipes/bioconductor-cancerdata/meta.yaml b/recipes/bioconductor-cancerdata/meta.yaml new file mode 100644 index 0000000000000..1830ca2a52c93 --- /dev/null +++ b/recipes/bioconductor-cancerdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "cancerdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2fb3c2815ba70f6edcf0254c19afed66 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Dataset for the R package cancerclass' + diff --git a/recipes/bioconductor-cancerdata/post-link.sh b/recipes/bioconductor-cancerdata/post-link.sh new file mode 100644 index 0000000000000..86e4cc27ae742 --- /dev/null +++ b/recipes/bioconductor-cancerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cancerdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cancerdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/cancerdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cancerdata/bioconductor-cancerdata_1.20.0_src_all.tar.gz" +) +MD5="2fb3c2815ba70f6edcf0254c19afed66" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cancerdata/pre-unlink.sh b/recipes/bioconductor-cancerdata/pre-unlink.sh new file mode 100644 index 0000000000000..f5aab06d2b8bc --- /dev/null +++ b/recipes/bioconductor-cancerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cancerdata diff --git a/recipes/bioconductor-cancerinsilico/build.sh b/recipes/bioconductor-cancerinsilico/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cancerinsilico/build.sh +++ b/recipes/bioconductor-cancerinsilico/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancerinsilico/meta.yaml b/recipes/bioconductor-cancerinsilico/meta.yaml index fcfd0f1d11951..862e509fd7e11 100644 --- a/recipes/bioconductor-cancerinsilico/meta.yaml +++ b/recipes/bioconductor-cancerinsilico/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "CancerInSilico" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c35f23004342562d43e5aa42da890d446eeaf9703eaa353a76356a08eba29caa + md5: b217be189972423f40efc7548f418a88 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle, Rtsne, viridis, rgl requirements: host: - r-base @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The CancerInSilico package provides an R interface for running mathematical models of tumor progresson and generating gene expression data from the results. This package has the underlying models implemented in C++ and the output and analysis features implemented in R.' extra: identifiers: - biotools:cancerinsilico - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cancerinsilico + path: recipes/bioconductor-cancerinsilico + version: 2.0.0 + diff --git a/recipes/bioconductor-cancermutationanalysis/build.sh b/recipes/bioconductor-cancermutationanalysis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cancermutationanalysis/build.sh +++ b/recipes/bioconductor-cancermutationanalysis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancermutationanalysis/meta.yaml b/recipes/bioconductor-cancermutationanalysis/meta.yaml index f2fb1ea998c10..54d3fa32dbeca 100644 --- a/recipes/bioconductor-cancermutationanalysis/meta.yaml +++ b/recipes/bioconductor-cancermutationanalysis/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CancerMutationAnalysis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 749165ff107d99e4b7d5ad341ce1411e25349f25e70c3b9e3e090b141231d3a4 + md5: 6b4c874482fba54cb147332073586193 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: KEGG.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base build: - {{ compiler('c') }} @@ -34,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'This package implements gene and gene-set level analysis methods for somatic mutation studies of cancer. The gene-level methods distinguish between driver genes (which play an active role in tumorigenesis) and passenger genes (which are mutated in tumor samples, but have no role in tumorigenesis) and incorporate a two-stage study design. The gene-set methods implement a patient-oriented approach, which calculates gene-set scores for each sample, then combines them across samples; a gene-oriented approach which uses the Wilcoxon test is also provided for comparison.' extra: identifiers: - biotools:cancermutationanalysis - doi:10.1007/978-1-62703-721-1_7 + parent_recipe: + name: bioconductor-cancermutationanalysis + path: recipes/bioconductor-cancermutationanalysis + version: 1.22.0 + diff --git a/recipes/bioconductor-cancersubtypes/build.sh b/recipes/bioconductor-cancersubtypes/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cancersubtypes/build.sh +++ b/recipes/bioconductor-cancersubtypes/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cancersubtypes/meta.yaml b/recipes/bioconductor-cancersubtypes/meta.yaml index 97da03742dbc3..00a10ae771fa6 100644 --- a/recipes/bioconductor-cancersubtypes/meta.yaml +++ b/recipes/bioconductor-cancersubtypes/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CancerSubtypes" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e365e26d253616dfdcf85a146a79bafbefa3c91604c35beac9807c9bc9e774bf + md5: f5f9711de5b16e3b4f2ddb908bc44aa7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit, knitr, RTCGA.mRNA, RTCGA.clinical requirements: host: - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-cluster - r-icluster @@ -29,9 +31,9 @@ requirements: - r-snftool - r-survival run: - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-cluster - r-icluster @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'CancerSubtypes integrates the current common computational biology methods for cancer subtypes identification and provides a standardized framework for cancer subtype analysis based multi-omics data, such as gene expression, miRNA expression, DNA methylation and others.' extra: identifiers: - biotools:cancersubtypes - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cancersubtypes + path: recipes/bioconductor-cancersubtypes + version: 1.6.0 + diff --git a/recipes/bioconductor-cand/build.sh b/recipes/bioconductor-cand/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cand/build.sh +++ b/recipes/bioconductor-cand/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cand/meta.yaml b/recipes/bioconductor-cand/meta.yaml index 58a366017a00f..c6ba36df57a50 100644 --- a/recipes/bioconductor-cand/meta.yaml +++ b/recipes/bioconductor-cand/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CAnD" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 59d74d2e70ccd062c5ad282d12fbd4229d5dde90dbd3dc9db15132a4f8b17ab5 + md5: fd13a36a530e102aa5f1b9c2ba8eb65f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions to perform the CAnD test on a set of ancestry proportions. For a particular ancestral subpopulation, a user will supply the estimated ancestry proportion for each sample, and each chromosome or chromosomal segment of interest. A p-value for each chromosome as well as an overall CAnD p-value will be returned for each test. Plotting functions are also available.' extra: identifiers: - biotools:cand - doi:10.1534/genetics.115.184184 + parent_recipe: + name: bioconductor-cand + path: recipes/bioconductor-cand + version: 1.12.0 + diff --git a/recipes/bioconductor-canine.db/meta.yaml b/recipes/bioconductor-canine.db/meta.yaml new file mode 100644 index 0000000000000..6e96260c1fc3f --- /dev/null +++ b/recipes/bioconductor-canine.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "canine.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 313097118354c68b3b6fb348eb55720e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix canine annotation data (chip canine) assembled using data from public repositories' + diff --git a/recipes/bioconductor-canine.db/post-link.sh b/recipes/bioconductor-canine.db/post-link.sh new file mode 100644 index 0000000000000..8a443b6905c29 --- /dev/null +++ b/recipes/bioconductor-canine.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canine.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/canine.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine.db/bioconductor-canine.db_3.2.3_src_all.tar.gz" +) +MD5="313097118354c68b3b6fb348eb55720e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canine.db/pre-unlink.sh b/recipes/bioconductor-canine.db/pre-unlink.sh new file mode 100644 index 0000000000000..1fe9d6e5da662 --- /dev/null +++ b/recipes/bioconductor-canine.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canine.db diff --git a/recipes/bioconductor-canine.db0/meta.yaml b/recipes/bioconductor-canine.db0/meta.yaml new file mode 100644 index 0000000000000..b057a8de02b7a --- /dev/null +++ b/recipes/bioconductor-canine.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "canine.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f2c7805b097ff757f07a47efcdd17f4f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for canine, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-canine.db0/post-link.sh b/recipes/bioconductor-canine.db0/post-link.sh new file mode 100644 index 0000000000000..679bbf721d23b --- /dev/null +++ b/recipes/bioconductor-canine.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canine.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/canine.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine.db0/bioconductor-canine.db0_3.7.1_src_all.tar.gz" +) +MD5="f2c7805b097ff757f07a47efcdd17f4f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canine.db0/pre-unlink.sh b/recipes/bioconductor-canine.db0/pre-unlink.sh new file mode 100644 index 0000000000000..d90bc1bf88068 --- /dev/null +++ b/recipes/bioconductor-canine.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canine.db0 diff --git a/recipes/bioconductor-canine2.db/meta.yaml b/recipes/bioconductor-canine2.db/meta.yaml new file mode 100644 index 0000000000000..b18bddc919b40 --- /dev/null +++ b/recipes/bioconductor-canine2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "canine2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5c393ea8e91c4d3eb08137bc2f301ca7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.cf.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix canine2 annotation data (chip canine2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-canine2.db/post-link.sh b/recipes/bioconductor-canine2.db/post-link.sh new file mode 100644 index 0000000000000..f1dd2bc14bbdc --- /dev/null +++ b/recipes/bioconductor-canine2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canine2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/canine2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2.db/bioconductor-canine2.db_3.2.3_src_all.tar.gz" +) +MD5="5c393ea8e91c4d3eb08137bc2f301ca7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canine2.db/pre-unlink.sh b/recipes/bioconductor-canine2.db/pre-unlink.sh new file mode 100644 index 0000000000000..85fa00d7cd89a --- /dev/null +++ b/recipes/bioconductor-canine2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canine2.db diff --git a/recipes/bioconductor-canine2cdf/meta.yaml b/recipes/bioconductor-canine2cdf/meta.yaml new file mode 100644 index 0000000000000..0afc2fd42139b --- /dev/null +++ b/recipes/bioconductor-canine2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "canine2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 78740cde98c75e6680470564a4df74c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Canine_2.cdf file.' + diff --git a/recipes/bioconductor-canine2cdf/post-link.sh b/recipes/bioconductor-canine2cdf/post-link.sh new file mode 100644 index 0000000000000..38f8978039d24 --- /dev/null +++ b/recipes/bioconductor-canine2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canine2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/canine2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2cdf/bioconductor-canine2cdf_2.18.0_src_all.tar.gz" +) +MD5="78740cde98c75e6680470564a4df74c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canine2cdf/pre-unlink.sh b/recipes/bioconductor-canine2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..bab53c0191c50 --- /dev/null +++ b/recipes/bioconductor-canine2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canine2cdf diff --git a/recipes/bioconductor-canine2probe/meta.yaml b/recipes/bioconductor-canine2probe/meta.yaml new file mode 100644 index 0000000000000..902ba243c21a1 --- /dev/null +++ b/recipes/bioconductor-canine2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "canine2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7de0f4ea616e8662dc2eaa9ab78d1f13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-canine2probe/post-link.sh b/recipes/bioconductor-canine2probe/post-link.sh new file mode 100644 index 0000000000000..8bf3e02d73a2b --- /dev/null +++ b/recipes/bioconductor-canine2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canine2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canine2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/canine2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canine2probe/bioconductor-canine2probe_2.18.0_src_all.tar.gz" +) +MD5="7de0f4ea616e8662dc2eaa9ab78d1f13" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canine2probe/pre-unlink.sh b/recipes/bioconductor-canine2probe/pre-unlink.sh new file mode 100644 index 0000000000000..0c586bd68ccd8 --- /dev/null +++ b/recipes/bioconductor-canine2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canine2probe diff --git a/recipes/bioconductor-caninecdf/meta.yaml b/recipes/bioconductor-caninecdf/meta.yaml new file mode 100644 index 0000000000000..aeb97a6b98f25 --- /dev/null +++ b/recipes/bioconductor-caninecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "caninecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 656f845cc66890015a4e13c5304ec262 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Canine.cdf file.' + diff --git a/recipes/bioconductor-caninecdf/post-link.sh b/recipes/bioconductor-caninecdf/post-link.sh new file mode 100644 index 0000000000000..93bed19dd6070 --- /dev/null +++ b/recipes/bioconductor-caninecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="caninecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/caninecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/caninecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-caninecdf/bioconductor-caninecdf_2.18.0_src_all.tar.gz" +) +MD5="656f845cc66890015a4e13c5304ec262" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-caninecdf/pre-unlink.sh b/recipes/bioconductor-caninecdf/pre-unlink.sh new file mode 100644 index 0000000000000..807355f19cf4c --- /dev/null +++ b/recipes/bioconductor-caninecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ caninecdf diff --git a/recipes/bioconductor-canineprobe/meta.yaml b/recipes/bioconductor-canineprobe/meta.yaml new file mode 100644 index 0000000000000..bf637da974db7 --- /dev/null +++ b/recipes/bioconductor-canineprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "canineprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e5467bc9b7e54c5adce6b409ba7df767 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Canine\_probe\_tab.' + diff --git a/recipes/bioconductor-canineprobe/post-link.sh b/recipes/bioconductor-canineprobe/post-link.sh new file mode 100644 index 0000000000000..e0e06346be571 --- /dev/null +++ b/recipes/bioconductor-canineprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="canineprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/canineprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/canineprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-canineprobe/bioconductor-canineprobe_2.18.0_src_all.tar.gz" +) +MD5="e5467bc9b7e54c5adce6b409ba7df767" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-canineprobe/pre-unlink.sh b/recipes/bioconductor-canineprobe/pre-unlink.sh new file mode 100644 index 0000000000000..6d9e340e9ef40 --- /dev/null +++ b/recipes/bioconductor-canineprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ canineprobe diff --git a/recipes/bioconductor-caomicsv/build.sh b/recipes/bioconductor-caomicsv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-caomicsv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-caomicsv/meta.yaml b/recipes/bioconductor-caomicsv/meta.yaml new file mode 100644 index 0000000000000..15c3c998c1862 --- /dev/null +++ b/recipes/bioconductor-caomicsv/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.12.0" %} +{% set name = "caOmicsV" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8d0bb960067a952a6a69805df7dc125 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - 'r-bc3net >=1.0.2' + - 'r-igraph >=0.7.1' + run: + - r-base + - 'r-bc3net >=1.0.2' + - 'r-igraph >=0.7.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2.0)' + summary: 'caOmicsV package provides methods to visualize multi-dimentional cancer genomics data including of patient information, gene expressions, DNA methylations, DNA copy number variations, and SNP/mutations in matrix layout or network layout.' + diff --git a/recipes/bioconductor-cardinal/build.sh b/recipes/bioconductor-cardinal/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cardinal/build.sh +++ b/recipes/bioconductor-cardinal/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cardinal/meta.yaml b/recipes/bioconductor-cardinal/meta.yaml index 23a28227f9e38..0f3616f4ebdca 100644 --- a/recipes/bioconductor-cardinal/meta.yaml +++ b/recipes/bioconductor-cardinal/meta.yaml @@ -1,40 +1,51 @@ -{% set version = "1.12.1" %} +{% set version = "2.0.2" %} {% set name = "Cardinal" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d72bb63d15040fcc46b97022a45a92bb3c1ecb2cafc1b9806f746e1e8d12a1f7 + md5: f8989d89d5841359e9966f50760fba41 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-matter >=1.6.0,<1.8.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-matter >=1.8.0,<1.9.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-dplyr - r-irlba - r-lattice + - r-magrittr - r-signal - r-sp run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-matter >=1.6.0,<1.8.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-matter >=1.8.0,<1.9.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-dplyr - r-irlba - r-lattice + - r-magrittr - r-signal - r-sp build: @@ -45,9 +56,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Implements statistical & computational tools for analyzing mass spectrometry imaging datasets, including methods for efficient pre-processing, spatial segmentation, and classification.' extra: identifiers: - biotools:cardinal + parent_recipe: + name: bioconductor-cardinal + path: recipes/bioconductor-cardinal + version: 1.12.1 + diff --git a/recipes/bioconductor-cardinalworkflows/meta.yaml b/recipes/bioconductor-cardinalworkflows/meta.yaml new file mode 100644 index 0000000000000..2ead086df4572 --- /dev/null +++ b/recipes/bioconductor-cardinalworkflows/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.14.0" %} +{% set name = "CardinalWorkflows" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5c7621b5e018a39a1dc3f2ea76532695 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-cardinal >=2.0.0,<2.1.0' + - r-base + run: + - 'bioconductor-cardinal >=2.0.0,<2.1.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Datasets and workflows for Cardinal: DESI and MALDI examples including pig fetus, cardinal painting, and human RCC.' + diff --git a/recipes/bioconductor-cardinalworkflows/post-link.sh b/recipes/bioconductor-cardinalworkflows/post-link.sh new file mode 100644 index 0000000000000..a36bd132eb299 --- /dev/null +++ b/recipes/bioconductor-cardinalworkflows/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CardinalWorkflows_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CardinalWorkflows_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/CardinalWorkflows_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cardinalworkflows/bioconductor-cardinalworkflows_1.14.0_src_all.tar.gz" +) +MD5="5c7621b5e018a39a1dc3f2ea76532695" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cardinalworkflows/pre-unlink.sh b/recipes/bioconductor-cardinalworkflows/pre-unlink.sh new file mode 100644 index 0000000000000..be72f4ca10e9a --- /dev/null +++ b/recipes/bioconductor-cardinalworkflows/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CardinalWorkflows diff --git a/recipes/bioconductor-casper/build.sh b/recipes/bioconductor-casper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-casper/build.sh +++ b/recipes/bioconductor-casper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-casper/meta.yaml b/recipes/bioconductor-casper/meta.yaml index d6bbe54976ed4..d4d50160598bb 100644 --- a/recipes/bioconductor-casper/meta.yaml +++ b/recipes/bioconductor-casper/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "casper" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ceada9d23d5da7e0f65bd6355722ba1d25f979318b0c7e0e0242149b44e68a37 + md5: f6de73dd1b5f4e0ee0118b65837c547b build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - - 'bioconductor-gaga >=2.26.0,<2.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-gaga >=2.28.0,<2.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-coda - r-gtools @@ -38,18 +38,18 @@ requirements: - r-survival - r-vgam run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - - 'bioconductor-gaga >=2.26.0,<2.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-gaga >=2.28.0,<2.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-coda - r-gtools @@ -65,9 +65,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.' extra: identifiers: - biotools:casper + parent_recipe: + name: bioconductor-casper + path: recipes/bioconductor-casper + version: 2.14.0 + diff --git a/recipes/bioconductor-catalyst/build.sh b/recipes/bioconductor-catalyst/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-catalyst/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-catalyst/meta.yaml b/recipes/bioconductor-catalyst/meta.yaml new file mode 100644 index 0000000000000..41b5780bf7462 --- /dev/null +++ b/recipes/bioconductor-catalyst/meta.yaml @@ -0,0 +1,95 @@ +{% set version = "1.6.0" %} +{% set name = "CATALYST" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 023f69e0aaf615cfb1acc1efa8093b2f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, diffcyt +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-dplyr + - r-drc + - r-dt + - r-ggplot2 + - r-ggrepel + - r-ggridges + - r-gridextra + - r-htmltools + - r-magrittr + - r-matrix + - r-matrixstats + - r-nnls + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-rtsne + - r-scales + - r-shiny + - r-shinybs + - r-shinydashboard + - r-shinyjs + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-dplyr + - r-drc + - r-dt + - r-ggplot2 + - r-ggrepel + - r-ggridges + - r-gridextra + - r-htmltools + - r-magrittr + - r-matrix + - r-matrixstats + - r-nnls + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-rtsne + - r-scales + - r-shiny + - r-shinybs + - r-shinydashboard + - r-shinyjs + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Mass cytometry (CyTOF) uses heavy metal isotopes rather than fluorescent tags as reporters to label antibodies, thereby substantially decreasing spectral overlap and allowing for examination of over 50 parameters at the single cell level. While spectral overlap is significantly less pronounced in CyTOF than flow cytometry, spillover due to detection sensitivity, isotopic impurities, and oxide formation can impede data interpretability. We designed CATALYST (Cytometry dATa anALYSis Tools) to provide a pipeline for preprocessing of cytometry data, including i) normalization using bead standards, ii) single-cell deconvolution, and iii) bead-based compensation.' + diff --git a/recipes/bioconductor-category/build.sh b/recipes/bioconductor-category/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-category/build.sh +++ b/recipes/bioconductor-category/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-category/meta.yaml b/recipes/bioconductor-category/meta.yaml index 4de199737bb1e..fe1909125660d 100644 --- a/recipes/bioconductor-category/meta.yaml +++ b/recipes/bioconductor-category/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "Category" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a0bf452fcfd0513f3e46a98880e1af03b783e7ad82fe2346d5fcb5d090c28e0f + md5: 062f06f66067dcbb4d21fe9dd714eff9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: EBarrays, ALL, Rgraphviz, RColorBrewer, xtable (>= 1.4-6), hgu95av2.db, KEGG.db, SNPchip, geneplotter, limma, lattice, RUnit, org.Sc.sgd.db, GOstats, GO.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-dbi - r-matrix run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-dbi - r-matrix @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of tools for performing category (gene set enrichment) analysis.' extra: identifiers: - biotools:category - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-category + path: recipes/bioconductor-category + version: 2.46.0 + diff --git a/recipes/bioconductor-categorycompare/build.sh b/recipes/bioconductor-categorycompare/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-categorycompare/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-categorycompare/meta.yaml b/recipes/bioconductor-categorycompare/meta.yaml new file mode 100644 index 0000000000000..802f4d8d2377b --- /dev/null +++ b/recipes/bioconductor-categorycompare/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.26.0" %} +{% set name = "categoryCompare" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0651838e9b5b0d85c2100aee6deca3c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, GO.db, KEGG.db, estrogen, org.Hs.eg.db, hgu95av2.db, limma, affy, genefilter +# SystemRequirements: Cytoscape (>= 3.6.1) (if used for visualization of results, heavily suggested) +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - r-base + - r-colorspace + - r-hwriter + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rcy3 >=2.2.0,<2.3.0' + - r-base + - r-colorspace + - r-hwriter +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested).' + diff --git a/recipes/bioconductor-causalr/build.sh b/recipes/bioconductor-causalr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-causalr/build.sh +++ b/recipes/bioconductor-causalr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-causalr/meta.yaml b/recipes/bioconductor-causalr/meta.yaml index fce4bd7e61c80..ccbc0287efb19 100644 --- a/recipes/bioconductor-causalr/meta.yaml +++ b/recipes/bioconductor-causalr/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CausalR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1f542a9ffc79fe02f79892d9161db85b8c782e011d1f16790c58699e0a3521bf + md5: 78c4a5ee311f07a75d8ba98136314ba3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Causal network analysis methods for regulator prediction and network reconstruction from genome scale data.' extra: identifiers: - biotools:causalr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-causalr + path: recipes/bioconductor-causalr + version: 1.12.0 + diff --git a/recipes/bioconductor-cbaf/build.sh b/recipes/bioconductor-cbaf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cbaf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cbaf/meta.yaml b/recipes/bioconductor-cbaf/meta.yaml new file mode 100644 index 0000000000000..f21eb571010a6 --- /dev/null +++ b/recipes/bioconductor-cbaf/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "cbaf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c9f3c048d7b4e87473f694c927c9dc71 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - r-base + - r-cgdsr + - r-gplots + - r-rcolorbrewer + - r-xlsx + run: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - r-base + - r-cgdsr + - r-gplots + - r-rcolorbrewer + - r-xlsx +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains functions that allow analysing and comparing various gene groups from different cancers/cancer subgroups easily. So far, it is compatible with RNA-seq, microRNA-seq, microarray and methylation datasets that are stored on cbioportal.org.' + diff --git a/recipes/bioconductor-ccdata/meta.yaml b/recipes/bioconductor-ccdata/meta.yaml new file mode 100644 index 0000000000000..0e0c56adc4b5e --- /dev/null +++ b/recipes/bioconductor-ccdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.8.0" %} +{% set name = "ccdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 43a2ecfa4bf126deb0a2ef4abf1c349e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package contains microarray gene expression data generated from the Connectivity Map build 02 and LINCS l1000. The data are used by the ccmap package to find drugs and drug combinations to mimic or reverse a gene expression signature.' + diff --git a/recipes/bioconductor-ccdata/post-link.sh b/recipes/bioconductor-ccdata/post-link.sh new file mode 100644 index 0000000000000..d993090a7a313 --- /dev/null +++ b/recipes/bioconductor-ccdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ccdata_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ccdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/ccdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ccdata/bioconductor-ccdata_1.8.0_src_all.tar.gz" +) +MD5="43a2ecfa4bf126deb0a2ef4abf1c349e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ccdata/pre-unlink.sh b/recipes/bioconductor-ccdata/pre-unlink.sh new file mode 100644 index 0000000000000..aebc9f2ac27f9 --- /dev/null +++ b/recipes/bioconductor-ccdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ccdata diff --git a/recipes/bioconductor-ccfindr/build.sh b/recipes/bioconductor-ccfindr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccfindr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccfindr/meta.yaml b/recipes/bioconductor-ccfindr/meta.yaml new file mode 100644 index 0000000000000..8dde81cbec88b --- /dev/null +++ b/recipes/bioconductor-ccfindr/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.2.0" %} +{% set name = "ccfindR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d2dae166f7d062b6fe3aded90a1ba724 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-gtools + - r-irlba + - r-matrix + - r-rcolorbrewer + - r-rcpp + - r-rcppeigen + - r-rmpi + - r-rtsne + run: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-gtools + - r-irlba + - r-matrix + - r-rcolorbrewer + - r-rcpp + - r-rcppeigen + - r-rmpi + - r-rtsne + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A collection of tools for cancer genomic data clustering analyses, including those for single cell RNA-seq. Cell clustering and feature gene selection analysis employ Bayesian (and maximum likelihood) non-negative matrix factorization (NMF) algorithm. Input data set consists of RNA count matrix, gene, and cell bar code annotations. Analysis outputs are factor matrices for multiple ranks and marginal likelihood values for each rank. The package includes utilities for downstream analyses, including meta-gene identification, visualization, and construction of rank-based trees for clusters.' + diff --git a/recipes/bioconductor-ccl4/meta.yaml b/recipes/bioconductor-ccl4/meta.yaml new file mode 100644 index 0000000000000..7b796019164c2 --- /dev/null +++ b/recipes/bioconductor-ccl4/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "CCl4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f8e6ef164ec15f7b8af5bfcd78fcc34b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'NChannelSet for rat hepatocytes treated with Carbon Tetrachloride (CCl4) data from LGC company.' + diff --git a/recipes/bioconductor-ccl4/post-link.sh b/recipes/bioconductor-ccl4/post-link.sh new file mode 100644 index 0000000000000..3c72b4825ea52 --- /dev/null +++ b/recipes/bioconductor-ccl4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CCl4_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CCl4_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/CCl4_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ccl4/bioconductor-ccl4_1.20.0_src_all.tar.gz" +) +MD5="f8e6ef164ec15f7b8af5bfcd78fcc34b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ccl4/pre-unlink.sh b/recipes/bioconductor-ccl4/pre-unlink.sh new file mode 100644 index 0000000000000..9b5872be6fbb0 --- /dev/null +++ b/recipes/bioconductor-ccl4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CCl4 diff --git a/recipes/bioconductor-ccmap/build.sh b/recipes/bioconductor-ccmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccmap/meta.yaml b/recipes/bioconductor-ccmap/meta.yaml new file mode 100644 index 0000000000000..45b4bf36ee117 --- /dev/null +++ b/recipes/bioconductor-ccmap/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.8.0" %} +{% set name = "ccmap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d603b7771a6fac35514db7eb9818bf57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: crossmeta, knitr, rmarkdown, testthat, lydata +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-ccdata >=1.8.0,<1.9.0' + - r-base + - 'r-biocmanager >=1.24.0' + - 'r-data.table >=1.10.4' + - 'r-doparallel >=1.0.10' + - 'r-foreach >=1.4.3' + - 'r-lsa >=0.73.1' + - 'r-xgboost >=0.6.4' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-ccdata >=1.8.0,<1.9.0' + - r-base + - 'r-biocmanager >=1.24.0' + - 'r-data.table >=1.10.4' + - 'r-doparallel >=1.0.10' + - 'r-foreach >=1.4.3' + - 'r-lsa >=0.73.1' + - 'r-xgboost >=0.6.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Finds drugs and drug combinations that are predicted to reverse or mimic gene expression signatures. These drugs might reverse diseases or mimic healthy lifestyles.' + diff --git a/recipes/bioconductor-ccpromise/build.sh b/recipes/bioconductor-ccpromise/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccpromise/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccpromise/meta.yaml b/recipes/bioconductor-ccpromise/meta.yaml new file mode 100644 index 0000000000000..3255d36bc831d --- /dev/null +++ b/recipes/bioconductor-ccpromise/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.8.0" %} +{% set name = "CCPROMISE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 73f58481f1fabc4fbd97d0b1e9647071 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-promise >=1.34.0,<1.35.0' + - r-base + - r-ccp + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-promise >=1.34.0,<1.35.0' + - r-base + - r-ccp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Perform Canonical correlation between two forms of high demensional genetic data, and associate the first compoent of each form of data with a specific biologically interesting pattern of associations with multiple endpoints. A probe level analysis is also implemented.' + diff --git a/recipes/bioconductor-ccrepe/build.sh b/recipes/bioconductor-ccrepe/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ccrepe/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ccrepe/meta.yaml b/recipes/bioconductor-ccrepe/meta.yaml new file mode 100644 index 0000000000000..d26708950ff6a --- /dev/null +++ b/recipes/bioconductor-ccrepe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "ccrepe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e35b42d7bc9c9a2dc8e4826d8c958290 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, BiocGenerics, testthat +requirements: + host: + - r-base + - 'r-infotheo >=1.1' + run: + - r-base + - 'r-infotheo >=1.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The CCREPE (Compositionality Corrected by REnormalizaion and PErmutation) package is designed to assess the significance of general similarity measures in compositional datasets. In microbial abundance data, for example, the total abundances of all microbes sum to one; CCREPE is designed to take this constraint into account when assigning p-values to similarity measures between the microbes. The package has two functions: ccrepe: Calculates similarity measures, p-values and q-values for relative abundances of bugs in one or two body sites using bootstrap and permutation matrices of the data. nc.score: Calculates species-level co-variation and co-exclusion patterns based on an extension of the checkerboard score to ordinal data.' + diff --git a/recipes/bioconductor-cctutorial/meta.yaml b/recipes/bioconductor-cctutorial/meta.yaml new file mode 100644 index 0000000000000..3ba732d14aa62 --- /dev/null +++ b/recipes/bioconductor-cctutorial/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.20.0" %} +{% set name = "ccTutorial" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bf29fe20285bcedbd73d52a641ebb751 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: biomaRt, Biobase(>= 2.5.5), xtable +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This is a data package that accompanies a ChIP-chip tutorial, which has been published in PLoS Computational Biology. The data and source code in this package allow the reader to completely reproduce the steps in the tutorial.' + diff --git a/recipes/bioconductor-cctutorial/post-link.sh b/recipes/bioconductor-cctutorial/post-link.sh new file mode 100644 index 0000000000000..a6db3d439b25f --- /dev/null +++ b/recipes/bioconductor-cctutorial/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ccTutorial_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ccTutorial_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ccTutorial_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cctutorial/bioconductor-cctutorial_1.20.0_src_all.tar.gz" +) +MD5="bf29fe20285bcedbd73d52a641ebb751" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cctutorial/pre-unlink.sh b/recipes/bioconductor-cctutorial/pre-unlink.sh new file mode 100644 index 0000000000000..9c95592be75f0 --- /dev/null +++ b/recipes/bioconductor-cctutorial/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ccTutorial diff --git a/recipes/bioconductor-celaref/build.sh b/recipes/bioconductor-celaref/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-celaref/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-celaref/meta.yaml b/recipes/bioconductor-celaref/meta.yaml new file mode 100644 index 0000000000000..0ec433e941990 --- /dev/null +++ b/recipes/bioconductor-celaref/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "celaref" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d19bfcefa4ddc3730276a4b44b81ba18 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, parallel, knitr, rmarkdown, ExperimentHub +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-matrix + - r-readr + - r-rlang + - r-tibble + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-mast >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-matrix + - r-readr + - r-rlang + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'After the clustering step of a single-cell RNAseq experiment, this package aims to suggest labels/cell types for the clusters, on the basis of similarity to a reference dataset. It requires a table of read counts per cell per gene, and a list of the cells belonging to each of the clusters, (for both test and reference data).' + diff --git a/recipes/bioconductor-celarefdata/meta.yaml b/recipes/bioconductor-celarefdata/meta.yaml new file mode 100644 index 0000000000000..99df8611a3a57 --- /dev/null +++ b/recipes/bioconductor-celarefdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "celarefData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fcf4c1723f025947fa6012f02e2aa33c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ExperimentHub, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This experiment data contains some processed data used in the celaref package vignette. These are publically available datasets, that have been processed by celaref package, and can be manipulated further with it.' + diff --git a/recipes/bioconductor-celarefdata/post-link.sh b/recipes/bioconductor-celarefdata/post-link.sh new file mode 100644 index 0000000000000..1859b9b54adc2 --- /dev/null +++ b/recipes/bioconductor-celarefdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="celarefData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/celarefData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/celarefData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celarefdata/bioconductor-celarefdata_1.0.0_src_all.tar.gz" +) +MD5="fcf4c1723f025947fa6012f02e2aa33c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-celarefdata/pre-unlink.sh b/recipes/bioconductor-celarefdata/pre-unlink.sh new file mode 100644 index 0000000000000..a6394ae768802 --- /dev/null +++ b/recipes/bioconductor-celarefdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ celarefData diff --git a/recipes/bioconductor-celegans.db/meta.yaml b/recipes/bioconductor-celegans.db/meta.yaml new file mode 100644 index 0000000000000..31ee2555f7880 --- /dev/null +++ b/recipes/bioconductor-celegans.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "celegans.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fb4631ee29a20c20d5766aed4c04cac1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.ce.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.ce.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix celegans annotation data (chip celegans) assembled using data from public repositories' + diff --git a/recipes/bioconductor-celegans.db/post-link.sh b/recipes/bioconductor-celegans.db/post-link.sh new file mode 100644 index 0000000000000..32c78c87b4d04 --- /dev/null +++ b/recipes/bioconductor-celegans.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="celegans.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celegans.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/celegans.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celegans.db/bioconductor-celegans.db_3.2.3_src_all.tar.gz" +) +MD5="fb4631ee29a20c20d5766aed4c04cac1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-celegans.db/pre-unlink.sh b/recipes/bioconductor-celegans.db/pre-unlink.sh new file mode 100644 index 0000000000000..864167c84d87a --- /dev/null +++ b/recipes/bioconductor-celegans.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ celegans.db diff --git a/recipes/bioconductor-celeganscdf/meta.yaml b/recipes/bioconductor-celeganscdf/meta.yaml new file mode 100644 index 0000000000000..586ccb512e9f3 --- /dev/null +++ b/recipes/bioconductor-celeganscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "celeganscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1098cd99bfc5000bf9858e4a3acaf452 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Celegans.CDF file.' + diff --git a/recipes/bioconductor-celeganscdf/post-link.sh b/recipes/bioconductor-celeganscdf/post-link.sh new file mode 100644 index 0000000000000..5b6c47b20da91 --- /dev/null +++ b/recipes/bioconductor-celeganscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="celeganscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celeganscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/celeganscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celeganscdf/bioconductor-celeganscdf_2.18.0_src_all.tar.gz" +) +MD5="1098cd99bfc5000bf9858e4a3acaf452" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-celeganscdf/pre-unlink.sh b/recipes/bioconductor-celeganscdf/pre-unlink.sh new file mode 100644 index 0000000000000..c6350bead89f0 --- /dev/null +++ b/recipes/bioconductor-celeganscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ celeganscdf diff --git a/recipes/bioconductor-celegansprobe/meta.yaml b/recipes/bioconductor-celegansprobe/meta.yaml new file mode 100644 index 0000000000000..9dd5d3cbdd8b0 --- /dev/null +++ b/recipes/bioconductor-celegansprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "celegansprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7454bba10ff2dd7c03bfe0f9d450f148 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was C\_elegans\_probe\_tab.' + diff --git a/recipes/bioconductor-celegansprobe/post-link.sh b/recipes/bioconductor-celegansprobe/post-link.sh new file mode 100644 index 0000000000000..32c59e2cd641b --- /dev/null +++ b/recipes/bioconductor-celegansprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="celegansprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/celegansprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/celegansprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-celegansprobe/bioconductor-celegansprobe_2.18.0_src_all.tar.gz" +) +MD5="7454bba10ff2dd7c03bfe0f9d450f148" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-celegansprobe/pre-unlink.sh b/recipes/bioconductor-celegansprobe/pre-unlink.sh new file mode 100644 index 0000000000000..7a554ef6b14f8 --- /dev/null +++ b/recipes/bioconductor-celegansprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ celegansprobe diff --git a/recipes/bioconductor-cellbaser/build.sh b/recipes/bioconductor-cellbaser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellbaser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellbaser/meta.yaml b/recipes/bioconductor-cellbaser/meta.yaml new file mode 100644 index 0000000000000..763bfd6026732 --- /dev/null +++ b/recipes/bioconductor-cellbaser/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "cellbaseR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9078d93a013e860fe491397e945ddd0a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, Gviz, VariantAnnotation +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-data.table + - r-doparallel + - r-foreach + - r-httr + - r-jsonlite + - r-pbapply + - r-r.utils + - r-tidyr + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-data.table + - r-doparallel + - r-foreach + - r-httr + - r-jsonlite + - r-pbapply + - r-r.utils + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (== 2.0)' + summary: 'This R package makes use of the exhaustive RESTful Web service API that has been implemented for the Cellabase database. It enable researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.' + diff --git a/recipes/bioconductor-cellgrowth/build.sh b/recipes/bioconductor-cellgrowth/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cellgrowth/build.sh +++ b/recipes/bioconductor-cellgrowth/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellgrowth/meta.yaml b/recipes/bioconductor-cellgrowth/meta.yaml index bd9def2beeb8f..2bf850dd1244b 100644 --- a/recipes/bioconductor-cellgrowth/meta.yaml +++ b/recipes/bioconductor-cellgrowth/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cellGrowth" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 641735000edf3981d23ebf871b2617e20576151411509d1e02af1d973b17400f + md5: 8d1c09814d5c5e354d9a11894e1f3b42 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides functionalities for the fitting of cell population growth models on experimental OD curves.' extra: identifiers: - biotools:cellgrowth - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cellgrowth + path: recipes/bioconductor-cellgrowth + version: 1.24.0 + diff --git a/recipes/bioconductor-cellhts2/build.sh b/recipes/bioconductor-cellhts2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cellhts2/build.sh +++ b/recipes/bioconductor-cellhts2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellhts2/conda_build_config.yaml b/recipes/bioconductor-cellhts2/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-cellhts2/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-cellhts2/meta.yaml b/recipes/bioconductor-cellhts2/meta.yaml index 58c4173232b2b..d449342d967aa 100644 --- a/recipes/bioconductor-cellhts2/meta.yaml +++ b/recipes/bioconductor-cellhts2/meta.yaml @@ -1,44 +1,46 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "cellHTS2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 90c46478b3a0e3e3b812b20c311cf41899bb94965e30820bb174e15904548a4a + md5: b0b4a06e25549a92e8239883e2fb533b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-prada >=1.56.0,<1.58.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-hwriter - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-prada >=1.56.0,<1.58.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-hwriter - r-locfit @@ -47,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides tools for the analysis of high-throughput assays that were performed in microtitre plate formats (including but not limited to 384-well plates). The functionality includes data import and management, normalisation, quality assessment, replicate summarisation and statistical scoring. A webpage that provides a detailed graphical overview over the data and analysis results is produced. In our work, we have applied the package to RNAi screens on fly and human cells, and for screens of yeast libraries. See ?cellHTS2 for a brief introduction.' extra: identifiers: - biotools:cellhts2 + parent_recipe: + name: bioconductor-cellhts2 + path: recipes/bioconductor-cellhts2 + version: 2.44.0 + diff --git a/recipes/bioconductor-cellity/build.sh b/recipes/bioconductor-cellity/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellity/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellity/meta.yaml b/recipes/bioconductor-cellity/meta.yaml new file mode 100644 index 0000000000000..57561730b97a8 --- /dev/null +++ b/recipes/bioconductor-cellity/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.10.0" %} +{% set name = "cellity" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f3b201ec288008e1ecba4a4937573082 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, caret, knitr, testthat, rmarkdown +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-e1071 + - r-ggplot2 + - r-mvoutlier + - r-robustbase + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-e1071 + - r-ggplot2 + - r-mvoutlier + - r-robustbase +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A support vector machine approach to identifying and filtering low quality cells from single-cell RNA-seq datasets.' + diff --git a/recipes/bioconductor-cellmapper/build.sh b/recipes/bioconductor-cellmapper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cellmapper/build.sh +++ b/recipes/bioconductor-cellmapper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellmapper/meta.yaml b/recipes/bioconductor-cellmapper/meta.yaml index 84d978dd1996b..90906331e98cb 100644 --- a/recipes/bioconductor-cellmapper/meta.yaml +++ b/recipes/bioconductor-cellmapper/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CellMapper" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d01348fa8b262193fbe2277418931e9440ae460a2bd257f279034b36db78967a + md5: a7a9cd05f7a9f5fad346faf0cdbd8224 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: CellMapperData, Biobase, HumanAffyData, ALL, BiocStyle, ExperimentHub requirements: host: - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Infers cell type-specific expression based on co-expression similarity with known cell type marker genes. Can make accurate predictions using publicly available expression data, even when a cell type has not been isolated before.' extra: identifiers: - biotools:cellmapper + parent_recipe: + name: bioconductor-cellmapper + path: recipes/bioconductor-cellmapper + version: 1.6.0 + diff --git a/recipes/bioconductor-cellmapperdata/meta.yaml b/recipes/bioconductor-cellmapperdata/meta.yaml new file mode 100644 index 0000000000000..b9abbf5412dbd --- /dev/null +++ b/recipes/bioconductor-cellmapperdata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.8.0" %} +{% set name = "CellMapperData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ac7ff311f02953168d5cb3f829fd1e1c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-cellmapper >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-cellmapper >=1.8.0,<1.9.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Experiment data package. Contains microarray data from several large expression compendia that have been pre-processed for use with the CellMapper package. This pre-processed data is recommended for routine searches using the CellMapper package.' + diff --git a/recipes/bioconductor-cellmapperdata/post-link.sh b/recipes/bioconductor-cellmapperdata/post-link.sh new file mode 100644 index 0000000000000..1b1de2c5f9880 --- /dev/null +++ b/recipes/bioconductor-cellmapperdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CellMapperData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CellMapperData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/CellMapperData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cellmapperdata/bioconductor-cellmapperdata_1.8.0_src_all.tar.gz" +) +MD5="ac7ff311f02953168d5cb3f829fd1e1c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cellmapperdata/pre-unlink.sh b/recipes/bioconductor-cellmapperdata/pre-unlink.sh new file mode 100644 index 0000000000000..a63506a240388 --- /dev/null +++ b/recipes/bioconductor-cellmapperdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CellMapperData diff --git a/recipes/bioconductor-cellnoptr/build.sh b/recipes/bioconductor-cellnoptr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cellnoptr/build.sh +++ b/recipes/bioconductor-cellnoptr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellnoptr/meta.yaml b/recipes/bioconductor-cellnoptr/meta.yaml index b799b0ae99c3d..29f3596e35d71 100644 --- a/recipes/bioconductor-cellnoptr/meta.yaml +++ b/recipes/bioconductor-cellnoptr/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CellNOptR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1eb26216d20f4a4a6824b4bea4c328c794143280c51a5eb4e5251033d708776f + md5: 896919b3c3f1d53863345c5afb1d3a69 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, igraph, stringi, stringr +# SystemRequirements: Graphviz version >= 2.2 requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-ggplot2 - r-hash - r-rcurl - r-xml run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-ggplot2 - r-hash @@ -42,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package does optimisation of boolean logic networks of signalling pathways based on a previous knowledge network and a set of data upon perturbation of the nodes in the network.' extra: identifiers: - biotools:cellnoptr - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cellnoptr + path: recipes/bioconductor-cellnoptr + version: 1.26.0 + diff --git a/recipes/bioconductor-cellscape/build.sh b/recipes/bioconductor-cellscape/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellscape/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellscape/meta.yaml b/recipes/bioconductor-cellscape/meta.yaml new file mode 100644 index 0000000000000..1f67b4dc0f7ad --- /dev/null +++ b/recipes/bioconductor-cellscape/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.6.0" %} +{% set name = "cellscape" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fca7882d296832aed78b674d1bb92f18 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - 'r-dplyr >=0.4.3' + - 'r-gtools >=3.5.0' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-plyr >=1.8.3' + - 'r-reshape2 >=1.4.1' + - 'r-stringr >=1.0.0' + run: + - r-base + - 'r-dplyr >=0.4.3' + - 'r-gtools >=3.5.0' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-plyr >=1.8.3' + - 'r-reshape2 >=1.4.1' + - 'r-stringr >=1.0.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'CellScape facilitates interactive browsing of single cell clonal evolution datasets. The tool requires two main inputs: (i) the genomic content of each single cell in the form of either copy number segments or targeted mutation values, and (ii) a single cell phylogeny. Phylogenetic formats can vary from dendrogram-like phylogenies with leaf nodes to evolutionary model-derived phylogenies with observed or latent internal nodes. The CellScape phylogeny is flexibly input as a table of source-target edges to support arbitrary representations, where each node may or may not have associated genomic data. The output of CellScape is an interactive interface displaying a single cell phylogeny and a cell-by-locus genomic heatmap representing the mutation status in each cell for each locus.' + diff --git a/recipes/bioconductor-cellscore/build.sh b/recipes/bioconductor-cellscore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cellscore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cellscore/meta.yaml b/recipes/bioconductor-cellscore/meta.yaml new file mode 100644 index 0000000000000..1851641bac91e --- /dev/null +++ b/recipes/bioconductor-cellscore/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "CellScore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e9b84c8c0cbd7bbe43cbe7c71af89342 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: hgu133plus2CellScore, knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-gplots >=3.0.1' + - 'r-lsa >=0.73.1' + - 'r-rcolorbrewer >=1.1-2' + - 'r-squash >=1.0.8' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-gplots >=3.0.1' + - 'r-lsa >=0.73.1' + - 'r-rcolorbrewer >=1.1-2' + - 'r-squash >=1.0.8' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The CellScore package contains functions to evaluate the cell identity of a test sample, given a cell transition defined with a starting (donor) cell type and a desired target cell type. The evaluation is based upon a scoring system, which uses a set of standard samples of known cell types, as the reference set. The functions have been carried out on a large set of microarray data from one platform (Affymetrix Human Genome U133 Plus 2.0). In principle, the method could be applied to any expression dataset, provided that there are a sufficient number of standard samples and that the data are normalized.' + diff --git a/recipes/bioconductor-celltrails/build.sh b/recipes/bioconductor-celltrails/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-celltrails/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-celltrails/meta.yaml b/recipes/bioconductor-celltrails/meta.yaml new file mode 100644 index 0000000000000..789e7edc792de --- /dev/null +++ b/recipes/bioconductor-celltrails/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.0" %} +{% set name = "CellTrails" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ae463a8b64790828bda20cc7d0521655 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationDbi, destiny, RUnit, scater, scran, knitr, org.Mm.eg.db, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cba + - r-dendextend + - r-dtw + - r-envstats + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-maptree + - r-mgcv + - r-reshape2 + - r-rtsne + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cba + - r-dendextend + - r-dtw + - r-envstats + - r-ggplot2 + - r-ggrepel + - r-igraph + - r-maptree + - r-mgcv + - r-reshape2 + - r-rtsne +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CellTrails is an unsupervised algorithm for the de novo chronological ordering, visualization and analysis of single-cell expression data. CellTrails makes use of a geometrically motivated concept of lower-dimensional manifold learning, which exhibits a multitude of virtues that counteract intrinsic noise of single cell data caused by drop-outs, technical variance, and redundancy of predictive variables. CellTrails enables the reconstruction of branching trajectories and provides an intuitive graphical representation of expression patterns along all branches simultaneously. It allows the user to define and infer the expression dynamics of individual and multiple pathways towards distinct phenotypes.' + diff --git a/recipes/bioconductor-celltree/build.sh b/recipes/bioconductor-celltree/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-celltree/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-celltree/meta.yaml b/recipes/bioconductor-celltree/meta.yaml new file mode 100644 index 0000000000000..b70794a49087f --- /dev/null +++ b/recipes/bioconductor-celltree/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.12.0" %} +{% set name = "cellTree" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d9840be22b8ca149f718dc8f5d7a07c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, HSMMSingleCell, biomaRt, org.Hs.eg.db, Biobase, tools +requirements: + host: + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-gplots + - r-igraph + - r-maptpx + - r-slam + - r-topicmodels + - r-xtable + run: + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-gplots + - r-igraph + - r-maptpx + - r-slam + - r-topicmodels + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This packages computes a Latent Dirichlet Allocation (LDA) model of single-cell RNA-seq data and builds a compact tree modelling the relationship between individual cells over time or space.' + diff --git a/recipes/bioconductor-cemitool/build.sh b/recipes/bioconductor-cemitool/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cemitool/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cemitool/meta.yaml b/recipes/bioconductor-cemitool/meta.yaml new file mode 100644 index 0000000000000..00a7070ff028f --- /dev/null +++ b/recipes/bioconductor-cemitool/meta.yaml @@ -0,0 +1,97 @@ +{% set version = "1.6.7" %} +{% set name = "CEMiTool" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db8e5d430c424e6d4482c5be2c248b88 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocManager +requirements: + host: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-geneoverlap >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-data.table >=1.9.4' + - r-dplyr + - r-dt + - r-ff + - r-ffbase + - r-ggdendro + - r-ggplot2 + - r-ggpmisc + - r-ggrepel + - r-ggthemes + - r-grbase + - r-gridextra + - r-gtable + - r-htmltools + - r-igraph + - r-intergraph + - r-knitr + - r-matrixstats + - r-network + - r-plyr + - r-pracma + - r-rcolorbrewer + - r-rmarkdown + - r-scales + - r-sna + - r-stringr + - r-tidyr + - r-wgcna + run: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-geneoverlap >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-data.table >=1.9.4' + - r-dplyr + - r-dt + - r-ff + - r-ffbase + - r-ggdendro + - r-ggplot2 + - r-ggpmisc + - r-ggrepel + - r-ggthemes + - r-grbase + - r-gridextra + - r-gtable + - r-htmltools + - r-igraph + - r-intergraph + - r-knitr + - r-matrixstats + - r-network + - r-plyr + - r-pracma + - r-rcolorbrewer + - r-rmarkdown + - r-scales + - r-sna + - r-stringr + - r-tidyr + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The CEMiTool package unifies the discovery and the analysis of coexpression gene modules in a fully automatic manner, while providing a user-friendly html report with high quality graphs. Our tool evaluates if modules contain genes that are over-represented by specific pathways or that are altered in a specific sample group. Additionally, CEMiTool is able to integrate transcriptomic data with interactome information, identifying the potential hubs on each network.' + diff --git a/recipes/bioconductor-ceu1kg/meta.yaml b/recipes/bioconductor-ceu1kg/meta.yaml new file mode 100644 index 0000000000000..16e7c5b072082 --- /dev/null +++ b/recipes/bioconductor-ceu1kg/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.20.0" %} +{% set name = "ceu1kg" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 039d5e0ba8ee673cbd97d636f30d379e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP.20101109 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'CEU genotypes from 1000 genomes "low coverage" pilot phase I (approx 8 million SNP calls released July 2010); includes Wellcome trust GENEVAR expression for 43 indiv' + diff --git a/recipes/bioconductor-ceu1kg/post-link.sh b/recipes/bioconductor-ceu1kg/post-link.sh new file mode 100644 index 0000000000000..9dee80c1528fc --- /dev/null +++ b/recipes/bioconductor-ceu1kg/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ceu1kg_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceu1kg_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceu1kg_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceu1kg/bioconductor-ceu1kg_0.20.0_src_all.tar.gz" +) +MD5="039d5e0ba8ee673cbd97d636f30d379e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ceu1kg/pre-unlink.sh b/recipes/bioconductor-ceu1kg/pre-unlink.sh new file mode 100644 index 0000000000000..1f46aa3c77624 --- /dev/null +++ b/recipes/bioconductor-ceu1kg/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ceu1kg diff --git a/recipes/bioconductor-ceu1kgv/meta.yaml b/recipes/bioconductor-ceu1kgv/meta.yaml new file mode 100644 index 0000000000000..e0100536c73ce --- /dev/null +++ b/recipes/bioconductor-ceu1kgv/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.24.0" %} +{% set name = "ceu1kgv" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c972c7288208ef044f986bbfd8fab71c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'expression + genotype on 79 unrelated CEU individuals' + diff --git a/recipes/bioconductor-ceu1kgv/post-link.sh b/recipes/bioconductor-ceu1kgv/post-link.sh new file mode 100644 index 0000000000000..5ac623df8befe --- /dev/null +++ b/recipes/bioconductor-ceu1kgv/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ceu1kgv_0.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceu1kgv_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceu1kgv_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceu1kgv/bioconductor-ceu1kgv_0.24.0_src_all.tar.gz" +) +MD5="c972c7288208ef044f986bbfd8fab71c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ceu1kgv/pre-unlink.sh b/recipes/bioconductor-ceu1kgv/pre-unlink.sh new file mode 100644 index 0000000000000..358da9d928105 --- /dev/null +++ b/recipes/bioconductor-ceu1kgv/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ceu1kgv diff --git a/recipes/bioconductor-ceuhm3/meta.yaml b/recipes/bioconductor-ceuhm3/meta.yaml new file mode 100644 index 0000000000000..1937bb99e7b1b --- /dev/null +++ b/recipes/bioconductor-ceuhm3/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.20.0" %} +{% set name = "ceuhm3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0255a0481a74261e5d40cbc1c00bd46f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'ceuhm3: genotype (HapMap phase III) and expression data for CEPH CEU cohort' + diff --git a/recipes/bioconductor-ceuhm3/post-link.sh b/recipes/bioconductor-ceuhm3/post-link.sh new file mode 100644 index 0000000000000..5570db21a6baa --- /dev/null +++ b/recipes/bioconductor-ceuhm3/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ceuhm3_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ceuhm3_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ceuhm3_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ceuhm3/bioconductor-ceuhm3_0.20.0_src_all.tar.gz" +) +MD5="0255a0481a74261e5d40cbc1c00bd46f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ceuhm3/pre-unlink.sh b/recipes/bioconductor-ceuhm3/pre-unlink.sh new file mode 100644 index 0000000000000..32e465a82d646 --- /dev/null +++ b/recipes/bioconductor-ceuhm3/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ceuhm3 diff --git a/recipes/bioconductor-cexor/build.sh b/recipes/bioconductor-cexor/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cexor/build.sh +++ b/recipes/bioconductor-cexor/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cexor/meta.yaml b/recipes/bioconductor-cexor/meta.yaml index 6304de1badf34..5ab15527834ee 100644 --- a/recipes/bioconductor-cexor/meta.yaml +++ b/recipes/bioconductor-cexor/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "CexoR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b337039bb3db90dc74f1367868ba39379cc752eb5bc546ce9efbbea2e91cfba0 + md5: adc301c13a685ebcb765a611268f6612 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-idr - r-rcolorbrewer run: - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-idr - r-rcolorbrewer @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | GPL-2 + file LICENSE' summary: 'Strand specific peak-pair calling in ChIP-exo replicates. The cumulative Skellam distribution function (package ''skellam'') is used to detect significant normalised count differences of opposed sign at each DNA strand (peak-pairs). Irreproducible discovery rate for overlapping peak-pairs across biological replicates is estimated using the package ''idr''.' extra: identifiers: - biotools:cexor - doi:10.14806/ej.21.0.837 + parent_recipe: + name: bioconductor-cexor + path: recipes/bioconductor-cexor + version: 1.18.0 + diff --git a/recipes/bioconductor-cfassay/build.sh b/recipes/bioconductor-cfassay/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cfassay/build.sh +++ b/recipes/bioconductor-cfassay/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cfassay/meta.yaml b/recipes/bioconductor-cfassay/meta.yaml index 6494e124400a1..00b394adde0ed 100644 --- a/recipes/bioconductor-cfassay/meta.yaml +++ b/recipes/bioconductor-cfassay/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "CFAssay" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5187e9a3b990f447d7b84e274051e9ea44be03b574127c53fdde1d8c6ad6baca + md5: fa7e613db23c139fa4f6f6b13fe2dc7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The package provides functions for calculation of linear-quadratic cell survival curves and for ANOVA of experimental 2-way designs along with the colony formation assay.' extra: identifiers: - biotools:cfassay - doi:10.1186/s13014-015-0529-y + parent_recipe: + name: bioconductor-cfassay + path: recipes/bioconductor-cfassay + version: 1.14.0 + diff --git a/recipes/bioconductor-cgdv17/meta.yaml b/recipes/bioconductor-cgdv17/meta.yaml new file mode 100644 index 0000000000000..7dde6bf14ac01 --- /dev/null +++ b/recipes/bioconductor-cgdv17/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.20.0" %} +{% set name = "cgdv17" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f099ccc73aef5fb29585a9f7a026f29f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: parallel, GGtools, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, illuminaHumanv1.db +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Complete Genomics Diversity Panel, chr17 on 46 individuals' + diff --git a/recipes/bioconductor-cgdv17/post-link.sh b/recipes/bioconductor-cgdv17/post-link.sh new file mode 100644 index 0000000000000..a3b38f46eb94b --- /dev/null +++ b/recipes/bioconductor-cgdv17/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cgdv17_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cgdv17_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/cgdv17_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cgdv17/bioconductor-cgdv17_0.20.0_src_all.tar.gz" +) +MD5="f099ccc73aef5fb29585a9f7a026f29f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cgdv17/pre-unlink.sh b/recipes/bioconductor-cgdv17/pre-unlink.sh new file mode 100644 index 0000000000000..43a8f72f6cb7e --- /dev/null +++ b/recipes/bioconductor-cgdv17/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cgdv17 diff --git a/recipes/bioconductor-cgen/build.sh b/recipes/bioconductor-cgen/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cgen/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cgen/meta.yaml b/recipes/bioconductor-cgen/meta.yaml new file mode 100644 index 0000000000000..8354391ad1caf --- /dev/null +++ b/recipes/bioconductor-cgen/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "3.18.0" %} +{% set name = "CGEN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8de652a5e02f957223ebbe1923ed9886 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: cluster +requirements: + host: + - r-base + - r-mvtnorm + - r-survival + run: + - r-base + - r-mvtnorm + - r-survival + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 + file LICENSE' + summary: 'An R package for analysis of case-control studies in genetic epidemiology.' + diff --git a/recipes/bioconductor-cghbase/build.sh b/recipes/bioconductor-cghbase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cghbase/build.sh +++ b/recipes/bioconductor-cghbase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghbase/meta.yaml b/recipes/bioconductor-cghbase/meta.yaml index d70a282bf1e2d..1f2ed670a0338 100644 --- a/recipes/bioconductor-cghbase/meta.yaml +++ b/recipes/bioconductor-cghbase/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "CGHbase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 58f12ed6f5ebb38d996d355465b15c486d35bbdb5f2f3983c9fccda1ea26c4c1 + md5: 8e5a1db8a434a7a03a7f0298a6e466a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Contains functions and classes that are needed by arrayCGH packages.' extra: identifiers: - biotools:cghbase - doi:10.1016/j.ejmg.2005.10.046 + parent_recipe: + name: bioconductor-cghbase + path: recipes/bioconductor-cghbase + version: 1.40.0 + diff --git a/recipes/bioconductor-cghcall/build.sh b/recipes/bioconductor-cghcall/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cghcall/build.sh +++ b/recipes/bioconductor-cghcall/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghcall/meta.yaml b/recipes/bioconductor-cghcall/meta.yaml index 84df548d0f8bd..da9c81f3585c1 100644 --- a/recipes/bioconductor-cghcall/meta.yaml +++ b/recipes/bioconductor-cghcall/meta.yaml @@ -1,44 +1,50 @@ -{% set version = "2.42.0" %} +{% set version = "2.44.0" %} {% set name = "CGHcall" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bf89e06a9600c589e70ebdc126923ff52c5652f64094bdfba80af4b4bbdbe178 + md5: 6adfe221a755373d03ab61d68c575c06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' - r-base - r-snowfall run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' - r-base - r-snowfall test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' summary: 'Calls aberrations for array CGH data using a six state mixture model as well as several biological concepts that are ignored by existing algorithms. Visualization of profiles is also provided.' extra: identifiers: - biotools:cghcall - doi:10.1093/bioinformatics/btm030 + parent_recipe: + name: bioconductor-cghcall + path: recipes/bioconductor-cghcall + version: 2.42.0 + diff --git a/recipes/bioconductor-cghmcr/build.sh b/recipes/bioconductor-cghmcr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cghmcr/build.sh +++ b/recipes/bioconductor-cghmcr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghmcr/meta.yaml b/recipes/bioconductor-cghmcr/meta.yaml index f8c377c1c6d6e..7b9a8e3bd36a5 100644 --- a/recipes/bioconductor-cghmcr/meta.yaml +++ b/recipes/bioconductor-cghmcr/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "cghMCR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7a483c8f37fe841e4029634ffaa9a9fc502cd16824e98b037ad77ea60d057a75 + md5: ee9010fd0cda4e0454890e547be251fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-cntools >=1.36.0,<1.38.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cntools >=1.38.0,<1.39.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-cntools >=1.36.0,<1.38.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cntools >=1.38.0,<1.39.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides functions to identify genomic regions of interests based on segmented copy number data from multiple samples.' extra: identifiers: - biotools:cghmcr - doi:10.1093/bioinformatics/btv298 + parent_recipe: + name: bioconductor-cghmcr + path: recipes/bioconductor-cghmcr + version: 1.38.0 + diff --git a/recipes/bioconductor-cghnormaliter/build.sh b/recipes/bioconductor-cghnormaliter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cghnormaliter/build.sh +++ b/recipes/bioconductor-cghnormaliter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghnormaliter/meta.yaml b/recipes/bioconductor-cghnormaliter/meta.yaml index 3e1343cb97f8b..b9e3f21cc4ece 100644 --- a/recipes/bioconductor-cghnormaliter/meta.yaml +++ b/recipes/bioconductor-cghnormaliter/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "CGHnormaliter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3c36826990685373baaf34836520e28c8b8425dc19a6870b6473baa80680d4dd + md5: 864c1f86399bde28c8deea6390e8f03f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Normalization and centralization of array comparative genomic hybridization (aCGH) data. The algorithm uses an iterative procedure that effectively eliminates the influence of imbalanced copy numbers. This leads to a more reliable assessment of copy number alterations (CNAs).' extra: identifiers: - biotools:cghnormaliter - doi:10.1186/1471-2164-10-401 + parent_recipe: + name: bioconductor-cghnormaliter + path: recipes/bioconductor-cghnormaliter + version: 1.34.0 + diff --git a/recipes/bioconductor-cghregions/build.sh b/recipes/bioconductor-cghregions/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cghregions/build.sh +++ b/recipes/bioconductor-cghregions/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cghregions/meta.yaml b/recipes/bioconductor-cghregions/meta.yaml index 0fc4628de0594..337ee48b81f81 100644 --- a/recipes/bioconductor-cghregions/meta.yaml +++ b/recipes/bioconductor-cghregions/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CGHregions" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ab10d41625ea1b4004bc0cb4d3a7ada2964b5bfd29cb5f8f9f242ba991c5b79 + md5: 83a3b0748e057ec4ca72aa1866f9b030 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (http://www.gnu.org/copyleft/gpl.html)' summary: 'Dimension Reduction for Array CGH Data with Minimal Information Loss' extra: identifiers: - biotools:cghregions - doi:10.1002/9783527678679.dg00687 + parent_recipe: + name: bioconductor-cghregions + path: recipes/bioconductor-cghregions + version: 1.38.0 + diff --git a/recipes/bioconductor-champ/build.sh b/recipes/bioconductor-champ/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-champ/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-champ/meta.yaml b/recipes/bioconductor-champ/meta.yaml new file mode 100644 index 0000000000000..73cc6c9effb98 --- /dev/null +++ b/recipes/bioconductor-champ/meta.yaml @@ -0,0 +1,107 @@ +{% set version = "2.12.0" %} +{% set name = "ChAMP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8e68fa277534fb313d680db8d1044684 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr,rmarkdown +requirements: + host: + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-champdata >=2.14.0,<2.15.0' + - 'bioconductor-dmrcate >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-fem >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-illumina450probevariants.db >=1.18.0,<1.19.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-combinat + - r-dendextend + - r-doparallel + - r-hmisc + - r-isva + - r-matrixstats + - 'r-plotly >=4.5.6' + - r-plyr + - r-prettydoc + - r-quadprog + - r-rcolorbrewer + - r-rmarkdown + - r-rpmm + - r-shiny + - r-shinythemes + run: + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-champdata >=2.14.0,<2.15.0' + - 'bioconductor-dmrcate >=1.18.0,<1.19.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-fem >=3.10.0,<3.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-illumina450probevariants.db >=1.18.0,<1.19.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-combinat + - r-dendextend + - r-doparallel + - r-hmisc + - r-isva + - r-matrixstats + - 'r-plotly >=4.5.6' + - r-plyr + - r-prettydoc + - r-quadprog + - r-rcolorbrewer + - r-rmarkdown + - r-rpmm + - r-shiny + - r-shinythemes +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The package includes quality control metrics, a selection of normalization methods and novel methods to identify differentially methylated regions and to highlight copy number alterations.' + diff --git a/recipes/bioconductor-champdata/meta.yaml b/recipes/bioconductor-champdata/meta.yaml new file mode 100644 index 0000000000000..b3cb39985fee2 --- /dev/null +++ b/recipes/bioconductor-champdata/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.14.0" %} +{% set name = "ChAMPdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 45ef9f402b16c268d28853e51b26ffd0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides datasets needed for ChAMP including a test dataset and blood controls for CNA analysis.' + diff --git a/recipes/bioconductor-champdata/post-link.sh b/recipes/bioconductor-champdata/post-link.sh new file mode 100644 index 0000000000000..a9ab679e049df --- /dev/null +++ b/recipes/bioconductor-champdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChAMPdata_2.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChAMPdata_2.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChAMPdata_2.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-champdata/bioconductor-champdata_2.14.0_src_all.tar.gz" +) +MD5="45ef9f402b16c268d28853e51b26ffd0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-champdata/pre-unlink.sh b/recipes/bioconductor-champdata/pre-unlink.sh new file mode 100644 index 0000000000000..2524c9ef66e06 --- /dev/null +++ b/recipes/bioconductor-champdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChAMPdata diff --git a/recipes/bioconductor-charge/build.sh b/recipes/bioconductor-charge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-charge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-charge/meta.yaml b/recipes/bioconductor-charge/meta.yaml new file mode 100644 index 0000000000000..b8fc6c400748d --- /dev/null +++ b/recipes/bioconductor-charge/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.2.0" %} +{% set name = "CHARGE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5c4c8debe46ce9db6a724b4bc94e6f06 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: roxygen2, EnsDb.Hsapiens.v86 +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-diptest + - r-factoextra + - r-factominer + - r-matrixstats + - r-modes + - r-plyr + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-diptest + - r-factoextra + - r-factominer + - r-matrixstats + - r-modes + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifies genomic duplications or deletions from gene expression data.' + diff --git a/recipes/bioconductor-charm/build.sh b/recipes/bioconductor-charm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-charm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-charm/meta.yaml b/recipes/bioconductor-charm/meta.yaml new file mode 100644 index 0000000000000..d866f710106d6 --- /dev/null +++ b/recipes/bioconductor-charm/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "2.28.0" %} +{% set name = "charm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 63fa78f4ef43f5c8ea4f2fe33885e184 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: charmData, BSgenome.Hsapiens.UCSC.hg18, corpcor +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ff + - r-fields + - r-gtools + - r-nor1mix + - r-rcolorbrewer + - r-sqn + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ff + - r-fields + - r-gtools + - r-nor1mix + - r-rcolorbrewer + - r-sqn +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'This package implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol. It finds differentially methylated regions between samples, calculates percentage methylation estimates and includes array quality assessment tools.' + diff --git a/recipes/bioconductor-charmdata/meta.yaml b/recipes/bioconductor-charmdata/meta.yaml new file mode 100644 index 0000000000000..bd7aaef89b145 --- /dev/null +++ b/recipes/bioconductor-charmdata/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.18.0" %} +{% set name = "charmData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8a33b09e3b618b0aae3f3ca0ec5acc9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-charm >=2.28.0,<2.29.0' + - 'bioconductor-pd.charm.hg18.example >=0.99.0,<0.100.0' + - r-base + run: + - 'bioconductor-charm >=2.28.0,<2.29.0' + - 'bioconductor-pd.charm.hg18.example >=0.99.0,<0.100.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'An example dataset for use with the charm package' + diff --git a/recipes/bioconductor-charmdata/post-link.sh b/recipes/bioconductor-charmdata/post-link.sh new file mode 100644 index 0000000000000..043d3e4c0b774 --- /dev/null +++ b/recipes/bioconductor-charmdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="charmData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/charmData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/charmData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-charmdata/bioconductor-charmdata_1.18.0_src_all.tar.gz" +) +MD5="b8a33b09e3b618b0aae3f3ca0ec5acc9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-charmdata/pre-unlink.sh b/recipes/bioconductor-charmdata/pre-unlink.sh new file mode 100644 index 0000000000000..9ba2c146f1c6e --- /dev/null +++ b/recipes/bioconductor-charmdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ charmData diff --git a/recipes/bioconductor-chemminedrugs/meta.yaml b/recipes/bioconductor-chemminedrugs/meta.yaml new file mode 100644 index 0000000000000..f2b83a5228653 --- /dev/null +++ b/recipes/bioconductor-chemminedrugs/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.2" %} +{% set name = "ChemmineDrugs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2a3646e5173e93080fb5b49564f5d545 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle,knitcitations,knitr +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An annotation package for use with ChemmineR. This package includes data from DrugBank. DUD data can be downloaded using the "DUD()" function in ChemmineR.' + diff --git a/recipes/bioconductor-chemminedrugs/post-link.sh b/recipes/bioconductor-chemminedrugs/post-link.sh new file mode 100644 index 0000000000000..e582a5c13f482 --- /dev/null +++ b/recipes/bioconductor-chemminedrugs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChemmineDrugs_1.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ChemmineDrugs_1.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/ChemmineDrugs_1.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chemminedrugs/bioconductor-chemminedrugs_1.0.2_src_all.tar.gz" +) +MD5="2a3646e5173e93080fb5b49564f5d545" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chemminedrugs/pre-unlink.sh b/recipes/bioconductor-chemminedrugs/pre-unlink.sh new file mode 100644 index 0000000000000..40f25bb9e67f8 --- /dev/null +++ b/recipes/bioconductor-chemminedrugs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChemmineDrugs diff --git a/recipes/bioconductor-chemmineob/build.sh b/recipes/bioconductor-chemmineob/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chemmineob/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chemmineob/meta.yaml b/recipes/bioconductor-chemmineob/meta.yaml new file mode 100644 index 0000000000000..8f36061f56c78 --- /dev/null +++ b/recipes/bioconductor-chemmineob/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.20.0" %} +{% set name = "ChemmineOB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e22ab70101dfc90ee6432269eb9d2adb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ChemmineR, BiocStyle, knitr, knitcitations, knitrBootstrap, BiocManager +# SystemRequirements: OpenBabel (>= 2.3.1) with headers (http://openbabel.org). +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-bh + - 'r-rcpp >=0.11.0' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-bh + - 'r-rcpp >=0.11.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'ChemmineOB provides an R interface to a subset of cheminformatics functionalities implemented by the OpelBabel C++ project. OpenBabel is an open source cheminformatics toolbox that includes utilities for structure format interconversions, descriptor calculations, compound similarity searching and more. ChemineOB aims to make a subset of these utilities available from within R. For non-developers, ChemineOB is primarily intended to be used from ChemmineR as an add-on package rather than used directly.' + diff --git a/recipes/bioconductor-chemminer/build.sh b/recipes/bioconductor-chemminer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chemminer/build.sh +++ b/recipes/bioconductor-chemminer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chemminer/meta.yaml b/recipes/bioconductor-chemminer/meta.yaml index be8af210f3cc8..ceb4604e63dbe 100644 --- a/recipes/bioconductor-chemminer/meta.yaml +++ b/recipes/bioconductor-chemminer/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "3.32.1" %} +{% set version = "3.34.1" %} {% set name = "ChemmineR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1cd0a789ea9e1da73f40ca0fc585b370044447507731eef6cc95df666145ef87 + md5: e271de186e07cdbb5195645bbab04f13 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RSQLite, scatterplot3d, gplots, fmcsR, snow, RPostgreSQL, BiocStyle, knitr, knitcitations, knitrBootstrap, ChemmineOB (>= 1.16.1), ChemmineDrugs, png,rmarkdown, BiocManager +# SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-base64enc - r-bh @@ -33,7 +35,7 @@ requirements: - r-rjson - r-rsvg run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-base64enc - r-bh @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'ChemmineR is a cheminformatics package for analyzing drug-like small molecule data in R. Its latest version contains functions for efficient processing of large numbers of molecules, physicochemical/structural property predictions, structural similarity searching, classification and clustering of compound libraries with a wide spectrum of algorithms. In addition, it offers visualization functions for compound clustering results and chemical structures.' extra: identifiers: - biotools:chemminer + parent_recipe: + name: bioconductor-chemminer + path: recipes/bioconductor-chemminer + version: 3.32.1 + diff --git a/recipes/bioconductor-chic.data/meta.yaml b/recipes/bioconductor-chic.data/meta.yaml new file mode 100644 index 0000000000000..8b81764b11aa5 --- /dev/null +++ b/recipes/bioconductor-chic.data/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "ChIC.data" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4bee195762ecb4bfce23bc3f841cc5cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - 'r-caret >=6.0-78' + run: + - r-base + - 'r-caret >=6.0-78' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains annotation and metagene profile data for the ChIC package.' + diff --git a/recipes/bioconductor-chic.data/post-link.sh b/recipes/bioconductor-chic.data/post-link.sh new file mode 100644 index 0000000000000..d01b740e31baf --- /dev/null +++ b/recipes/bioconductor-chic.data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChIC.data_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIC.data_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIC.data_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chic.data/bioconductor-chic.data_1.2.0_src_all.tar.gz" +) +MD5="4bee195762ecb4bfce23bc3f841cc5cb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chic.data/pre-unlink.sh b/recipes/bioconductor-chic.data/pre-unlink.sh new file mode 100644 index 0000000000000..fdc7298b1390f --- /dev/null +++ b/recipes/bioconductor-chic.data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChIC.data diff --git a/recipes/bioconductor-chic/build.sh b/recipes/bioconductor-chic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chic/meta.yaml b/recipes/bioconductor-chic/meta.yaml new file mode 100644 index 0000000000000..02cc0c8613327 --- /dev/null +++ b/recipes/bioconductor-chic/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.2.0" %} +{% set name = "ChIC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dcf74f7e88f59bb8965f1d0202651109 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chic.data >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-caret + - r-catools + - r-progress + - r-spp + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chic.data >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-caret + - r-catools + - r-progress + - r-spp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Quality control (QC) pipeline for ChIP-seq data using a comprehensive set of QC metrics, including previously proposed metrics as well as novel ones, based on local characteristics of the enrichment profile. The package provides functions to calculate a set of QC metrics, a compendium with reference values and machine learning models to score sample quality.' + diff --git a/recipes/bioconductor-chicago/build.sh b/recipes/bioconductor-chicago/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chicago/build.sh +++ b/recipes/bioconductor-chicago/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chicago/meta.yaml b/recipes/bioconductor-chicago/meta.yaml index 971813f3c899e..bb6410571bde7 100644 --- a/recipes/bioconductor-chicago/meta.yaml +++ b/recipes/bioconductor-chicago/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Chicago" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0d938792567088e2458762df32ef40c845cc9070a8932c7e5a7fb9517f9e2954 + md5: 8533dfb490d2389e4a9eda3f81fa6481 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: argparser, BiocStyle, knitr, rmarkdown, PCHiCdata, testthat, Rsamtools, GenomicInteractions, GenomicRanges, IRanges, AnnotationHub requirements: host: - r-base @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A pipeline for analysing Capture Hi-C data.' extra: identifiers: - biotools:chicago + parent_recipe: + name: bioconductor-chicago + path: recipes/bioconductor-chicago + version: 1.8.0 + diff --git a/recipes/bioconductor-chicken.db/meta.yaml b/recipes/bioconductor-chicken.db/meta.yaml new file mode 100644 index 0000000000000..bd190acbf18eb --- /dev/null +++ b/recipes/bioconductor-chicken.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "chicken.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e093b861c4688cf10e53a3124ee8bfc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.gg.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.gg.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix chicken annotation data (chip chicken) assembled using data from public repositories' + diff --git a/recipes/bioconductor-chicken.db/post-link.sh b/recipes/bioconductor-chicken.db/post-link.sh new file mode 100644 index 0000000000000..efcf3f7a17cc1 --- /dev/null +++ b/recipes/bioconductor-chicken.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chicken.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chicken.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/chicken.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chicken.db/bioconductor-chicken.db_3.2.3_src_all.tar.gz" +) +MD5="e093b861c4688cf10e53a3124ee8bfc0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chicken.db/pre-unlink.sh b/recipes/bioconductor-chicken.db/pre-unlink.sh new file mode 100644 index 0000000000000..af3b26df34e7e --- /dev/null +++ b/recipes/bioconductor-chicken.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chicken.db diff --git a/recipes/bioconductor-chicken.db0/meta.yaml b/recipes/bioconductor-chicken.db0/meta.yaml new file mode 100644 index 0000000000000..b3fa5f26582a1 --- /dev/null +++ b/recipes/bioconductor-chicken.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "chicken.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 948b616eea6f7bda986dfc115842279e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for chicken, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-chicken.db0/post-link.sh b/recipes/bioconductor-chicken.db0/post-link.sh new file mode 100644 index 0000000000000..8cb76018eb88c --- /dev/null +++ b/recipes/bioconductor-chicken.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chicken.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chicken.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/chicken.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chicken.db0/bioconductor-chicken.db0_3.7.1_src_all.tar.gz" +) +MD5="948b616eea6f7bda986dfc115842279e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chicken.db0/pre-unlink.sh b/recipes/bioconductor-chicken.db0/pre-unlink.sh new file mode 100644 index 0000000000000..97cfd6430b1dc --- /dev/null +++ b/recipes/bioconductor-chicken.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chicken.db0 diff --git a/recipes/bioconductor-chickencdf/meta.yaml b/recipes/bioconductor-chickencdf/meta.yaml new file mode 100644 index 0000000000000..57e679d5bb849 --- /dev/null +++ b/recipes/bioconductor-chickencdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "chickencdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ab0097b4b7b6c4d94360feb84ab69972 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Chicken.cdf file.' + diff --git a/recipes/bioconductor-chickencdf/post-link.sh b/recipes/bioconductor-chickencdf/post-link.sh new file mode 100644 index 0000000000000..53fe7ec7d2034 --- /dev/null +++ b/recipes/bioconductor-chickencdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chickencdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chickencdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/chickencdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chickencdf/bioconductor-chickencdf_2.18.0_src_all.tar.gz" +) +MD5="ab0097b4b7b6c4d94360feb84ab69972" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chickencdf/pre-unlink.sh b/recipes/bioconductor-chickencdf/pre-unlink.sh new file mode 100644 index 0000000000000..dc6b8636bfb65 --- /dev/null +++ b/recipes/bioconductor-chickencdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chickencdf diff --git a/recipes/bioconductor-chickenprobe/meta.yaml b/recipes/bioconductor-chickenprobe/meta.yaml new file mode 100644 index 0000000000000..59d38673354c4 --- /dev/null +++ b/recipes/bioconductor-chickenprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "chickenprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b33599081ce1ba768ff7992e143c01d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Chicken\_probe\_tab.' + diff --git a/recipes/bioconductor-chickenprobe/post-link.sh b/recipes/bioconductor-chickenprobe/post-link.sh new file mode 100644 index 0000000000000..705ddb10b71e1 --- /dev/null +++ b/recipes/bioconductor-chickenprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chickenprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chickenprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/chickenprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chickenprobe/bioconductor-chickenprobe_2.18.0_src_all.tar.gz" +) +MD5="b33599081ce1ba768ff7992e143c01d0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chickenprobe/pre-unlink.sh b/recipes/bioconductor-chickenprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3e9bd41af0495 --- /dev/null +++ b/recipes/bioconductor-chickenprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chickenprobe diff --git a/recipes/bioconductor-chimera/build.sh b/recipes/bioconductor-chimera/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chimera/build.sh +++ b/recipes/bioconductor-chimera/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chimera/meta.yaml b/recipes/bioconductor-chimera/meta.yaml index 4fae5141f57f2..00c58ba18ab14 100644 --- a/recipes/bioconductor-chimera/meta.yaml +++ b/recipes/bioconductor-chimera/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "chimera" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b24054dd8cfccd9fcb5ae546a8b220c91eac68a8e965ddd1bd224ec3dfc16ccf + md5: 3245d0c076c17bc1b850d377cf15070a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocParallel, geneplotter +# SystemRequirements: STAR, TopHat, bowtie and samtools are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base build: - {{ compiler('c') }} @@ -45,8 +47,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.' - + summary: 'This package facilitates the characterisation of fusion products events. It allows to import fusion data results from the following fusion finders: chimeraScan, bellerophontes, deFuse, FusionFinder, FusionHunter, mapSplice, tophat-fusion, FusionMap, STAR, Rsubread, fusionCatcher.' +extra: + parent_recipe: + name: bioconductor-chimera + path: recipes/bioconductor-chimera + version: 1.22.0 diff --git a/recipes/bioconductor-chimeraviz/build.sh b/recipes/bioconductor-chimeraviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chimeraviz/build.sh +++ b/recipes/bioconductor-chimeraviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chimeraviz/meta.yaml b/recipes/bioconductor-chimeraviz/meta.yaml index 6cf8b6199ec0a..1687deeefd57e 100644 --- a/recipes/bioconductor-chimeraviz/meta.yaml +++ b/recipes/bioconductor-chimeraviz/meta.yaml @@ -1,39 +1,42 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "chimeraviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 72155e7a9e6ae51f6ad588d6ee0d98cbcda3710d9794eb6c6f03d3d502f1d5a9 + md5: 88df77f2bd025b9416ec3b0538c97b19 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, roxygen2, devtools, knitr, lintr +# SystemRequirements: bowtie, samtools, and egrep are required for some functionalities requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-argumentcheck - r-base - r-data.table @@ -44,22 +47,22 @@ requirements: - r-rcolorbrewer - r-rmarkdown run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-argumentcheck - r-base - r-data.table @@ -73,8 +76,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'chimeraviz manages data from fusion gene finders and provides useful visualization tools.' - +extra: + parent_recipe: + name: bioconductor-chimeraviz + path: recipes/bioconductor-chimeraviz + version: 1.6.2 diff --git a/recipes/bioconductor-chimp.db0/meta.yaml b/recipes/bioconductor-chimp.db0/meta.yaml new file mode 100644 index 0000000000000..d81afbe73f9e7 --- /dev/null +++ b/recipes/bioconductor-chimp.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "chimp.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e9b8c6525777c4474e79ed1edc5c5f05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for chimp, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-chimp.db0/post-link.sh b/recipes/bioconductor-chimp.db0/post-link.sh new file mode 100644 index 0000000000000..145c60524fdde --- /dev/null +++ b/recipes/bioconductor-chimp.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chimp.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/chimp.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/chimp.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chimp.db0/bioconductor-chimp.db0_3.7.1_src_all.tar.gz" +) +MD5="e9b8c6525777c4474e79ed1edc5c5f05" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chimp.db0/pre-unlink.sh b/recipes/bioconductor-chimp.db0/pre-unlink.sh new file mode 100644 index 0000000000000..acfa313fb9213 --- /dev/null +++ b/recipes/bioconductor-chimp.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chimp.db0 diff --git a/recipes/bioconductor-chimphumanbraindata/meta.yaml b/recipes/bioconductor-chimphumanbraindata/meta.yaml new file mode 100644 index 0000000000000..313b306c3a162 --- /dev/null +++ b/recipes/bioconductor-chimphumanbraindata/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "ChimpHumanBrainData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ea5241df1f05ea48aa510de5a2a3efb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - r-hexbin + - r-statmod + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - r-hexbin + - r-statmod + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: MIT + summary: 'This data package contains chimp and human brain data extracted from the ArrayExpress accession E-AFMX-2. Both human and chimp RNAs were run on human hgu95av2 Affymetrix arrays. It is a useful dataset for tutorials.' + diff --git a/recipes/bioconductor-chimphumanbraindata/post-link.sh b/recipes/bioconductor-chimphumanbraindata/post-link.sh new file mode 100644 index 0000000000000..0e79dca87316b --- /dev/null +++ b/recipes/bioconductor-chimphumanbraindata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChimpHumanBrainData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChimpHumanBrainData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChimpHumanBrainData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chimphumanbraindata/bioconductor-chimphumanbraindata_1.20.0_src_all.tar.gz" +) +MD5="ea5241df1f05ea48aa510de5a2a3efb9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chimphumanbraindata/pre-unlink.sh b/recipes/bioconductor-chimphumanbraindata/pre-unlink.sh new file mode 100644 index 0000000000000..cde37354eedfe --- /dev/null +++ b/recipes/bioconductor-chimphumanbraindata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChimpHumanBrainData diff --git a/recipes/bioconductor-chipanalyser/build.sh b/recipes/bioconductor-chipanalyser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chipanalyser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipanalyser/meta.yaml b/recipes/bioconductor-chipanalyser/meta.yaml new file mode 100644 index 0000000000000..d5218b1126936 --- /dev/null +++ b/recipes/bioconductor-chipanalyser/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.4.0" %} +{% set name = "ChIPanalyser" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4f3fdeed3fb1ba02a78e56d70f1a9098 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Dmelanogaster.UCSC.dm3,knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-rcpproll + - r-rocr + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-rcpproll + - r-rocr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Based on a statistical thermodynamic framework, ChIPanalyser tries to produce ChIP-seq like profile. The model relies on four consideration: TF binding sites can be scored using a Position weight Matrix, DNA accessibility plays a role in Transcription Factor binding, binding profiles are dependant on the number of transcription factors bound to DNA and finally binding energy (another way of describing PWM''s) or binding specificity should be modulated (hence the introduction of a binding specificity modulator). The end result of ChIPanalyser is to produce profiles simulating real ChIP-seq profile and provide accuracy measurements of these predicted profiles after being compared to real ChIP-seq data. The ultimate goal is to produce ChIP-seq like profiles predicting ChIP-seq like profile to circumvent the need to produce costly ChIP-seq experiments.' + diff --git a/recipes/bioconductor-chipcomp/build.sh b/recipes/bioconductor-chipcomp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipcomp/build.sh +++ b/recipes/bioconductor-chipcomp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipcomp/meta.yaml b/recipes/bioconductor-chipcomp/meta.yaml index fb74682688bdd..71e3eb7516049 100644 --- a/recipes/bioconductor-chipcomp/meta.yaml +++ b/recipes/bioconductor-chipcomp/meta.yaml @@ -1,45 +1,46 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ChIPComp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1a43058202e3fbf2e0e8265d9113d0187d0885513ce54386eb0d8ff18f8b3649 + md5: de5f56eb79ef4dab25dd22ac8aa20b0e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle,RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base build: - {{ compiler('c') }} @@ -48,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'ChIPComp detects differentially bound sharp binding sites across multiple conditions considering matching control.' extra: identifiers: - biotools:chipcomp + parent_recipe: + name: bioconductor-chipcomp + path: recipes/bioconductor-chipcomp + version: 1.10.0 + diff --git a/recipes/bioconductor-chipenrich.data/meta.yaml b/recipes/bioconductor-chipenrich.data/meta.yaml new file mode 100644 index 0000000000000..3ae9fa7344a7e --- /dev/null +++ b/recipes/bioconductor-chipenrich.data/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "2.6.0" %} +{% set name = "chipenrich.data" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cd762813ed7fcc7e0ef6d0be7de5047b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat, GO.db, org.Dm.eg.db, org.Dr.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Dmelanogaster.UCSC.dm6.ensGene, TxDb.Drerio.UCSC.danRer10.refGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Mmusculus.UCSC.mm9.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Rnorvegicus.UCSC.rn4.ensGene, TxDb.Rnorvegicus.UCSC.rn5.refGene, TxDb.Rnorvegicus.UCSC.rn6.refGene +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-readr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-readr + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Supporting data for the chipenrich package. Includes pre-defined gene sets, gene locus definitions, and mappability estimates.' + diff --git a/recipes/bioconductor-chipenrich.data/post-link.sh b/recipes/bioconductor-chipenrich.data/post-link.sh new file mode 100644 index 0000000000000..e567dee9fa807 --- /dev/null +++ b/recipes/bioconductor-chipenrich.data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="chipenrich.data_2.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/chipenrich.data_2.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/chipenrich.data_2.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipenrich.data/bioconductor-chipenrich.data_2.6.0_src_all.tar.gz" +) +MD5="cd762813ed7fcc7e0ef6d0be7de5047b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chipenrich.data/pre-unlink.sh b/recipes/bioconductor-chipenrich.data/pre-unlink.sh new file mode 100644 index 0000000000000..7a901aa78b44a --- /dev/null +++ b/recipes/bioconductor-chipenrich.data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ chipenrich.data diff --git a/recipes/bioconductor-chipenrich/build.sh b/recipes/bioconductor-chipenrich/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chipenrich/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipenrich/meta.yaml b/recipes/bioconductor-chipenrich/meta.yaml new file mode 100644 index 0000000000000..18d496d26c5d8 --- /dev/null +++ b/recipes/bioconductor-chipenrich/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "2.6.0" %} +{% set name = "chipenrich" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: de5edd323cf961e677b6b7fc52f1c0d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, devtools, knitr, rmarkdown, roxygen2, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chipenrich.data >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-lattice + - r-latticeextra + - r-mgcv + - r-plyr + - r-rms + - r-stringr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chipenrich.data >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-lattice + - r-latticeextra + - r-mgcv + - r-plyr + - r-rms + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'ChIP-Enrich performs gene set enrichment testing using peaks called from a ChIP-seq experiment. The method empirically corrects for confounding factors such as the length of genes, and the mappability of the sequence surrounding genes.' + diff --git a/recipes/bioconductor-chipexoqual/build.sh b/recipes/bioconductor-chipexoqual/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chipexoqual/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipexoqual/meta.yaml b/recipes/bioconductor-chipexoqual/meta.yaml new file mode 100644 index 0000000000000..c4ff40299cc1a --- /dev/null +++ b/recipes/bioconductor-chipexoqual/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.6.0" %} +{% set name = "ChIPexoQual" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 611bcc06f4a538ad75e2233cbf3c88ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ChIPexoQualExample (>= 0.99.1), knitr (>= 1.10), BiocStyle, gridExtra (>= 2.2), testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-broom >=0.4' + - 'r-data.table >=1.9.6' + - 'r-dplyr >=0.5' + - 'r-ggplot2 >=1.0' + - 'r-hexbin >=1.27' + - 'r-rcolorbrewer >=1.1' + - r-rmarkdown + - 'r-scales >=0.4.0' + - 'r-viridis >=0.3' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-broom >=0.4' + - 'r-data.table >=1.9.6' + - 'r-dplyr >=0.5' + - 'r-ggplot2 >=1.0' + - 'r-hexbin >=1.27' + - 'r-rcolorbrewer >=1.1' + - r-rmarkdown + - 'r-scales >=0.4.0' + - 'r-viridis >=0.3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Package with a quality control pipeline for ChIP-exo/nexus data.' + diff --git a/recipes/bioconductor-chipexoqualexample/meta.yaml b/recipes/bioconductor-chipexoqualexample/meta.yaml new file mode 100644 index 0000000000000..ebadeacbb80e1 --- /dev/null +++ b/recipes/bioconductor-chipexoqualexample/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "ChIPexoQualExample" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 18e7a340ba4586efebd01c0eaa2de1b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data for the ChIPexoQual package, consisting of (3) chromosome 1 aligned reads from a ChIP-exo experiment for FoxA1 in mouse liver cell lines aligned to the mm9 genome.' + diff --git a/recipes/bioconductor-chipexoqualexample/post-link.sh b/recipes/bioconductor-chipexoqualexample/post-link.sh new file mode 100644 index 0000000000000..646b804921e47 --- /dev/null +++ b/recipes/bioconductor-chipexoqualexample/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ChIPexoQualExample_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIPexoQualExample_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPexoQualExample_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipexoqualexample/bioconductor-chipexoqualexample_1.6.0_src_all.tar.gz" +) +MD5="18e7a340ba4586efebd01c0eaa2de1b4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-chipexoqualexample/pre-unlink.sh b/recipes/bioconductor-chipexoqualexample/pre-unlink.sh new file mode 100644 index 0000000000000..2794021df5a4f --- /dev/null +++ b/recipes/bioconductor-chipexoqualexample/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ChIPexoQualExample diff --git a/recipes/bioconductor-chippeakanno/build.sh b/recipes/bioconductor-chippeakanno/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chippeakanno/build.sh +++ b/recipes/bioconductor-chippeakanno/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chippeakanno/conda_build_config.yaml b/recipes/bioconductor-chippeakanno/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-chippeakanno/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-chippeakanno/meta.yaml b/recipes/bioconductor-chippeakanno/meta.yaml index 6a77f5238d575..85b2ab2c8ae07 100644 --- a/recipes/bioconductor-chippeakanno/meta.yaml +++ b/recipes/bioconductor-chippeakanno/meta.yaml @@ -1,77 +1,79 @@ -{% set version = "3.14.2" %} +{% set version = "3.16.0" %} {% set name = "ChIPpeakAnno" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4c73984fc86297346ade9747fe408ce5feb77f3790aa1702f7bf775a0cd3338f + md5: 5e52ae5329247caf5e5b29de1051c5b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: reactome.db, BSgenome.Ecoli.NCBI.20080805, BSgenome.Hsapiens.UCSC.hg19, org.Ce.eg.db, org.Hs.eg.db, BSgenome.Celegans.UCSC.ce10, BSgenome.Drerio.UCSC.danRer7, EnsDb.Hsapiens.v75, EnsDb.Hsapiens.v79, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Hsapiens.UCSC.hg38.knownGene, gplots, BiocStyle, rtracklayer, knitr, rmarkdown, testthat, trackViewer, motifStack, OrganismDbi requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-regioner >=1.12.0,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dbi - r-idr - r-matrixstats - r-seqinr - r-venndiagram run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-regioner >=1.12.0,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dbi - r-idr - r-matrixstats @@ -81,9 +83,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package includes functions to retrieve the sequences around the peak, obtain enriched Gene Ontology (GO) terms, find the nearest gene, exon, miRNA or custom features such as most conserved elements and other transcription factor binding sites supplied by users. Starting 2.0.5, new functions have been added for finding the peaks with bi-directional promoters with summary statistics (peaksNearBDP), for summarizing the occurrence of motifs in peaks (summarizePatternInPeaks) and for adding other IDs to annotated peaks or enrichedGO (addGeneIDs). This package leverages the biomaRt, IRanges, Biostrings, BSgenome, GO.db, multtest and stat packages.' extra: identifiers: - biotools:chippeakanno + parent_recipe: + name: bioconductor-chippeakanno + path: recipes/bioconductor-chippeakanno + version: 3.14.2 + diff --git a/recipes/bioconductor-chipqc/build.sh b/recipes/bioconductor-chipqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipqc/build.sh +++ b/recipes/bioconductor-chipqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipqc/conda_build_config.yaml b/recipes/bioconductor-chipqc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-chipqc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-chipqc/meta.yaml b/recipes/bioconductor-chipqc/meta.yaml index 9cd63a962e5d9..c25206b7c285a 100644 --- a/recipes/bioconductor-chipqc/meta.yaml +++ b/recipes/bioconductor-chipqc/meta.yaml @@ -1,65 +1,67 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "ChIPQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fdebb0fdc165e292b0141a2f540f6bb24c112202b0b8a6a4bed41394e9687abc + md5: e6be25df0cd0a858e838143c5cb61d43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-diffbind >=2.8.0,<2.10.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.6.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-diffbind >=2.10.0,<2.11.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0' - r-base - r-ggplot2 - r-gtools - r-nozzle.r1 - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-diffbind >=2.8.0,<2.10.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.6.0' - - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.2,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-diffbind >=2.10.0,<2.11.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.celegans.ucsc.ce6.ensgene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene >=3.2.0,<3.3.0' - r-base - r-ggplot2 - r-gtools @@ -69,9 +71,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Quality metrics for ChIPseq data.' extra: identifiers: - biotools:chipqc + parent_recipe: + name: bioconductor-chipqc + path: recipes/bioconductor-chipqc + version: 1.16.1 + diff --git a/recipes/bioconductor-chipseeker/build.sh b/recipes/bioconductor-chipseeker/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipseeker/build.sh +++ b/recipes/bioconductor-chipseeker/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipseeker/meta.yaml b/recipes/bioconductor-chipseeker/meta.yaml index f593667c36008..73c680fdbf297 100644 --- a/recipes/bioconductor-chipseeker/meta.yaml +++ b/recipes/bioconductor-chipseeker/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "ChIPseeker" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fe358c80a1a5f2d4ccbadcca59a23074aa5f81b681384fc1106066defa3581d6 + md5: ef4405a995f3e80a672528ddb20d0279 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: clusterProfiler, ReactomePA, org.Hs.eg.db, knitr, BiocStyle, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-boot - r-dplyr @@ -40,16 +42,16 @@ requirements: - r-rcolorbrewer - r-upsetr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - r-boot - r-dplyr @@ -65,9 +67,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements functions to retrieve the nearest genes around the peak, annotate genomic region of the peak, statstical methods for estimate the significance of overlap among ChIP peak data sets, and incorporate GEO database for user to compare the own dataset with those deposited in database. The comparison can be used to infer cooperative regulation and thus can be used to generate hypotheses. Several visualization functions are implemented to summarize the coverage of the peak experiment, average profile and heatmap of peaks binding to TSS regions, genomic annotation, distance to TSS, and overlap of peaks or genes.' extra: identifiers: - biotools:chipseeker + parent_recipe: + name: bioconductor-chipseeker + path: recipes/bioconductor-chipseeker + version: 1.16.1 + diff --git a/recipes/bioconductor-chipseq/build.sh b/recipes/bioconductor-chipseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipseq/build.sh +++ b/recipes/bioconductor-chipseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipseq/meta.yaml b/recipes/bioconductor-chipseq/meta.yaml index c4ce3c4dea605..e24b5bfe3e249 100644 --- a/recipes/bioconductor-chipseq/meta.yaml +++ b/recipes/bioconductor-chipseq/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "chipseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a767466f1511d1d3682a7a8ed5c9a6f7e63832bf776f7bdcc4e5445be86bc825 + md5: 290f7ce079aa0d77772ce81d8499f3af build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome, GenomicFeatures, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-lattice run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-lattice build: @@ -40,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for helping process short read data for chipseq experiments' extra: identifiers: - biotools:chipseq - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chipseq + path: recipes/bioconductor-chipseq + version: 1.30.0 + diff --git a/recipes/bioconductor-chipseqr/build.sh b/recipes/bioconductor-chipseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chipseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipseqr/meta.yaml b/recipes/bioconductor-chipseqr/meta.yaml new file mode 100644 index 0000000000000..323e6f80e3c1b --- /dev/null +++ b/recipes/bioconductor-chipseqr/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.36.0" %} +{% set name = "ChIPseqR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 546c295c55884109a0a1e834b58c41b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-fbasics + - r-timsac + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-fbasics + - r-timsac + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'ChIPseqR identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. The model used to describe binding events was developed to locate nucleosomes but should flexible enough to handle other types of experiments as well.' + diff --git a/recipes/bioconductor-chipseqspike/build.sh b/recipes/bioconductor-chipseqspike/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chipseqspike/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipseqspike/meta.yaml b/recipes/bioconductor-chipseqspike/meta.yaml new file mode 100644 index 0000000000000..aabcf4db3dcd5 --- /dev/null +++ b/recipes/bioconductor-chipseqspike/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "ChIPSeqSpike" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d22e39a23ca76f29f3d1ad621c608f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqplots >=1.20.0,<1.21.0' + - r-base + - r-corrplot + - r-ggplot2 + - r-lsd + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqplots >=1.20.0,<1.21.0' + - r-base + - r-corrplot + - r-ggplot2 + - r-lsd + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Chromatin Immuno-Precipitation followed by Sequencing (ChIP-Seq) is used to determine the binding sites of any protein of interest, such as transcription factors or histones with or without a specific modification, at a genome scale. The many steps of the protocol can introduce biases that make ChIP-Seq more qualitative than quantitative. For instance, it was shown that global histone modification differences are not caught by traditional downstream data normalization techniques. A case study reported no differences in histone H3 lysine-27 trimethyl (H3K27me3) upon Ezh2 inhibitor treatment. To tackle this problem, external spike-in control were used to keep track of technical biases between conditions. Exogenous DNA from a different non-closely related species was inserted during the protocol to infer scaling factors that enabled an accurate normalization, thus revealing the inhibitor effect. ChIPSeqSpike offers tools for ChIP-Seq spike-in normalization. Ready to use scaled bigwig files and scaling factors values are obtained as output. ChIPSeqSpike also provides tools for ChIP-Seq spike-in assessment and analysis through a versatile collection of graphical functions.' + diff --git a/recipes/bioconductor-chipsim/build.sh b/recipes/bioconductor-chipsim/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipsim/build.sh +++ b/recipes/bioconductor-chipsim/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipsim/meta.yaml b/recipes/bioconductor-chipsim/meta.yaml index c3db1989f8772..9fd4a68c795af 100644 --- a/recipes/bioconductor-chipsim/meta.yaml +++ b/recipes/bioconductor-chipsim/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ChIPsim" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2d0d5fb309ed681962dba1698158df8f4612316d5adf8570c94c46c3a17c676e + md5: 807aa8e54aeac47c04e3b4173118482a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: actuar, zoo requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A general framework for the simulation of ChIP-seq data. Although currently focused on nucleosome positioning the package is designed to support different types of experiments.' extra: identifiers: - biotools:chipsim - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chipsim + path: recipes/bioconductor-chipsim + version: 1.34.0 + diff --git a/recipes/bioconductor-chipxpress/build.sh b/recipes/bioconductor-chipxpress/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chipxpress/build.sh +++ b/recipes/bioconductor-chipxpress/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chipxpress/conda_build_config.yaml b/recipes/bioconductor-chipxpress/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-chipxpress/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-chipxpress/meta.yaml b/recipes/bioconductor-chipxpress/meta.yaml index 4c177ebc4fa06..79397fe7400eb 100644 --- a/recipes/bioconductor-chipxpress/meta.yaml +++ b/recipes/bioconductor-chipxpress/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ChIPXpress" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b64b509939b988973f09aaf715529d8a5e9eb84f83d2aefd88cc3ea633ae53a1 + md5: 42bb787851b0c8b7875266dff5128c4e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: mouse4302frmavecs, mouse4302.db, mouse4302cdf, RUnit, BiocGenerics requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-chipxpressdata >=1.18.0,<1.20.0' - - 'bioconductor-frma >=1.32.0,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-chipxpressdata >=1.20.0,<1.21.0' + - 'bioconductor-frma >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' - r-base - r-biganalytics - r-bigmemory run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-chipxpressdata >=1.18.0,<1.20.0' - - 'bioconductor-frma >=1.32.0,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-chipxpressdata >=1.20.0,<1.21.0' + - 'bioconductor-frma >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' - r-base - r-biganalytics - r-bigmemory @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'ChIPXpress takes as input predicted TF bound genes from ChIPx data and uses a corresponding database of gene expression profiles downloaded from NCBI GEO to rank the TF bound targets in order of which gene is most likely to be functional TF target.' extra: identifiers: - biotools:chipxpress - doi:10.1186/1471-2105-14-188 + parent_recipe: + name: bioconductor-chipxpress + path: recipes/bioconductor-chipxpress + version: 1.24.0 + diff --git a/recipes/bioconductor-chipxpressdata/meta.yaml b/recipes/bioconductor-chipxpressdata/meta.yaml index a1bb8c58862ba..392d73f7396e7 100644 --- a/recipes/bioconductor-chipxpressdata/meta.yaml +++ b/recipes/bioconductor-chipxpressdata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "ChIPXpressData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2fc3ca28b77347bddde703816a892f8874d855d146245452cd6230d05df1e6a4 + md5: a22a580a546729aa51a3e5899c047f1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -28,8 +29,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Contains pre-built mouse (GPL1261) and human (GPL570) database of gene expression profiles to be used for ChIPXpress ranking.' - +extra: + parent_recipe: + name: bioconductor-chipxpressdata + path: recipes/bioconductor-chipxpressdata + version: 1.18.0 diff --git a/recipes/bioconductor-chipxpressdata/post-link.sh b/recipes/bioconductor-chipxpressdata/post-link.sh index def21373b1b00..e98475ddc773f 100644 --- a/recipes/bioconductor-chipxpressdata/post-link.sh +++ b/recipes/bioconductor-chipxpressdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ChIPXpressData_1.18.0.tar.gz" +FN="ChIPXpressData_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ChIPXpressData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/ChIPXpressData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ChIPXpressData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ChIPXpressData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chipxpressdata/bioconductor-chipxpressdata_1.20.0_src_all.tar.gz" ) -MD5="5c2695c0ef69ef1d8c5702a478667047" +MD5="a22a580a546729aa51a3e5899c047f1e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-chopsticks/build.sh b/recipes/bioconductor-chopsticks/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chopsticks/build.sh +++ b/recipes/bioconductor-chopsticks/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chopsticks/meta.yaml b/recipes/bioconductor-chopsticks/meta.yaml index d98e5c8c1922a..86dc8bcbc2245 100644 --- a/recipes/bioconductor-chopsticks/meta.yaml +++ b/recipes/bioconductor-chopsticks/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "chopsticks" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d9573d3caa31c7a200802b0a87070838531ff4a3c7c04fd8130f32dabd868c26 + md5: b808bcd49f1f23d35a2189e46df3a6de build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: hexbin requirements: host: - r-base @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Implements classes and methods for large-scale SNP association studies' extra: identifiers: - biotools:chopsticks - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chopsticks + path: recipes/bioconductor-chopsticks + version: 1.46.0 + diff --git a/recipes/bioconductor-chrogps/build.sh b/recipes/bioconductor-chrogps/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chrogps/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chrogps/meta.yaml b/recipes/bioconductor-chrogps/meta.yaml new file mode 100644 index 0000000000000..07a7983514b6a --- /dev/null +++ b/recipes/bioconductor-chrogps/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "2.0.0" %} +{% set name = "chroGPS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 14ccb84d998040aa8fab8a52b14d7d21 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-changepoint + - r-cluster + - r-dppackage + - r-ellipse + - r-icsnp + - r-mass + - r-vegan + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-changepoint + - r-cluster + - r-dppackage + - r-ellipse + - r-icsnp + - r-mass + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2.14)' + summary: 'We provide intuitive maps to visualize, analyze and compare the association between genetic elements based on their epigenetic profiles. The approach is based on Multi-Dimensional Scaling, and includes a parallelized implementation for handling high dimensional datasets. We provide several sensible distance metrics, and adjustment procedures to remove systematic biases typically observed when merging data obtained under different technologies or genetic backgrounds. We also provide functions and methods to perform differential analysis of epigenome maps at factor and gene level.' + diff --git a/recipes/bioconductor-chromdraw/build.sh b/recipes/bioconductor-chromdraw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chromdraw/build.sh +++ b/recipes/bioconductor-chromdraw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromdraw/meta.yaml b/recipes/bioconductor-chromdraw/meta.yaml index d4b4ded0a93f8..0b1f91a0bbb06 100644 --- a/recipes/bioconductor-chromdraw/meta.yaml +++ b/recipes/bioconductor-chromdraw/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "chromDraw" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8429d9c00418d6cd63180ee5763c8ef907cf8aa5855140553143830c47af59e7 + md5: c54bc321ee938793b8fcbb474ef540f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# SystemRequirements: Rtools (>= 3.1) requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - 'r-rcpp >=0.11.1' build: @@ -33,9 +34,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ChromDraw is a R package for drawing the schemes of karyotype(s) in the linear and circular fashion. It is possible to visualized cytogenetic marsk on the chromosomes. This tool has own input data format. Input data can be imported from the GenomicRanges data structure. This package can visualized the data in the BED file format. Here is requirement on to the first nine fields of the BED format. Output files format are *.eps and *.svg.' extra: identifiers: - biotools:chromdraw + parent_recipe: + name: bioconductor-chromdraw + path: recipes/bioconductor-chromdraw + version: 2.10.0 + diff --git a/recipes/bioconductor-chromheatmap/build.sh b/recipes/bioconductor-chromheatmap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chromheatmap/build.sh +++ b/recipes/bioconductor-chromheatmap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromheatmap/meta.yaml b/recipes/bioconductor-chromheatmap/meta.yaml index 80d100aea51a0..19398e5f69d82 100644 --- a/recipes/bioconductor-chromheatmap/meta.yaml +++ b/recipes/bioconductor-chromheatmap/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "ChromHeatMap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dbfd69528bb77da0fa85cb53b9feab831077f96e421f5ce75694b8fdb9bdca01 + md5: 8c849b949219b4a16234dc8850dd594e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ChromHeatMap package can be used to plot genome-wide data (e.g. expression, CGH, SNP) along each strand of a given chromosome as a heat map. The generated heat map can be used to interactively identify probes and genes of interest.' extra: identifiers: - biotools:chromheatmap - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-chromheatmap + path: recipes/bioconductor-chromheatmap + version: 1.34.0 + diff --git a/recipes/bioconductor-chromplot/build.sh b/recipes/bioconductor-chromplot/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chromplot/build.sh +++ b/recipes/bioconductor-chromplot/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromplot/meta.yaml b/recipes/bioconductor-chromplot/meta.yaml index 0438822e3d6b7..409b39de15bb2 100644 --- a/recipes/bioconductor-chromplot/meta.yaml +++ b/recipes/bioconductor-chromplot/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "chromPlot" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3f164cbb4f23dafec6352e6df2cd8bc5057a13553dcef0dcfc4d111efae6b5fc + md5: fd2da81e6c20c564f5b23a49c65e6847 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: qtl, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package designed to visualize genomic data along the chromosomes, where the vertical chromosomes are sorted by number, with sex chromosomes at the end.' extra: identifiers: - biotools:chromplot - doi:10.1093/bioinformatics/btw137 + parent_recipe: + name: bioconductor-chromplot + path: recipes/bioconductor-chromplot + version: 1.8.0 + diff --git a/recipes/bioconductor-chromstar/build.sh b/recipes/bioconductor-chromstar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chromstar/build.sh +++ b/recipes/bioconductor-chromstar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromstar/meta.yaml b/recipes/bioconductor-chromstar/meta.yaml index 6732eae31181b..c0e59fcb4933b 100644 --- a/recipes/bioconductor-chromstar/meta.yaml +++ b/recipes/bioconductor-chromstar/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "chromstaR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 14a2d48db46c858ee773b18c2bc72fb132a7438d9f66bb761074683d503fdf6d + md5: 0bcb2867e4f92b89a972829558250f3f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, BiocStyle, testthat, biomaRt requirements: host: - - 'bioconductor-bamsignals >=1.12.1,<1.14.0' - - 'bioconductor-chromstardata >=1.6.0,<1.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-chromstardata >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -33,14 +34,14 @@ requirements: - r-mvtnorm - r-reshape2 run: - - 'bioconductor-bamsignals >=1.12.1,<1.14.0' - - 'bioconductor-chromstardata >=1.6.0,<1.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-chromstardata >=1.8.0,<1.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -55,10 +56,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements functions for combinatorial and differential analysis of ChIP-seq data. It includes uni- and multivariate peak-calling, export to genome browser viewable files, and functions for enrichment analyses.' extra: identifiers: - biotools:chromstar - doi:10.1101/038612 + parent_recipe: + name: bioconductor-chromstar + path: recipes/bioconductor-chromstar + version: 1.6.2 + diff --git a/recipes/bioconductor-chromstardata/meta.yaml b/recipes/bioconductor-chromstardata/meta.yaml index 6b53f576bf9ff..c445e57853988 100644 --- a/recipes/bioconductor-chromstardata/meta.yaml +++ b/recipes/bioconductor-chromstardata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "chromstaRData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: df7d487f0d792f3b22df14408855b6c6b32b6c9185e4d0b171c341b726e97f24 + md5: 6de05adbae8cdeacaad09e20b18bbf95 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'ChIP-seq data for demonstration purposes in the chromstaR package.' - +extra: + parent_recipe: + name: bioconductor-chromstardata + path: recipes/bioconductor-chromstardata + version: 1.6.0 diff --git a/recipes/bioconductor-chromstardata/post-link.sh b/recipes/bioconductor-chromstardata/post-link.sh index 9b4e472efcd0a..237bb7d6576a5 100644 --- a/recipes/bioconductor-chromstardata/post-link.sh +++ b/recipes/bioconductor-chromstardata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="chromstaRData_1.6.0.tar.gz" +FN="chromstaRData_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/chromstaRData_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/chromstaRData_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/chromstaRData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/chromstaRData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-chromstardata/bioconductor-chromstardata_1.8.0_src_all.tar.gz" ) -MD5="eda1145219cebb5688aa0043391b0270" +MD5="6de05adbae8cdeacaad09e20b18bbf95" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-chromswitch/build.sh b/recipes/bioconductor-chromswitch/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-chromswitch/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromswitch/meta.yaml b/recipes/bioconductor-chromswitch/meta.yaml new file mode 100644 index 0000000000000..97dcd75b35e1c --- /dev/null +++ b/recipes/bioconductor-chromswitch/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.0" %} +{% set name = "chromswitch" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 60f981b01486ea7e0c91c20cbf4ed531 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, DescTools (>= 0.99.19), devtools (>= 1.13.3), GenomeInfoDb (>= 1.16.0), knitr, rmarkdown, mclust (>= 5.3), testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-cluster >=2.0.6' + - 'r-dplyr >=0.5.0' + - 'r-gplots >=3.0.1' + - 'r-lazyeval >=0.2.0' + - 'r-magrittr >=1.5' + - 'r-matrixstats >=0.52' + - 'r-nmf >=0.20.6' + - 'r-tidyr >=0.6.3' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-cluster >=2.0.6' + - 'r-dplyr >=0.5.0' + - 'r-gplots >=3.0.1' + - 'r-lazyeval >=0.2.0' + - 'r-magrittr >=1.5' + - 'r-matrixstats >=0.52' + - 'r-nmf >=0.20.6' + - 'r-tidyr >=0.6.3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Chromswitch implements a flexible method to detect chromatin state switches between samples in two biological conditions in a specific genomic region of interest given peaks or chromatin state calls from ChIP-seq data.' + diff --git a/recipes/bioconductor-chromvar/build.sh b/recipes/bioconductor-chromvar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chromvar/build.sh +++ b/recipes/bioconductor-chromvar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chromvar/meta.yaml b/recipes/bioconductor-chromvar/meta.yaml index a473ebd08e3e2..c15f06e195480 100644 --- a/recipes/bioconductor-chromvar/meta.yaml +++ b/recipes/bioconductor-chromvar/meta.yaml @@ -1,76 +1,88 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "chromVAR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 484a08055f35c6c9fbe7963e3e265058664dae8328afd55ccd432912872a627c + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2f2af9a568f88511eb19c286fdf7caaf build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: JASPAR2016, BSgenome.Hsapiens.UCSC.hg19, readr, testthat, knitr, rmarkdown, pheatmap, motifmatchr +# SystemRequirements: C++11 requirements: host: - - bioconductor-iranges - - bioconductor-genomicranges - - bioconductor-genomeinfodb - - bioconductor-biocparallel - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-tfbstools - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-bsgenome - - r-essentials + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' - r-base + - r-dt - r-ggplot2 + - r-matrix + - r-miniui + - r-nabor + - r-plotly + - r-rcolorbrewer - r-rcpp - r-rcpparmadillo - r-rtsne - - r-plotly - r-shiny - - r-miniui - - r-dt - - r-nabor run: - - bioconductor-iranges - - bioconductor-genomicranges - - bioconductor-genomeinfodb - - bioconductor-biocparallel - - bioconductor-biocgenerics - - bioconductor-biostrings - - bioconductor-tfbstools - - bioconductor-rsamtools - - bioconductor-s4vectors - - bioconductor-summarizedexperiment - - bioconductor-bsgenome - - r-essentials + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' - r-base + - r-dt - r-ggplot2 + - r-matrix + - r-miniui + - r-nabor + - r-plotly + - r-rcolorbrewer - r-rcpp - r-rcpparmadillo - r-rtsne - - r-plotly - r-shiny - - r-miniui - - r-dt - - r-nabor - + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: GPL-2 + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' summary: 'Determine variation in chromatin accessibility across sets of annotations or peaks. Designed primarily for single-cell or sparse chromatin accessibility data, e.g. from scATAC-seq or sparse bulk ATAC or DNAse-seq experiments.' - extra: identifiers: - biotools:chromvar + parent_recipe: + name: bioconductor-chromvar + path: recipes/bioconductor-chromvar + version: 1.2.0 + diff --git a/recipes/bioconductor-chronos/build.sh b/recipes/bioconductor-chronos/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-chronos/build.sh +++ b/recipes/bioconductor-chronos/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-chronos/conda_build_config.yaml b/recipes/bioconductor-chronos/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-chronos/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-chronos/meta.yaml b/recipes/bioconductor-chronos/meta.yaml index dd70faff781e5..5b36eb53ba4dc 100644 --- a/recipes/bioconductor-chronos/meta.yaml +++ b/recipes/bioconductor-chronos/meta.yaml @@ -1,26 +1,29 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "CHRONOS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 75c03fbb73ce2c2561005feeb65c757798be41cabe7742a8eb00c8932cdf1234 + md5: 0fdab9e25f3a8db821e653397297b081 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +# SystemRequirements: Java version >= 1.7, Pandoc requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-circlize - r-doparallel @@ -29,9 +32,9 @@ requirements: - r-rcurl - r-xml run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - r-circlize - r-doparallel @@ -43,9 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package used for efficient unraveling of the inherent dynamic properties of pathways. MicroRNA-mediated subpathway topologies are extracted and evaluated by exploiting the temporal transition and the fold change activity of the linked genes/microRNAs.' extra: identifiers: - biotools:CHRONOS + parent_recipe: + name: bioconductor-chronos + path: recipes/bioconductor-chronos + version: 1.8.1 + diff --git a/recipes/bioconductor-cicero/build.sh b/recipes/bioconductor-cicero/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cicero/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cicero/meta.yaml b/recipes/bioconductor-cicero/meta.yaml new file mode 100644 index 0000000000000..32cb30cfe4719 --- /dev/null +++ b/recipes/bioconductor-cicero/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.13" %} +{% set name = "cicero" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0adf35ffd0c0887513a9be7f558164ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationDbi (>= 1.38.2), knitr, rmarkdown, rtracklayer (>= 1.36.6), testthat, vdiffr (>= 0.2.3), covr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-monocle >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-assertthat >=0.2.0' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.7.4' + - 'r-fnn >=1.1' + - 'r-ggplot2 >=2.2.1' + - 'r-glasso >=1.8' + - 'r-igraph >=1.1.0' + - 'r-matrix >=1.2-12' + - 'r-plyr >=1.8.4' + - 'r-reshape2 >=1.4.3' + - 'r-stringr >=1.2.0' + - 'r-tibble >=1.4.2' + - 'r-vgam >=1.0-5' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-monocle >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-assertthat >=0.2.0' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.7.4' + - 'r-fnn >=1.1' + - 'r-ggplot2 >=2.2.1' + - 'r-glasso >=1.8' + - 'r-igraph >=1.1.0' + - 'r-matrix >=1.2-12' + - 'r-plyr >=1.8.4' + - 'r-reshape2 >=1.4.3' + - 'r-stringr >=1.2.0' + - 'r-tibble >=1.4.2' + - 'r-vgam >=1.0-5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Cicero computes putative cis-regulatory maps from single-cell chromatin accessibility data. It also extends monocle 2 for use in chromatin accessibility data.' + diff --git a/recipes/bioconductor-cindex/build.sh b/recipes/bioconductor-cindex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cindex/build.sh +++ b/recipes/bioconductor-cindex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cindex/meta.yaml b/recipes/bioconductor-cindex/meta.yaml index ee7a3ad0edd0f..3f72c25ed4ec3 100644 --- a/recipes/bioconductor-cindex/meta.yaml +++ b/recipes/bioconductor-cindex/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CINdex" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5d482deea03bc6ef5b1813448c69bc2e027014c4b7dfa53cc06e64f6ae868a9d + md5: 429ec61774d457ec691f01d418bb6ff1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat, ReactomePA, RUnit, BiocGenerics, AnnotationHub, rtracklayer, pd.genomewidesnp.6, org.Hs.eg.db, biovizBase, TxDb.Hsapiens.UCSC.hg18.knownGene, methods, Biostrings,Homo.sapiens requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-bitops - r-dplyr @@ -31,10 +33,10 @@ requirements: - r-som - r-stringr run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-bitops - r-dplyr @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The CINdex package addresses important area of high-throughput genomic analysis. It allows the automated processing and analysis of the experimental DNA copy number data generated by Affymetrix SNP 6.0 arrays or similar high throughput technologies. It calculates the chromosome instability (CIN) index that allows to quantitatively characterize genome-wide DNA copy number alterations as a measure of chromosomal instability. This package calculates not only overall genomic instability, but also instability in terms of copy number gains and losses separately at the chromosome and cytoband level.' extra: identifiers: - biotools:cindex - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cindex + path: recipes/bioconductor-cindex + version: 1.8.0 + diff --git a/recipes/bioconductor-cispath/build.sh b/recipes/bioconductor-cispath/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cispath/build.sh +++ b/recipes/bioconductor-cispath/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cispath/meta.yaml b/recipes/bioconductor-cispath/meta.yaml index b6aa04e645bfb..0542d6b1237e4 100644 --- a/recipes/bioconductor-cispath/meta.yaml +++ b/recipes/bioconductor-cispath/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "cisPath" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bd458092836f93f9995167f1aa8816efefc3e215191fc88c11481b1514c48ef4 + md5: f599dcd8049193817764ff0114785078 build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'cisPath is an R package that uses web browsers to visualize and manage protein-protein interaction networks.' extra: identifiers: - biotools:cispath - doi:10.1186/1752-0509-9-s1-s1 + parent_recipe: + name: bioconductor-cispath + path: recipes/bioconductor-cispath + version: 1.20.0 + diff --git a/recipes/bioconductor-citruscdf/meta.yaml b/recipes/bioconductor-citruscdf/meta.yaml new file mode 100644 index 0000000000000..493097039a05f --- /dev/null +++ b/recipes/bioconductor-citruscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "citruscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4af821a0c1ae1adf42b7dc5ce7458593 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Citrus.cdf file.' + diff --git a/recipes/bioconductor-citruscdf/post-link.sh b/recipes/bioconductor-citruscdf/post-link.sh new file mode 100644 index 0000000000000..266f10bd165ed --- /dev/null +++ b/recipes/bioconductor-citruscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="citruscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/citruscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/citruscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-citruscdf/bioconductor-citruscdf_2.18.0_src_all.tar.gz" +) +MD5="4af821a0c1ae1adf42b7dc5ce7458593" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-citruscdf/pre-unlink.sh b/recipes/bioconductor-citruscdf/pre-unlink.sh new file mode 100644 index 0000000000000..1e38454583d5d --- /dev/null +++ b/recipes/bioconductor-citruscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ citruscdf diff --git a/recipes/bioconductor-citrusprobe/meta.yaml b/recipes/bioconductor-citrusprobe/meta.yaml new file mode 100644 index 0000000000000..1edc7075239a7 --- /dev/null +++ b/recipes/bioconductor-citrusprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "citrusprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 259b114f96d5307c447d000bd27a7d15 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Citrus\_probe\_tab.' + diff --git a/recipes/bioconductor-citrusprobe/post-link.sh b/recipes/bioconductor-citrusprobe/post-link.sh new file mode 100644 index 0000000000000..c1b5e46c67e4f --- /dev/null +++ b/recipes/bioconductor-citrusprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="citrusprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/citrusprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/citrusprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-citrusprobe/bioconductor-citrusprobe_2.18.0_src_all.tar.gz" +) +MD5="259b114f96d5307c447d000bd27a7d15" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-citrusprobe/pre-unlink.sh b/recipes/bioconductor-citrusprobe/pre-unlink.sh new file mode 100644 index 0000000000000..7e229504957e4 --- /dev/null +++ b/recipes/bioconductor-citrusprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ citrusprobe diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml new file mode 100644 index 0000000000000..6a6490e1c7677 --- /dev/null +++ b/recipes/bioconductor-clariomdhumanprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomdhumanprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3f390b06a44187e10e4e8a60af16375b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomdhuman annotation data (chip clariomdhumanprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh b/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh new file mode 100644 index 0000000000000..4e840b8594fd6 --- /dev/null +++ b/recipes/bioconductor-clariomdhumanprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomdhumanprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomdhumanprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomdhumanprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomdhumanprobeset.db/bioconductor-clariomdhumanprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="3f390b06a44187e10e4e8a60af16375b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomdhumanprobeset.db/pre-unlink.sh b/recipes/bioconductor-clariomdhumanprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..5371dc13687ff --- /dev/null +++ b/recipes/bioconductor-clariomdhumanprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomdhumanprobeset.db diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..8173e6ce75810 --- /dev/null +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomdhumantranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a460203ad96a4ada92b495ac0811cbe3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomdhuman annotation data (chip clariomdhumantranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..0f69e7cf22dab --- /dev/null +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomdhumantranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomdhumantranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomdhumantranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomdhumantranscriptcluster.db/bioconductor-clariomdhumantranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="a460203ad96a4ada92b495ac0811cbe3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomdhumantranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomdhumantranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..7d82f9ae0164f --- /dev/null +++ b/recipes/bioconductor-clariomdhumantranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomdhumantranscriptcluster.db diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..7dc188a8b7553 --- /dev/null +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomshumanhttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fce4e730f50b068d8f91319754f8024f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomshumanht annotation data (chip clariomshumanhttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..971a1d44f30a5 --- /dev/null +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomshumanhttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomshumanhttranscriptcluster.db/bioconductor-clariomshumanhttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="fce4e730f50b068d8f91319754f8024f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomshumanhttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..b7935f94bb1d3 --- /dev/null +++ b/recipes/bioconductor-clariomshumanhttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomshumanhttranscriptcluster.db diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..7060dbd8345bc --- /dev/null +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomshumantranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0b92969a4bb4a2d8e972602f68c7ad1b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomshuman annotation data (chip clariomshumantranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..0e8f413578139 --- /dev/null +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomshumantranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomshumantranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomshumantranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomshumantranscriptcluster.db/bioconductor-clariomshumantranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="0b92969a4bb4a2d8e972602f68c7ad1b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomshumantranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomshumantranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..ecb0ee3bf3099 --- /dev/null +++ b/recipes/bioconductor-clariomshumantranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomshumantranscriptcluster.db diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..fa983f6e50b0d --- /dev/null +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomsmousehttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ba6fdb1816669b4ffb2707a0fe89ef59 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomsmouseht annotation data (chip clariomsmousehttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..de2bb4041027c --- /dev/null +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomsmousehttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsmousehttranscriptcluster.db/bioconductor-clariomsmousehttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="ba6fdb1816669b4ffb2707a0fe89ef59" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomsmousehttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..9e1547297ae9e --- /dev/null +++ b/recipes/bioconductor-clariomsmousehttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomsmousehttranscriptcluster.db diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..01e5a799e42b9 --- /dev/null +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomsmousetranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a70687be504281a4ec08c0535da4121f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomsmouse annotation data (chip clariomsmousetranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..72ff07bef19d2 --- /dev/null +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomsmousetranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsmousetranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomsmousetranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsmousetranscriptcluster.db/bioconductor-clariomsmousetranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="a70687be504281a4ec08c0535da4121f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomsmousetranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomsmousetranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..ed62c16ea72ef --- /dev/null +++ b/recipes/bioconductor-clariomsmousetranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomsmousetranscriptcluster.db diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..8c0a08bb3ed68 --- /dev/null +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomsrathttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 50399fde7380b015da941f36362a3f78 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomsratht annotation data (chip clariomsrathttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..dff9d73bb5269 --- /dev/null +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomsrathttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsrathttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomsrathttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsrathttranscriptcluster.db/bioconductor-clariomsrathttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="50399fde7380b015da941f36362a3f78" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomsrathttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomsrathttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..8cf73ac63fcc3 --- /dev/null +++ b/recipes/bioconductor-clariomsrathttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomsrathttranscriptcluster.db diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..10346dbed76d3 --- /dev/null +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "clariomsrattranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 34d0c761a038f5f28f6b5db4b7e575a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix clariomsrat annotation data (chip clariomsrattranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh b/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..353d6ec67de40 --- /dev/null +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="clariomsrattranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/clariomsrattranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/clariomsrattranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-clariomsrattranscriptcluster.db/bioconductor-clariomsrattranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="34d0c761a038f5f28f6b5db4b7e575a7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-clariomsrattranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-clariomsrattranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..3ee1fddb827d8 --- /dev/null +++ b/recipes/bioconductor-clariomsrattranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ clariomsrattranscriptcluster.db diff --git a/recipes/bioconductor-classifyr/build.sh b/recipes/bioconductor-classifyr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-classifyr/build.sh +++ b/recipes/bioconductor-classifyr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-classifyr/conda_build_config.yaml b/recipes/bioconductor-classifyr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-classifyr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-classifyr/meta.yaml b/recipes/bioconductor-classifyr/meta.yaml index 043c5d728078e..ec4460255bd1a 100644 --- a/recipes/bioconductor-classifyr/meta.yaml +++ b/recipes/bioconductor-classifyr/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.0.10" %} +{% set version = "2.2.2" %} {% set name = "ClassifyR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b313c24b6825c35f0b90957fb2eec6d79ce12b95a6cb79a17273128871eb0c1 + md5: 694c05bae86b05e915ed5c891132d0c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma, genefilter, edgeR, car, Rmixmod, ggplot2 (>= 3.0.0), gridExtra (>= 2.0.0), cowplot, BiocStyle, pamr, PoiClaClu, parathyroidSE, knitr, htmltools, gtable, scales, e1071, rmarkdown, IRanges, randomForest, robustbase, mlogit, mnlogit, glmnet, class requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-locfit - r-plyr run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-locfit - r-plyr @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The software formalises a framework for classification in R. There are four stages; Data transformation, feature selection, classifier training, and prediction. The requirements of variable types and names are fixed, but specialised variables for functions can also be provided. The classification framework is wrapped in a driver loop, that reproducibly carries out a number of cross-validation schemes. Functions for differential expression, differential variability, and differential distribution are included. Additional functions may be developed by the user, by creating an interface to the framework.' extra: identifiers: - biotools:classifyr + parent_recipe: + name: bioconductor-classifyr + path: recipes/bioconductor-classifyr + version: 2.0.10 + diff --git a/recipes/bioconductor-cleanupdtseq/build.sh b/recipes/bioconductor-cleanupdtseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cleanupdtseq/build.sh +++ b/recipes/bioconductor-cleanupdtseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cleanupdtseq/meta.yaml b/recipes/bioconductor-cleanupdtseq/meta.yaml index 48b07865b1386..7ca85ac775ee7 100644 --- a/recipes/bioconductor-cleanupdtseq/meta.yaml +++ b/recipes/bioconductor-cleanupdtseq/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cleanUpdTSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d055b4e455bd9be214baa9229a03c6a73f1f00a39cdeddfd61e93020fbb1d42f + md5: 4bcb20170e1ccbcfc1c93d2adb6e0e0d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-e1071 - r-seqinr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.drerio.ucsc.danrer7 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-e1071 - r-seqinr @@ -37,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package uses the Naive Bayes classifier (from e1071) to assign probability values to putative polyadenylation sites (pA sites) based on training data from zebrafish. This will allow the user to separate true, biologically relevant pA sites from false, oligodT primed pA sites.' extra: identifiers: - biotools:cleanupdtseq + parent_recipe: + name: bioconductor-cleanupdtseq + path: recipes/bioconductor-cleanupdtseq + version: 1.18.0 + diff --git a/recipes/bioconductor-cleaver/build.sh b/recipes/bioconductor-cleaver/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cleaver/build.sh +++ b/recipes/bioconductor-cleaver/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cleaver/meta.yaml b/recipes/bioconductor-cleaver/meta.yaml index 2c5770c9e6735..80824c48a3ea5 100644 --- a/recipes/bioconductor-cleaver/meta.yaml +++ b/recipes/bioconductor-cleaver/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "cleaver" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2d7a222959268fc5cc7d9048267d5993d0c97a3c60e5b4c23db7640eacfad764 + md5: 3ac18493a9e15c2f5e9679b96d9d3da7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat (>= 0.8), knitr, BiocStyle (>= 0.0.14), BRAIN, UniProt.ws (>= 2.1.4) requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'In-silico cleavage of polypeptide sequences. The cleavage rules are taken from: http://web.expasy.org/peptide_cutter/peptidecutter_enzymes.html' extra: identifiers: - biotools:cleaver - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cleaver + path: recipes/bioconductor-cleaver + version: 1.18.0 + diff --git a/recipes/bioconductor-clippda/build.sh b/recipes/bioconductor-clippda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clippda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clippda/meta.yaml b/recipes/bioconductor-clippda/meta.yaml new file mode 100644 index 0000000000000..a9f2294607e25 --- /dev/null +++ b/recipes/bioconductor-clippda/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.32.0" %} +{% set name = "clippda" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0d4835a20f6d5153606e6338f6933a85 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-lattice + - r-rgl + - r-scatterplot3d + - r-statmod + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-lattice + - r-rgl + - r-scatterplot3d + - r-statmod +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Methods for the nalysis of data from clinical proteomic profiling studies. The focus is on the studies of human subjects, which are often observational case-control by design and have technical replicates. A method for sample size determination for planning these studies is proposed. It incorporates routines for adjusting for the expected heterogeneities and imbalances in the data and the within-sample replicate correlations.' + diff --git a/recipes/bioconductor-clipper/build.sh b/recipes/bioconductor-clipper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clipper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clipper/meta.yaml b/recipes/bioconductor-clipper/meta.yaml new file mode 100644 index 0000000000000..b7cc3a9f109cf --- /dev/null +++ b/recipes/bioconductor-clipper/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.22.0" %} +{% set name = "clipper" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eb3ea7c60842da6cb778e932d303688f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics, graphite, ALL, hgu95av2.db, MASS, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-qpgraph >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-corpcor + - 'r-grbase >=1.6.6' + - r-igraph + - r-matrix + - r-rcpp + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-qpgraph >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-corpcor + - 'r-grbase >=1.6.6' + - r-igraph + - r-matrix + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Implements topological gene set analysis using a two-step empirical approach. It exploits graph decomposition theory to create a junction tree and reconstruct the most relevant signal path. In the first step clipper selects significant pathways according to statistical tests on the means and the concentration matrices of the graphs derived from pathway topologies. Then, it "clips" the whole pathway identifying the signal paths having the greatest association with a specific phenotype.' + diff --git a/recipes/bioconductor-cll/meta.yaml b/recipes/bioconductor-cll/meta.yaml new file mode 100644 index 0000000000000..3d0f56e98689e --- /dev/null +++ b/recipes/bioconductor-cll/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "CLL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3851a86f9abc1159d405cbbc03ecf405 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'The CLL package contains the chronic lymphocytic leukemia (CLL) gene expression data. The CLL data had 24 samples that were either classified as progressive or stable in regards to disease progression. The data came from Dr. Sabina Chiaretti at Division of Hematology, Department of Cellular Biotechnologies and Hematology, University La Sapienza, Rome, Italy and Dr. Jerome Ritz at Department of Medicine, Brigham and Women''s Hospital, Harvard Medical School, Boston, Massachusetts.' + diff --git a/recipes/bioconductor-cll/post-link.sh b/recipes/bioconductor-cll/post-link.sh new file mode 100644 index 0000000000000..ea682058d28c1 --- /dev/null +++ b/recipes/bioconductor-cll/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CLL_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CLL_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/CLL_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cll/bioconductor-cll_1.22.0_src_all.tar.gz" +) +MD5="3851a86f9abc1159d405cbbc03ecf405" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cll/pre-unlink.sh b/recipes/bioconductor-cll/pre-unlink.sh new file mode 100644 index 0000000000000..25bd306d6053f --- /dev/null +++ b/recipes/bioconductor-cll/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CLL diff --git a/recipes/bioconductor-cllmethylation/meta.yaml b/recipes/bioconductor-cllmethylation/meta.yaml new file mode 100644 index 0000000000000..69e88fba44b0b --- /dev/null +++ b/recipes/bioconductor-cllmethylation/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.2.0" %} +{% set name = "CLLmethylation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cd8a30818dd72030144bd4216d915569 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, ggplot2, knitr, rmarkdown +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'The package includes DNA methylation data for the primary Chronic Lymphocytic Leukemia samples included in the Primary Blood Cancer Encyclopedia (PACE) project. Raw data from the 450k DNA methylation arrays is stored in the European Genome-Phenome Archive (EGA) under accession number EGAS0000100174. For more information concerning the project please refer to the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) and R/Bioconductor package BloodCancerMultiOmics2017.' + diff --git a/recipes/bioconductor-cllmethylation/post-link.sh b/recipes/bioconductor-cllmethylation/post-link.sh new file mode 100644 index 0000000000000..0b5a50efe06f0 --- /dev/null +++ b/recipes/bioconductor-cllmethylation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CLLmethylation_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CLLmethylation_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/CLLmethylation_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cllmethylation/bioconductor-cllmethylation_1.2.0_src_all.tar.gz" +) +MD5="cd8a30818dd72030144bd4216d915569" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cllmethylation/pre-unlink.sh b/recipes/bioconductor-cllmethylation/pre-unlink.sh new file mode 100644 index 0000000000000..66b46f8d7c13f --- /dev/null +++ b/recipes/bioconductor-cllmethylation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CLLmethylation diff --git a/recipes/bioconductor-clomial/build.sh b/recipes/bioconductor-clomial/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clomial/build.sh +++ b/recipes/bioconductor-clomial/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clomial/meta.yaml b/recipes/bioconductor-clomial/meta.yaml index 6338f492c1240..76dd96f9489bb 100644 --- a/recipes/bioconductor-clomial/meta.yaml +++ b/recipes/bioconductor-clomial/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Clomial" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 011379922782078d02cb3ead86de0b2d0d1ebd93565a2b5ddcc424a41f6eb0cd + md5: 5df8f10dc7708504ed2aa694c13f55a6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,9 +30,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Clomial fits binomial distributions to counts obtained from Next Gen Sequencing data of multiple samples of the same tumor. The trained parameters can be interpreted to infer the clonal structure of the tumor.' extra: identifiers: - biotools:clomial + parent_recipe: + name: bioconductor-clomial + path: recipes/bioconductor-clomial + version: 1.16.0 + diff --git a/recipes/bioconductor-clonality/build.sh b/recipes/bioconductor-clonality/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clonality/build.sh +++ b/recipes/bioconductor-clonality/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clonality/meta.yaml b/recipes/bioconductor-clonality/meta.yaml index 07411cc14794b..416716e5c38d0 100644 --- a/recipes/bioconductor-clonality/meta.yaml +++ b/recipes/bioconductor-clonality/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Clonality" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e18af28e399c47a7c66649ef4f6555184537a979b5ac5aae365dae5549c95bf5 + md5: aa1dccf7e9baf578b9be782ec99278e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: gdata requirements: host: - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Statistical tests for clonality versus independence of tumors from the same patient based on their LOH or genomewide copy number profiles' extra: identifiers: - biotools:clonality - doi:10.1093/bioinformatics/btr268 + parent_recipe: + name: bioconductor-clonality + path: recipes/bioconductor-clonality + version: 1.28.0 + diff --git a/recipes/bioconductor-clonotyper/build.sh b/recipes/bioconductor-clonotyper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clonotyper/build.sh +++ b/recipes/bioconductor-clonotyper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clonotyper/meta.yaml b/recipes/bioconductor-clonotyper/meta.yaml index f0b4899f601ac..6b1750589a24e 100644 --- a/recipes/bioconductor-clonotyper/meta.yaml +++ b/recipes/bioconductor-clonotyper/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "clonotypeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f4d1afd969aa4b632be5b7ae702e0d55ece6ea2ba38fcf468f04c08e1307de31 + md5: ce60c01fcc6b07e75ad0047f74e308ec build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, edgeR, knitr, pvclust, RUnit, vegan requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'High throughput analysis of T cell antigen receptor sequences The genes encoding T cell receptors are created by somatic recombination, generating an immense combination of V, (D) and J segments. Additional processes during the recombination create extra sequence diversity between the V an J segments. Collectively, this hyper-variable region is called the CDR3 loop. The purpose of this package is to process and quantitatively analyse millions of V-CDR3-J combination, called clonotypes, from multiple sequence libraries.' extra: identifiers: - biotools:clonotyper + parent_recipe: + name: bioconductor-clonotyper + path: recipes/bioconductor-clonotyper + version: 1.18.0 + diff --git a/recipes/bioconductor-clst/build.sh b/recipes/bioconductor-clst/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clst/build.sh +++ b/recipes/bioconductor-clst/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clst/meta.yaml b/recipes/bioconductor-clst/meta.yaml index e7ce5e0a1d3ca..9dc37212eb2b9 100644 --- a/recipes/bioconductor-clst/meta.yaml +++ b/recipes/bioconductor-clst/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "clst" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 632521ce98e86024424a14ddca80ac0959056b40db8419ddc90340a7d31ee25d + md5: 03379c8704e8e7843e96d8feb82ac307 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-lattice run: - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-lattice test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Package for modified nearest-neighbor classification based on calculation of a similarity threshold distinguishing within-group from between-group comparisons.' extra: identifiers: - biotools:clst - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clst + path: recipes/bioconductor-clst + version: 1.28.0 + diff --git a/recipes/bioconductor-clstutils/build.sh b/recipes/bioconductor-clstutils/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clstutils/build.sh +++ b/recipes/bioconductor-clstutils/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clstutils/meta.yaml b/recipes/bioconductor-clstutils/meta.yaml index c2f9616d1c622..c8052498b4dfa 100644 --- a/recipes/bioconductor-clstutils/meta.yaml +++ b/recipes/bioconductor-clstutils/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "clstutils" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 628bc1297b326e4fc0c71280028726dfc1f4e7e921867d6539937d8ca8755136 + md5: e63fa92d5f3812877f3c9904b7530fe7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, RSVGTipsDevice requirements: host: - - 'bioconductor-clst >=1.28.0,<1.30.0' + - 'bioconductor-clst >=1.30.0,<1.31.0' - r-ape - r-base - r-lattice - r-rjson - r-rsqlite run: - - 'bioconductor-clst >=1.28.0,<1.30.0' + - 'bioconductor-clst >=1.30.0,<1.31.0' - r-ape - r-base - r-lattice @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Tools for performing taxonomic assignment based on phylogeny using pplacer and clst.' extra: identifiers: - biotools:clstutils - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clstutils + path: recipes/bioconductor-clstutils + version: 1.28.0 + diff --git a/recipes/bioconductor-clustcomp/build.sh b/recipes/bioconductor-clustcomp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clustcomp/build.sh +++ b/recipes/bioconductor-clustcomp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustcomp/meta.yaml b/recipes/bioconductor-clustcomp/meta.yaml index a2b12bab794df..79e4f867941fb 100644 --- a/recipes/bioconductor-clustcomp/meta.yaml +++ b/recipes/bioconductor-clustcomp/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "clustComp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f5e149b4bc931123d81416f289bb6454817e87648fa43bd2da12473521eaafad + md5: e6750fcee97be0e5706cb50e8d87f610 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, colonCA, RUnit, BiocGenerics requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'clustComp is a package that implements several techniques for the comparison and visualisation of relationships between different clustering results, either flat versus flat or hierarchical versus flat. These relationships among clusters are displayed using a weighted bi-graph, in which the nodes represent the clusters and the edges connect pairs of nodes with non-empty intersection; the weight of each edge is the number of elements in that intersection and is displayed through the edge thickness. The best layout of the bi-graph is provided by the barycentre algorithm, which minimises the weighted number of crossings. In the case of comparing a hierarchical and a non-hierarchical clustering, the dendrogram is pruned at different heights, selected by exploring the tree by depth-first search, starting at the root. Branches are decided to be split according to the value of a scoring function, that can be based either on the aesthetics of the bi-graph or on the mutual information between the hierarchical and the flat clusterings. A mapping between groups of clusters from each side is constructed with a greedy algorithm, and can be additionally visualised.' extra: identifiers: - biotools:clustcomp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clustcomp + path: recipes/bioconductor-clustcomp + version: 1.8.0 + diff --git a/recipes/bioconductor-clusterexperiment/build.sh b/recipes/bioconductor-clusterexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterexperiment/meta.yaml b/recipes/bioconductor-clusterexperiment/meta.yaml new file mode 100644 index 0000000000000..49b215ba80a32 --- /dev/null +++ b/recipes/bioconductor-clusterexperiment/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "2.2.0" %} +{% set name = "clusterExperiment" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d8125f0b838d2d47f45701e1ee5fc54a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, testthat, scRNAseq, MAST, Rtsne, scran, igraph +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.4.0,<1.5.0' + - 'r-ape >=5.0' + - r-base + - r-cluster + - r-dendextend + - r-howmany + - r-kernlab + - r-locfdr + - r-matrixstats + - r-nmf + - r-phylobase + - r-rcolorbrewer + - r-rcpp + - r-rspectra + - r-scales + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zinbwave >=1.4.0,<1.5.0' + - 'r-ape >=5.0' + - r-base + - r-cluster + - r-dendextend + - r-howmany + - r-kernlab + - r-locfdr + - r-matrixstats + - r-nmf + - r-phylobase + - r-rcolorbrewer + - r-rcpp + - r-rspectra + - r-scales + - r-stringr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides functionality for running and comparing many different clusterings of single-cell sequencing data or other large mRNA Expression data sets.' + diff --git a/recipes/bioconductor-clusterjudge/build.sh b/recipes/bioconductor-clusterjudge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterjudge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterjudge/meta.yaml b/recipes/bioconductor-clusterjudge/meta.yaml new file mode 100644 index 0000000000000..1b9e2e200e651 --- /dev/null +++ b/recipes/bioconductor-clusterjudge/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "ClusterJudge" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87cb47cba4bc6d197a97d2e50b814e0c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: yeastExpData, knitr, rmarkdown, devtools, testthat, biomaRt +requirements: + host: + - r-base + - r-httr + - r-infotheo + - r-jsonlite + - r-lattice + - r-latticeextra + run: + - r-base + - r-httr + - r-infotheo + - r-jsonlite + - r-lattice + - r-latticeextra +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'ClusterJudge implements the functions, examples and other software published as an algorithm by Gibbons, FD and Roth FP. The article is called "Judging the Quality of Gene Expression-Based Clustering Methods Using Gene Annotation" and it appeared in Genome Research, vol. 12, pp1574-1581 (2002). See package?ClusterJudge for an overview.' + diff --git a/recipes/bioconductor-clusterprofiler/build.sh b/recipes/bioconductor-clusterprofiler/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clusterprofiler/build.sh +++ b/recipes/bioconductor-clusterprofiler/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterprofiler/meta.yaml b/recipes/bioconductor-clusterprofiler/meta.yaml index ef7f762596ed7..e4192ed7a6ec0 100644 --- a/recipes/bioconductor-clusterprofiler/meta.yaml +++ b/recipes/bioconductor-clusterprofiler/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "3.8.1" %} +{% set version = "3.10.0" %} {% set name = "clusterProfiler" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1583d5fb93df68d8ae3e998138bd01d4287a1753ca0a558832fd9c660bc4a789 + md5: 56aca3fdbd28215e0027ebd27f953e72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: AnnotationHub, GSEABase, KEGG.db, knitr, org.Hs.eg.db, prettydoc, pathview, ReactomePA, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-magrittr @@ -31,12 +33,12 @@ requirements: - r-rvcheck - r-tidyr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-ggplot2 - r-magrittr @@ -47,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.' extra: identifiers: - biotools:clusterprofiler + parent_recipe: + name: bioconductor-clusterprofiler + path: recipes/bioconductor-clusterprofiler + version: 3.8.1 + diff --git a/recipes/bioconductor-clusterseq/build.sh b/recipes/bioconductor-clusterseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-clusterseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterseq/meta.yaml b/recipes/bioconductor-clusterseq/meta.yaml new file mode 100644 index 0000000000000..7116b8433c9a1 --- /dev/null +++ b/recipes/bioconductor-clusterseq/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.6.0" %} +{% set name = "clusterSeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de87aa6662095dfe988eff1c8c2c6bce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Identification of clusters of co-expressed genes based on their expression across multiple (replicated) biological samples.' + diff --git a/recipes/bioconductor-clustersignificance/build.sh b/recipes/bioconductor-clustersignificance/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clustersignificance/build.sh +++ b/recipes/bioconductor-clustersignificance/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clustersignificance/meta.yaml b/recipes/bioconductor-clustersignificance/meta.yaml index 23df69c895170..4c69142fe6d6d 100644 --- a/recipes/bioconductor-clustersignificance/meta.yaml +++ b/recipes/bioconductor-clustersignificance/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "ClusterSignificance" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 54c6d9c4a36ea55066761ceeb6c277e2c8e94e3890a29e97af12cdf68d8793d7 + md5: e9d0e4317b1a056b26796c4158d5b63f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, BiocStyle, ggplot2, plsgenomics, covr requirements: host: - r-base @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ClusterSignificance package provides tools to assess if class clusters in dimensionality reduced data representations have a separation different from permuted data. The term class clusters here refers to, clusters of points representing known classes in the data. This is particularly useful to determine if a subset of the variables, e.g. genes in a specific pathway, alone can separate samples into these established classes. ClusterSignificance accomplishes this by, projecting all points onto a one dimensional line. Cluster separations are then scored and the probability of the seen separation being due to chance is evaluated using a permutation method.' extra: identifiers: - biotools:clustersignificance - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clustersignificance + path: recipes/bioconductor-clustersignificance + version: 1.8.2 + diff --git a/recipes/bioconductor-clusterstab/build.sh b/recipes/bioconductor-clusterstab/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-clusterstab/build.sh +++ b/recipes/bioconductor-clusterstab/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-clusterstab/meta.yaml b/recipes/bioconductor-clusterstab/meta.yaml index 396aced2ff824..2cd1469300114 100644 --- a/recipes/bioconductor-clusterstab/meta.yaml +++ b/recipes/bioconductor-clusterstab/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "clusterStab" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 503836113b24f67107e42d1f9b05be501267f6f93edc8d75a377ffbb21e67528 + md5: 13e2412428edb769e74ebf828778f9e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: fibroEset, genefilter requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can be used to estimate the number of clusters in a set of microarray data, as well as test the stability of these clusters.' extra: identifiers: - biotools:clusterstab - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-clusterstab + path: recipes/bioconductor-clusterstab + version: 1.52.0 + diff --git a/recipes/bioconductor-cma/build.sh b/recipes/bioconductor-cma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cma/build.sh +++ b/recipes/bioconductor-cma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cma/meta.yaml b/recipes/bioconductor-cma/meta.yaml index 7dc01d2803e9f..985b9ed400636 100644 --- a/recipes/bioconductor-cma/meta.yaml +++ b/recipes/bioconductor-cma/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "CMA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 30cb1696be1ec077327992d7127cb08097be00ade8d3229205af383aafd73272 + md5: ae7cd551d9e6cf48713f81726e421044 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MASS, class, nnet, glmnet, e1071, randomForest, plsgenomics, gbm, mgcv, corpcor, limma, st, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides a comprehensive collection of various microarray-based classification algorithms both from Machine Learning and Statistics. Variable Selection, Hyperparameter tuning, Evaluation and Comparison can be performed combined or stepwise in a user-friendly environment.' extra: identifiers: - biotools:cma - doi:10.1186/1471-2105-9-439 + parent_recipe: + name: bioconductor-cma + path: recipes/bioconductor-cma + version: 1.38.0 + diff --git a/recipes/bioconductor-cmap/meta.yaml b/recipes/bioconductor-cmap/meta.yaml index 44b824176dcb4..bf2c78f959e64 100644 --- a/recipes/bioconductor-cmap/meta.yaml +++ b/recipes/bioconductor-cmap/meta.yaml @@ -1,21 +1,22 @@ {% set version = "1.15.1" %} {% set name = "cMAP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3bf24aca1ce63ebff4ac0172467ecd8acbb0c1f8a240cd0f8b8abd7c44fdf15f + md5: dbf8df4d4540151936884e1c5d747bcf build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: LGPL summary: 'Annotation data file for cMAP assembled using data from public data repositories' - +extra: + parent_recipe: + name: bioconductor-cmap + path: recipes/bioconductor-cmap + version: 1.15.1 diff --git a/recipes/bioconductor-cmap/post-link.sh b/recipes/bioconductor-cmap/post-link.sh index 4c76f2a85875d..171ddc53d512b 100644 --- a/recipes/bioconductor-cmap/post-link.sh +++ b/recipes/bioconductor-cmap/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="cMAP_1.15.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cMAP_1.15.1.tar.gz" "https://bioarchive.galaxyproject.org/cMAP_1.15.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-cmap/bioconductor-cmap_1.15.1_src_all.tar.gz" diff --git a/recipes/bioconductor-cmap2data/meta.yaml b/recipes/bioconductor-cmap2data/meta.yaml index bc5ae3c2da5cc..5631f39bc3e24 100644 --- a/recipes/bioconductor-cmap2data/meta.yaml +++ b/recipes/bioconductor-cmap2data/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "cMap2data" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4158c38925a807da44c0c3aaee568f39d64d1647589d1455fd06234cfaf3c05a + md5: 174f2e6265ede0b5e9163d7557f9e608 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data package which provides default drug profiles for the DrugVsDisease package as well as associated gene lists and data clusters used by the DrugVsDisease package.' - +extra: + parent_recipe: + name: bioconductor-cmap2data + path: recipes/bioconductor-cmap2data + version: 1.16.0 diff --git a/recipes/bioconductor-cmap2data/post-link.sh b/recipes/bioconductor-cmap2data/post-link.sh index f7b1a1e98a746..87f4f0cb57f30 100644 --- a/recipes/bioconductor-cmap2data/post-link.sh +++ b/recipes/bioconductor-cmap2data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="cMap2data_1.16.0.tar.gz" +FN="cMap2data_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/cMap2data_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/cMap2data_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cMap2data_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/cMap2data_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cmap2data/bioconductor-cmap2data_1.18.0_src_all.tar.gz" ) -MD5="07ed9ef43caf12a0f4250f7c6e2848ff" +MD5="174f2e6265ede0b5e9163d7557f9e608" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-cn.farms/build.sh b/recipes/bioconductor-cn.farms/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cn.farms/build.sh +++ b/recipes/bioconductor-cn.farms/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cn.farms/conda_build_config.yaml b/recipes/bioconductor-cn.farms/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-cn.farms/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-cn.farms/meta.yaml b/recipes/bioconductor-cn.farms/meta.yaml index f979c43c8c3ab..12c853ac590e0 100644 --- a/recipes/bioconductor-cn.farms/meta.yaml +++ b/recipes/bioconductor-cn.farms/meta.yaml @@ -1,41 +1,42 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "cn.farms" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ec995fc0d1a2cdd177db01916ab9a161b3fd8e08dcbe967313b58addfe022d7d + md5: 0182f9e0aa8c1ab548b761a264cf0926 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: pd.mapping250k.sty, pd.mapping250k.nsp, pd.genomewidesnp.5, pd.genomewidesnp.6 requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-ff - r-lattice - r-snow run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-ff @@ -49,10 +50,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package implements the cn.FARMS algorithm for copy number variation (CNV) analysis. cn.FARMS allows to analyze the most common Affymetrix (250K-SNP6.0) array types, supports high-performance computing using snow and ff.' extra: identifiers: - biotools:cn.farms - doi:10.1093/nar/gkr197 + parent_recipe: + name: bioconductor-cn.farms + path: recipes/bioconductor-cn.farms + version: 1.28.0 + diff --git a/recipes/bioconductor-cn.mops/build.sh b/recipes/bioconductor-cn.mops/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cn.mops/build.sh +++ b/recipes/bioconductor-cn.mops/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cn.mops/meta.yaml b/recipes/bioconductor-cn.mops/meta.yaml index 5166cb6d90c14..8dad2803eb29d 100644 --- a/recipes/bioconductor-cn.mops/meta.yaml +++ b/recipes/bioconductor-cn.mops/meta.yaml @@ -1,41 +1,42 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "cn.mops" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b9b0be3df2a0ebe6f77d2bfd6087b8f1fd03dc0327ea5e7066a97e64dca68cf5 + md5: c6736a533b5a4a5832b974bf0f33389b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: DNAcopy requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base build: - {{ compiler('c') }} @@ -45,9 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'cn.mops (Copy Number estimation by a Mixture Of PoissonS) is a data processing pipeline for copy number variations and aberrations (CNVs and CNAs) from next generation sequencing (NGS) data. The package supplies functions to convert BAM files into read count matrices or genomic ranges objects, which are the input objects for cn.mops. cn.mops models the depths of coverage across samples at each genomic position. Therefore, it does not suffer from read count biases along chromosomes. Using a Bayesian approach, cn.mops decomposes read variations across samples into integer copy numbers and noise by its mixture components and Poisson distributions, respectively. cn.mops guarantees a low FDR because wrong detections are indicated by high noise and filtered out. cn.mops is very fast and written in C++.' extra: identifiers: - biotools:cn.mops + parent_recipe: + name: bioconductor-cn.mops + path: recipes/bioconductor-cn.mops + version: 1.26.0 + diff --git a/recipes/bioconductor-cnanorm/build.sh b/recipes/bioconductor-cnanorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnanorm/build.sh +++ b/recipes/bioconductor-cnanorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnanorm/meta.yaml b/recipes/bioconductor-cnanorm/meta.yaml index f89c4ee933323..a837b4902f344 100644 --- a/recipes/bioconductor-cnanorm/meta.yaml +++ b/recipes/bioconductor-cnanorm/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "CNAnorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7be2b7579a6a3885bc1c01f287c43c4669235407827ec3576cbcb3e7430bdfe + md5: edd5ffe29a6af7360a99b61e85ae5292 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' - r-base build: - {{ compiler('c') }} @@ -31,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Performs ratio, GC content correction and normalization of data obtained using low coverage (one read every 100-10,000 bp) high troughput sequencing. It performs a "discrete" normalization looking for the ploidy of the genome. It will also provide tumour content if at least two ploidy states can be found.' extra: identifiers: - biotools:cnanorm + parent_recipe: + name: bioconductor-cnanorm + path: recipes/bioconductor-cnanorm + version: 1.26.0 + diff --git a/recipes/bioconductor-cner/build.sh b/recipes/bioconductor-cner/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cner/build.sh +++ b/recipes/bioconductor-cner/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cner/meta.yaml b/recipes/bioconductor-cner/meta.yaml index 30cc28e7d2160..0aa2e0f79d51c 100644 --- a/recipes/bioconductor-cner/meta.yaml +++ b/recipes/bioconductor-cner/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.1" %} {% set name = "CNEr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 431f04c9915af270b60e628737c53a0b3550d23c214f09eba6f172b456cbc425 + md5: d14b070544db2a224af7ddacd34e24ad build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Gviz (>= 1.7.4), BiocStyle, knitr, rmarkdown, testthat, BSgenome.Drerio.UCSC.danRer10, BSgenome.Hsapiens.UCSC.hg38, TxDb.Drerio.UCSC.danRer10.refGene, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Ggallus.UCSC.galGal3 requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -39,18 +40,18 @@ requirements: - 'r-reshape2 >=1.4.1' - 'r-rsqlite >=0.11.4' run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-dbi >=0.7' - 'r-ggplot2 >=2.1.0' @@ -66,10 +67,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | file LICENSE' summary: 'Large-scale identification and advanced visualization of sets of conserved noncoding elements.' extra: identifiers: - biotools:cner - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cner + path: recipes/bioconductor-cner + version: 1.16.1 + diff --git a/recipes/bioconductor-cnordt/build.sh b/recipes/bioconductor-cnordt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cnordt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnordt/meta.yaml b/recipes/bioconductor-cnordt/meta.yaml new file mode 100644 index 0000000000000..3e5d512c05069 --- /dev/null +++ b/recipes/bioconductor-cnordt/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.24.0" %} +{% set name = "CNORdt" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f4408254e7c371770f9212526209a36 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - r-abind + - r-base + run: + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - r-abind + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This add-on to the package CellNOptR handles time-course data, as opposed to steady state data in CellNOptR. It scales the simulation step to allow comparison and model fitting for time-course data. Future versions will optimize delays and strengths for each edge.' + diff --git a/recipes/bioconductor-cnorfeeder/build.sh b/recipes/bioconductor-cnorfeeder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cnorfeeder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnorfeeder/meta.yaml b/recipes/bioconductor-cnorfeeder/meta.yaml new file mode 100644 index 0000000000000..d0b066d9fa379 --- /dev/null +++ b/recipes/bioconductor-cnorfeeder/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "CNORfeeder" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d939f756f949292243ea621b99d9cf69 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: minet, catnet, Rgraphviz, RUnit, BiocGenerics, igraph +requirements: + host: + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package integrates literature-constrained and data-driven methods to infer signalling networks from perturbation experiments. It permits to extends a given network with links derived from the data via various inference methods and uses information on physical interactions of proteins to guide and validate the integration of links.' + diff --git a/recipes/bioconductor-cnorfuzzy/build.sh b/recipes/bioconductor-cnorfuzzy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnorfuzzy/build.sh +++ b/recipes/bioconductor-cnorfuzzy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnorfuzzy/meta.yaml b/recipes/bioconductor-cnorfuzzy/meta.yaml index d1f1ce716354c..f51a9c51f732b 100644 --- a/recipes/bioconductor-cnorfuzzy/meta.yaml +++ b/recipes/bioconductor-cnorfuzzy/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CNORfuzzy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a8fe42cbf825457625445bfaad7586b9757b98c1faa44016a34d4033e4c7a735 + md5: a81e01df30c7acdb9a966953fa009109 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: xtable, Rgraphviz, RUnit, BiocGenerics requirements: host: - - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - r-base - 'r-nloptr >=0.8.5' run: - - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - r-base - 'r-nloptr >=0.8.5' build: @@ -32,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package is an extension to CellNOptR. It contains additional functionality needed to simulate and train a prior knowledge network to experimental data using constrained fuzzy logic (cFL, rather than Boolean logic as is the case in CellNOptR). Additionally, this package will contain functions to use for the compilation of multiple optimization results (either Boolean or cFL).' extra: identifiers: - biotools:cnorfuzzy - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cnorfuzzy + path: recipes/bioconductor-cnorfuzzy + version: 1.22.0 + diff --git a/recipes/bioconductor-cnorode/build.sh b/recipes/bioconductor-cnorode/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnorode/build.sh +++ b/recipes/bioconductor-cnorode/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnorode/meta.yaml b/recipes/bioconductor-cnorode/meta.yaml index b05e515831b16..df3828e5ec538 100644 --- a/recipes/bioconductor-cnorode/meta.yaml +++ b/recipes/bioconductor-cnorode/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "CNORode" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c7b64bbe51cc9ad24a4eaceb1e12ff459817da059abaec683f60d16a50db016d + md5: f3ea74252b1ad73d7342f763e5ad55be build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - r-base - r-genalg run: - - 'bioconductor-cellnoptr >=1.26.0,<1.28.0' + - 'bioconductor-cellnoptr >=1.28.0,<1.29.0' - r-base - r-genalg build: @@ -32,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'ODE add-on to CellNOptR' extra: identifiers: - biotools:cnorode - doi:10.1186/1752-0509-6-133 + parent_recipe: + name: bioconductor-cnorode + path: recipes/bioconductor-cnorode + version: 1.22.0 + diff --git a/recipes/bioconductor-cnpbayes/build.sh b/recipes/bioconductor-cnpbayes/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cnpbayes/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnpbayes/meta.yaml b/recipes/bioconductor-cnpbayes/meta.yaml new file mode 100644 index 0000000000000..727d7223e3a7c --- /dev/null +++ b/recipes/bioconductor-cnpbayes/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.12.0" %} +{% set name = "CNPBayes" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b9231a3d34f0e502f273043d299f125d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, BiocStyle, rmarkdown, BiocCheck, MASS, VanillaICE, tidyverse +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coda + - r-combinat + - r-dplyr + - r-ggplot2 + - r-gtools + - r-magrittr + - r-matrixstats + - r-mclust + - r-purrr + - r-rcolorbrewer + - 'r-rcpp >=0.12.1' + - r-reshape2 + - r-scales + - r-tibble + - r-tidyr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coda + - r-combinat + - r-dplyr + - r-ggplot2 + - r-gtools + - r-magrittr + - r-matrixstats + - r-mclust + - r-purrr + - r-rcolorbrewer + - 'r-rcpp >=0.12.1' + - r-reshape2 + - r-scales + - r-tibble + - r-tidyr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Bayesian hierarchical mixture models for batch effects and copy number.' + diff --git a/recipes/bioconductor-cntools/build.sh b/recipes/bioconductor-cntools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cntools/build.sh +++ b/recipes/bioconductor-cntools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cntools/meta.yaml b/recipes/bioconductor-cntools/meta.yaml index 0d0048d00d995..927653b7bbcef 100644 --- a/recipes/bioconductor-cntools/meta.yaml +++ b/recipes/bioconductor-cntools/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "CNTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8b22ddb405bec464ede7b63cce655ddf4de3d93260de91b8ebb1a7a711e24375 + md5: 0a41c86ddaddf77e73f344fe7fa3c915 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides tools to convert the output of segmentation analysis using DNAcopy to a matrix structure with overlapping segments as rows and samples as columns so that other computational analyses can be applied to segmented data' extra: identifiers: - biotools:cntools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cntools + path: recipes/bioconductor-cntools + version: 1.36.0 + diff --git a/recipes/bioconductor-cnvgsa/build.sh b/recipes/bioconductor-cnvgsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnvgsa/build.sh +++ b/recipes/bioconductor-cnvgsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvgsa/meta.yaml b/recipes/bioconductor-cnvgsa/meta.yaml index ae882721e81f3..04b3b88565924 100644 --- a/recipes/bioconductor-cnvgsa/meta.yaml +++ b/recipes/bioconductor-cnvgsa/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "cnvGSA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6236cc65e337f5d84ef3f52b511b28ba0522f9261fdcb7c1521dcd35275cc5ec + md5: f178bf3793415071fcb3504af847f843 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: cnvGSAdata, org.Hs.eg.db requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-brglm - r-doparallel - r-foreach - r-splitstackshape run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-brglm - r-doparallel @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package is intended to facilitate gene-set association with rare CNVs in case-control studies.' extra: identifiers: - biotools:cnvgsa - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cnvgsa + path: recipes/bioconductor-cnvgsa + version: 1.24.0 + diff --git a/recipes/bioconductor-cnvgsadata/meta.yaml b/recipes/bioconductor-cnvgsadata/meta.yaml new file mode 100644 index 0000000000000..32edd34854046 --- /dev/null +++ b/recipes/bioconductor-cnvgsadata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "cnvGSAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9068308f3e9af11c862659158fc77687 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-cnvgsa >=1.26.0,<1.27.0' + - r-base + run: + - 'bioconductor-cnvgsa >=1.26.0,<1.27.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package contains the data used in the vignette of the cnvGSA package.' + diff --git a/recipes/bioconductor-cnvgsadata/post-link.sh b/recipes/bioconductor-cnvgsadata/post-link.sh new file mode 100644 index 0000000000000..6acc2ba8baecb --- /dev/null +++ b/recipes/bioconductor-cnvgsadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cnvGSAdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/cnvGSAdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/cnvGSAdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cnvgsadata/bioconductor-cnvgsadata_1.18.0_src_all.tar.gz" +) +MD5="9068308f3e9af11c862659158fc77687" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cnvgsadata/pre-unlink.sh b/recipes/bioconductor-cnvgsadata/pre-unlink.sh new file mode 100644 index 0000000000000..6cb998ec091e6 --- /dev/null +++ b/recipes/bioconductor-cnvgsadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cnvGSAdata diff --git a/recipes/bioconductor-cnvpanelizer/build.sh b/recipes/bioconductor-cnvpanelizer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnvpanelizer/build.sh +++ b/recipes/bioconductor-cnvpanelizer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvpanelizer/meta.yaml b/recipes/bioconductor-cnvpanelizer/meta.yaml index 5e41d7ea4e44a..24139a6ce3790 100644 --- a/recipes/bioconductor-cnvpanelizer/meta.yaml +++ b/recipes/bioconductor-cnvpanelizer/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CNVPanelizer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 36dd57265e65fae10b9339cd9671d60bcf148d96508dbbff8e9af41e2ce3d5cf + md5: 98e25515072bab932fb127f75cbfe980 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-noiseq >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-foreach - r-ggplot2 @@ -38,13 +40,13 @@ requirements: - r-stringr - r-testthat run: - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-noiseq >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-foreach - r-ggplot2 @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A method that allows for the use of a collection of non-matched normal tissue samples. Our approach uses a non-parametric bootstrap subsampling of the available reference samples to estimate the distribution of read counts from targeted sequencing. As inspired by random forest, this is combined with a procedure that subsamples the amplicons associated with each of the targeted genes. The obtained information allows us to reliably classify the copy number aberrations on the gene level.' extra: identifiers: - biotools:cnvpanelizer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cnvpanelizer + path: recipes/bioconductor-cnvpanelizer + version: 1.12.0 + diff --git a/recipes/bioconductor-cnvrd2/build.sh b/recipes/bioconductor-cnvrd2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cnvrd2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvrd2/meta.yaml b/recipes/bioconductor-cnvrd2/meta.yaml new file mode 100644 index 0000000000000..810421d5750c4 --- /dev/null +++ b/recipes/bioconductor-cnvrd2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.20.0" %} +{% set name = "CNVrd2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 43748a826e927c6f6c8a24789b709688 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-rjags + run: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-rjags +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'CNVrd2 uses next-generation sequencing data to measure human gene copy number for multiple samples, indentify SNPs tagging copy number variants and detect copy number polymorphic genomic regions.' + diff --git a/recipes/bioconductor-cnvtools/build.sh b/recipes/bioconductor-cnvtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cnvtools/build.sh +++ b/recipes/bioconductor-cnvtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cnvtools/meta.yaml b/recipes/bioconductor-cnvtools/meta.yaml index 037b2a1a1856a..5b048d3137f22 100644 --- a/recipes/bioconductor-cnvtools/meta.yaml +++ b/recipes/bioconductor-cnvtools/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.74.0" %} +{% set version = "1.76.0" %} {% set name = "CNVtools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d129df72861ec507dd4670fe8596b1378d4eba83631c1626fe354d3e24f2babc + md5: 8c7a391861a596b79dec372a8ed5fd92 build: number: 0 rpaths: @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is meant to facilitate the testing of Copy Number Variant data for genetic association, typically in case-control studies.' extra: identifiers: - biotools:cnvtools - doi:10.1038/ng.206 + parent_recipe: + name: bioconductor-cnvtools + path: recipes/bioconductor-cnvtools + version: 1.74.0 + diff --git a/recipes/bioconductor-cobindr/build.sh b/recipes/bioconductor-cobindr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cobindr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cobindr/meta.yaml b/recipes/bioconductor-cobindr/meta.yaml new file mode 100644 index 0000000000000..3ddc50d9510d2 --- /dev/null +++ b/recipes/bioconductor-cobindr/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.20.0" %} +{% set name = "cobindR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a311dfeeec28c8f77c993ace8a77b5c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-gmp + - r-gplots + - r-mclust + - r-rtfbs + - r-seqinr + - r-yaml + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-gmp + - r-gplots + - r-mclust + - r-rtfbs + - r-seqinr + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Finding and analysing co-occuring motifs of transcription factor binding sites in groups of genes' + diff --git a/recipes/bioconductor-cocitestats/build.sh b/recipes/bioconductor-cocitestats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cocitestats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cocitestats/meta.yaml b/recipes/bioconductor-cocitestats/meta.yaml new file mode 100644 index 0000000000000..859af5949fbe8 --- /dev/null +++ b/recipes/bioconductor-cocitestats/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.54.0" %} +{% set name = "CoCiteStats" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 631d2c987e3945ab37065b400165fd2f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: CPL + summary: 'A collection of software tools for dealing with co-citation data.' + diff --git a/recipes/bioconductor-cocoa/build.sh b/recipes/bioconductor-cocoa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cocoa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cocoa/meta.yaml b/recipes/bioconductor-cocoa/meta.yaml new file mode 100644 index 0000000000000..519c81e7f8199 --- /dev/null +++ b/recipes/bioconductor-cocoa/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.1" %} +{% set name = "COCOA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4daa8635624853e5bd208d15853d55d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mira >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-ggplot2 + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mira >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-ggplot2 + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'COCOA is a method for understanding variation among samples and can be used with data that includes genomic coordinates such as DNA methylation. On a high level, COCOA uses a database of "region sets" and principal component analysis (PCA) of your data to identify sources of variation among samples. A region set is a set of genomic regions that share a biological annotation, for instance, transcription factor binding regions, histone modification regions, or open chromatin regions. COCOA works in both supervised (known groups of samples) and unsupervised (no groups) situations and can be used as a complement to "differential" methods that find discrete differences between groups. COCOA can identify biologically meaningful sources of variation between samples and increase understanding of variation in your data.' + diff --git a/recipes/bioconductor-codelink/build.sh b/recipes/bioconductor-codelink/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-codelink/build.sh +++ b/recipes/bioconductor-codelink/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-codelink/meta.yaml b/recipes/bioconductor-codelink/meta.yaml index 7623bbcc4fc07..fcc8e141e3b47 100644 --- a/recipes/bioconductor-codelink/meta.yaml +++ b/recipes/bioconductor-codelink/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "codelink" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3455f089ce1063d6882a766752ee007a7e062082c77003155393073342338a4c + md5: 581f0dafd469d47a78e5c59c019d20fc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: genefilter, parallel, knitr requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package facilitates reading, preprocessing and manipulating Codelink microarray data. The raw data must be exported as text file using the Codelink software.' extra: identifiers: - biotools:codelink + parent_recipe: + name: bioconductor-codelink + path: recipes/bioconductor-codelink + version: 1.48.0 + diff --git a/recipes/bioconductor-codex/build.sh b/recipes/bioconductor-codex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-codex/build.sh +++ b/recipes/bioconductor-codex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-codex/meta.yaml b/recipes/bioconductor-codex/meta.yaml index d243dd27f1573..c66e3258865d9 100644 --- a/recipes/bioconductor-codex/meta.yaml +++ b/recipes/bioconductor-codex/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CODEX" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: facca69dfd7a7bf32333eab374c82dac6178da13408a19cfcbc3dd0a0c02c65b + md5: d25cc0d3a2df50fff53a274b3d634724 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: WES.1KG.WUGSC requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A normalization and copy number variation calling procedure for whole exome DNA sequencing data. CODEX relies on the availability of multiple samples processed using the same sequencing pipeline for normalization, and does not require matched controls. The normalization model in CODEX includes terms that specifically remove biases due to GC content, exon length and targeting and amplification efficiency, and latent systemic artifacts. CODEX also includes a Poisson likelihood-based recursive segmentation procedure that explicitly models the count-based exome sequencing data.' extra: identifiers: - biotools:codex - doi:10.1093/nar/gku1363 + parent_recipe: + name: bioconductor-codex + path: recipes/bioconductor-codex + version: 1.12.0 + diff --git a/recipes/bioconductor-coexnet/build.sh b/recipes/bioconductor-coexnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coexnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coexnet/meta.yaml b/recipes/bioconductor-coexnet/meta.yaml new file mode 100644 index 0000000000000..a1d2870e66a35 --- /dev/null +++ b/recipes/bioconductor-coexnet/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.4.0" %} +{% set name = "coexnet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9d8e6b5ab48da4a1ca2db90f2160c94f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +requirements: + host: + - 'bioconductor-acde >=1.12.0,<1.13.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-igraph + - r-rmarkdown + run: + - 'bioconductor-acde >=1.12.0,<1.13.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-igraph + - r-rmarkdown +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'Extracts the gene expression matrix from GEO DataSets (.CEL files) as a AffyBatch object. Additionally, can make the normalization process using two different methods (vsn and rma). The summarization (pass from multi-probe to one gene) uses two different criteria (Maximum value and Median of the samples expression data) and the process of gene differentially expressed analisys using two methods (sam and acde). The construction of the co-expression network can be conduced using two different methods, Pearson Correlation Coefficient (PCC) or Mutual Information (MI) and choosing a threshold value using a graph theory approach.' + diff --git a/recipes/bioconductor-cogaps/build.sh b/recipes/bioconductor-cogaps/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cogaps/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cogaps/meta.yaml b/recipes/bioconductor-cogaps/meta.yaml new file mode 100644 index 0000000000000..06a7ee5cafc7a --- /dev/null +++ b/recipes/bioconductor-cogaps/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "3.2.1" %} +{% set name = "CoGAPS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fe3ec2e7eb8cb5fb23894fd27bf856df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bh + - r-cluster + - r-data.table + - r-gplots + - r-rcolorbrewer + - r-rcpp + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bh + - r-cluster + - r-data.table + - r-gplots + - r-rcolorbrewer + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (==2)' + summary: 'Coordinated Gene Activity in Pattern Sets (CoGAPS) implements a Bayesian MCMC matrix factorization algorithm, GAPS, and links it to gene set statistic methods to infer biological process activity. It can be used to perform sparse matrix factorization on any data, and when this data represents biomolecules, to do gene set analysis.' + diff --git a/recipes/bioconductor-cogena/build.sh b/recipes/bioconductor-cogena/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cogena/build.sh +++ b/recipes/bioconductor-cogena/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cogena/meta.yaml b/recipes/bioconductor-cogena/meta.yaml index 0c42794065a59..9cb7d778b7abf 100644 --- a/recipes/bioconductor-cogena/meta.yaml +++ b/recipes/bioconductor-cogena/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "cogena" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: eb1d08e4601eef63e125212b63a93ecf156ff2bc4298056f407aabc212e60534 + md5: e2c7d73b261ab79838296c26f8b38878 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-amap - r-apcluster - r-base @@ -37,7 +39,7 @@ requirements: - r-mclust - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-amap - r-apcluster - r-base @@ -59,10 +61,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'cogena is a workflow for co-expressed gene-set enrichment analysis. It aims to discovery smaller scale, but highly correlated cellular events that may be of great biological relevance. A novel pipeline for drug discovery and drug repositioning based on the cogena workflow is proposed. Particularly, candidate drugs can be predicted based on the gene expression of disease-related data, or other similar drugs can be identified based on the gene expression of drug-related data. Moreover, the drug mode of action can be disclosed by the associated pathway analysis. In summary, cogena is a flexible workflow for various gene set enrichment analysis for co-expressed genes, with a focus on pathway/GO analysis and drug repositioning.' extra: identifiers: - biotools:cogena - doi:10.1186/s12864-016-2737-8 + parent_recipe: + name: bioconductor-cogena + path: recipes/bioconductor-cogena + version: 1.14.0 + diff --git a/recipes/bioconductor-cogps/build.sh b/recipes/bioconductor-cogps/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cogps/build.sh +++ b/recipes/bioconductor-cogps/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cogps/meta.yaml b/recipes/bioconductor-cogps/meta.yaml index 7ea1346b245cd..f3e1d372d58b7 100644 --- a/recipes/bioconductor-cogps/meta.yaml +++ b/recipes/bioconductor-cogps/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "coGPS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5f558092a19cbbc6ec45da9be8a691615b7e73a4fb100caa8b0419fbcbba7c16 + md5: e471e9f7a0a57988cbe0729d35712e77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Gene Set Enrichment Analysis of P-value based statistics for outlier gene detection in dataset merged from multiple studies' extra: identifiers: - biotools:cogps - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cogps + path: recipes/bioconductor-cogps + version: 1.24.0 + diff --git a/recipes/bioconductor-cohcap/build.sh b/recipes/bioconductor-cohcap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cohcap/build.sh +++ b/recipes/bioconductor-cohcap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cohcap/meta.yaml b/recipes/bioconductor-cohcap/meta.yaml index fb4cf9b923726..ebc68854ce81b 100644 --- a/recipes/bioconductor-cohcap/meta.yaml +++ b/recipes/bioconductor-cohcap/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.1" %} {% set name = "COHCAP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3d6ceaf99409025c1483957c229e42c149bc9e6f41d8618e928667038ab2cdf5 + md5: a00f1b04b6e4a464ab245bf79ebbb764 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# SystemRequirements: Perl requirements: host: - - 'bioconductor-cohcapanno >=1.16.0,<1.18.0' + - 'bioconductor-cohcapanno >=1.18.0,<1.19.0' - r-base - r-bh - r-gplots @@ -27,7 +28,7 @@ requirements: - r-rcpparmadillo - r-writexls run: - - 'bioconductor-cohcapanno >=1.16.0,<1.18.0' + - 'bioconductor-cohcapanno >=1.18.0,<1.19.0' - r-base - r-bh - r-gplots @@ -43,9 +44,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options.' + summary: 'This package provides a pipeline to analyze single-nucleotide resolution methylation data (Illumina 450k/EPIC methylation array, targeted BS-Seq, etc.). It provides differential methylation for CpG Sites, differential methylation for CpG Islands, integration with gene expression data, with visualizaton options. Discussion Group: https://sourceforge.net/p/cohcap/discussion/bioconductor/' extra: identifiers: - biotools:cohcap + parent_recipe: + name: bioconductor-cohcap + path: recipes/bioconductor-cohcap + version: 1.26.0 + diff --git a/recipes/bioconductor-cohcapanno/meta.yaml b/recipes/bioconductor-cohcapanno/meta.yaml index 951aadb003e70..94127de537585 100644 --- a/recipes/bioconductor-cohcapanno/meta.yaml +++ b/recipes/bioconductor-cohcapanno/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "COHCAPanno" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d5a74932f43dba6f89346f3e490642911d3fa4d9e885af76fb99b8d1d3b27e22 + md5: b68214a25ae7726c488dd5893cf6417a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Provides genomic location, nearby CpG island and nearby gene information for common Illumina methylation array platforms' - +extra: + parent_recipe: + name: bioconductor-cohcapanno + path: recipes/bioconductor-cohcapanno + version: 1.16.0 diff --git a/recipes/bioconductor-cohcapanno/post-link.sh b/recipes/bioconductor-cohcapanno/post-link.sh index 47ca84f9d718b..d69ac98cef541 100644 --- a/recipes/bioconductor-cohcapanno/post-link.sh +++ b/recipes/bioconductor-cohcapanno/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="COHCAPanno_1.16.0.tar.gz" +FN="COHCAPanno_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/COHCAPanno_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/COHCAPanno_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COHCAPanno_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/COHCAPanno_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cohcapanno/bioconductor-cohcapanno_1.18.0_src_all.tar.gz" ) -MD5="9b88358fffd88f0ff80cd3892e4d3604" +MD5="b68214a25ae7726c488dd5893cf6417a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-colonca/meta.yaml b/recipes/bioconductor-colonca/meta.yaml new file mode 100644 index 0000000000000..3baabfc07215f --- /dev/null +++ b/recipes/bioconductor-colonca/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "colonCA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 60d8c68d5e87c89a3fb08e63169e3ab0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'exprSet for Alon et al. (1999) colon cancer data' + diff --git a/recipes/bioconductor-colonca/post-link.sh b/recipes/bioconductor-colonca/post-link.sh new file mode 100644 index 0000000000000..3d43078230712 --- /dev/null +++ b/recipes/bioconductor-colonca/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="colonCA_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/colonCA_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/colonCA_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-colonca/bioconductor-colonca_1.24.0_src_all.tar.gz" +) +MD5="60d8c68d5e87c89a3fb08e63169e3ab0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-colonca/pre-unlink.sh b/recipes/bioconductor-colonca/pre-unlink.sh new file mode 100644 index 0000000000000..320e576236b94 --- /dev/null +++ b/recipes/bioconductor-colonca/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ colonCA diff --git a/recipes/bioconductor-comet/build.sh b/recipes/bioconductor-comet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-comet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-comet/meta.yaml b/recipes/bioconductor-comet/meta.yaml new file mode 100644 index 0000000000000..95c65d35f9597 --- /dev/null +++ b/recipes/bioconductor-comet/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.14.0" %} +{% set name = "coMET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 47824d638de57c2c0bc0c22a624fb0f2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-colortools + - r-corrplot + - r-gridextra + - r-hash + - r-psych + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-colortools + - r-corrplot + - r-gridextra + - r-hash + - r-psych +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Visualisation of EWAS results in a genomic region. In addition to phenotype-association P-values, coMET also generates plots of co-methylation patterns and provides a series of annotation tracks. It can be used to other omic-wide association scans as long as the data can be translated to genomic level and for any species.' + diff --git a/recipes/bioconductor-compartmap/build.sh b/recipes/bioconductor-compartmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-compartmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compartmap/meta.yaml b/recipes/bioconductor-compartmap/meta.yaml new file mode 100644 index 0000000000000..6ffcafe1d519a --- /dev/null +++ b/recipes/bioconductor-compartmap/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.2" %} +{% set name = "compartmap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 232abc83b25db9468001591dabba0f76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: covr, testthat, knitr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-mixomics >=6.6.0,<6.7.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gtools + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-mixomics >=6.6.0,<6.7.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Compartmap performs shrunken A/B compartment inference from ATAC-seq and methylation arrays.' + diff --git a/recipes/bioconductor-compass/build.sh b/recipes/bioconductor-compass/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-compass/build.sh +++ b/recipes/bioconductor-compass/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compass/meta.yaml b/recipes/bioconductor-compass/meta.yaml index ec454ae0f7efa..a59e94cd5f02d 100644 --- a/recipes/bioconductor-compass/meta.yaml +++ b/recipes/bioconductor-compass/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "COMPASS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: be92660b167bf8c89d6091e3e5b5cdc25a4d9e6d4881a7799a986504543a4da0 + md5: c3b0cc2a1dd6dceb06b05441ed1bf818 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: flowWorkspace (>= 3.9.66), flowCore, ncdfFlow, shiny, testthat, devtools, flowWorkspaceData requirements: host: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - r-abind - r-base - r-clue @@ -36,7 +37,7 @@ requirements: - r-scales - r-tidyr run: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' - r-abind - r-base - r-clue @@ -61,10 +62,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'COMPASS is a statistical framework that enables unbiased analysis of antigen-specific T-cell subsets. COMPASS uses a Bayesian hierarchical framework to model all observed cell-subsets and select the most likely to be antigen-specific while regularizing the small cell counts that often arise in multi-parameter space. The model provides a posterior probability of specificity for each cell subset and each sample, which can be used to profile a subject''s immune response to external stimuli such as infection or vaccination.' extra: identifiers: - biotools:compass - doi:10.1038/nbt.3187 + parent_recipe: + name: bioconductor-compass + path: recipes/bioconductor-compass + version: 1.18.1 + diff --git a/recipes/bioconductor-compcoder/build.sh b/recipes/bioconductor-compcoder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-compcoder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compcoder/meta.yaml b/recipes/bioconductor-compcoder/meta.yaml new file mode 100644 index 0000000000000..c0726e373e484 --- /dev/null +++ b/recipes/bioconductor-compcoder/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.18.0" %} +{% set name = "compcodeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1377c8378b5f0b53bc1e971fda7f645e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, EBSeq, DESeq, DESeq2 (>= 1.1.31), baySeq (>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0) +requirements: + host: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-catools + - r-gdata + - r-ggplot2 + - r-gplots + - r-gtools + - r-kernsmooth + - 'r-knitr >=1.2' + - 'r-lattice >=0.16' + - r-markdown + - r-mass + - r-modeest + - r-rocr + - r-sm + - r-stringr + - r-vioplot + run: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-catools + - r-gdata + - r-ggplot2 + - r-gplots + - r-gtools + - r-kernsmooth + - 'r-knitr >=1.2' + - 'r-lattice >=0.16' + - r-markdown + - r-mass + - r-modeest + - r-rocr + - r-sm + - r-stringr + - r-vioplot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data and interfaces to several packages for performing the differential expression analysis.' + diff --git a/recipes/bioconductor-compepitools/build.sh b/recipes/bioconductor-compepitools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-compepitools/build.sh +++ b/recipes/bioconductor-compepitools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compepitools/meta.yaml b/recipes/bioconductor-compepitools/meta.yaml index dd8b10e0394a7..2af08a34c7bcd 100644 --- a/recipes/bioconductor-compepitools/meta.yaml +++ b/recipes/bioconductor-compepitools/meta.yaml @@ -1,61 +1,68 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "compEpiTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 745c5f30b63520ac68a9d88aa78bbc7ca71ad0c0d5db6094f8de1cabbe1bce15 + md5: fb61333b079671d747268fb10a6b1188 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Mmusculus.UCSC.mm9, TxDb.Mmusculus.UCSC.mm9.knownGene, org.Mm.eg.db, knitr, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-methylpipe >=1.14.0,<1.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-gplots run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-methylpipe >=1.14.0,<1.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-gplots test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Tools for computational epigenomics developed for the analysis, integration and simultaneous visualization of various (epi)genomics data types across multiple genomic regions in multiple samples.' extra: identifiers: - biotools:compepitools + parent_recipe: + name: bioconductor-compepitools + path: recipes/bioconductor-compepitools + version: 1.14.1 + diff --git a/recipes/bioconductor-compgo/build.sh b/recipes/bioconductor-compgo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-compgo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-compgo/meta.yaml b/recipes/bioconductor-compgo/meta.yaml new file mode 100644 index 0000000000000..57cda3fdea4a4 --- /dev/null +++ b/recipes/bioconductor-compgo/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.18.0" %} +{% set name = "CompGO" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8d55397e57562db724c8714f2ca5b0c1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-rdavidwebservice >=1.20.0,<1.21.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-ggplot2 + - r-reshape2 + run: + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-rdavidwebservice >=1.20.0,<1.21.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-ggplot2 + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains functions to accomplish several tasks. It is able to download full genome databases from UCSC, import .bed files easily, annotate these .bed file regions with genes (plus distance) from aforementioned database dumps, interface with DAVID to create functional annotation and gene ontology enrichment charts based on gene lists (such as those generated from input .bed files) and finally visualise and compare these enrichments using either directed acyclic graphs or scatterplots.' + diff --git a/recipes/bioconductor-complexheatmap/build.sh b/recipes/bioconductor-complexheatmap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-complexheatmap/build.sh +++ b/recipes/bioconductor-complexheatmap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-complexheatmap/meta.yaml b/recipes/bioconductor-complexheatmap/meta.yaml index 793bd5dd7d076..e05dee47ded00 100644 --- a/recipes/bioconductor-complexheatmap/meta.yaml +++ b/recipes/bioconductor-complexheatmap/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "ComplexHeatmap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1661fa2af0cdf77bbe94cdfd81c58950836cdd8c53da182548cccafb61f85c62 + md5: 456f36170972af9de5e366781054c561 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat (>= 0.3), knitr, markdown, cluster, MASS, pvclust, dendsort, HilbertCurve, Cairo, png, jpeg, tiff, fastcluster, dendextend (>= 1.0.1) requirements: host: - r-base - 'r-circlize >=0.4.1' - r-colorspace - r-getoptlong - - 'r-globaloptions >=0.0.10' + - 'r-globaloptions >=0.1.0' - r-rcolorbrewer run: - r-base - 'r-circlize >=0.4.1' - r-colorspace - r-getoptlong - - 'r-globaloptions >=0.0.10' + - 'r-globaloptions >=0.1.0' - r-rcolorbrewer test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Complex heatmaps are efficient to visualize associations between different sources of data sets and reveal potential structures. Here the ComplexHeatmap package provides a highly flexible way to arrange multiple heatmaps and supports self-defined annotation graphics.' extra: identifiers: - biotools:complexheatmap + parent_recipe: + name: bioconductor-complexheatmap + path: recipes/bioconductor-complexheatmap + version: 1.18.1 + diff --git a/recipes/bioconductor-condcomp/build.sh b/recipes/bioconductor-condcomp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-condcomp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-condcomp/meta.yaml b/recipes/bioconductor-condcomp/meta.yaml new file mode 100644 index 0000000000000..7e4e68920b5ab --- /dev/null +++ b/recipes/bioconductor-condcomp/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "condcomp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eafc4b293b338b14acf0cb3a24064122 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, Matrix, Seurat, monocle, HSMMSingleCell +requirements: + host: + - r-base + - r-cluster + - r-ggplot2 + - r-ggrepel + - r-outliers + run: + - r-base + - r-cluster + - r-ggplot2 + - r-ggrepel + - r-outliers +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2) | file LICENSE' + summary: 'For a given clustered data, which can also be split into two conditions, this package provides a way to perform a condition comparison on said clustered data. The comparison is performed on each cluster. Several statistics are used and, when analysed in conjunction, they might give some insight regarding the heterogeneity of some of the clusters.' + diff --git a/recipes/bioconductor-confess/build.sh b/recipes/bioconductor-confess/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-confess/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-confess/meta.yaml b/recipes/bioconductor-confess/meta.yaml new file mode 100644 index 0000000000000..089d2b10d2077 --- /dev/null +++ b/recipes/bioconductor-confess/meta.yaml @@ -0,0 +1,85 @@ +{% set version = "1.10.0" %} +{% set name = "CONFESS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 688202920086c703ad3d06e249e62029 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, CONFESSdata +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowmeans >=1.42.0,<1.43.0' + - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - r-base + - r-changepoint + - r-cluster + - r-contrast + - 'r-data.table >=1.9.7' + - r-ecp + - r-flexmix + - r-foreach + - r-ggplot2 + - r-mass + - r-moments + - r-outliers + - r-plotrix + - r-raster + - r-readbitmap + - r-reshape2 + - r-waveslim + - r-wavethresh + - r-zoo + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowmeans >=1.42.0,<1.43.0' + - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - r-base + - r-changepoint + - r-cluster + - r-contrast + - 'r-data.table >=1.9.7' + - r-ecp + - r-flexmix + - r-foreach + - r-ggplot2 + - r-mass + - r-moments + - r-outliers + - r-plotrix + - r-raster + - r-readbitmap + - r-reshape2 + - r-waveslim + - r-wavethresh + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Single Cell Fluidigm Spot Detector.' + diff --git a/recipes/bioconductor-confessdata/meta.yaml b/recipes/bioconductor-confessdata/meta.yaml new file mode 100644 index 0000000000000..7de5b14bcb8ed --- /dev/null +++ b/recipes/bioconductor-confessdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.10.0" %} +{% set name = "CONFESSdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e44ef1d35b8701069ba3908770dbb1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Example text-converted C01 image files for use in the CONFESS Bioconductor package.' + diff --git a/recipes/bioconductor-confessdata/post-link.sh b/recipes/bioconductor-confessdata/post-link.sh new file mode 100644 index 0000000000000..c5e9aa7d1b533 --- /dev/null +++ b/recipes/bioconductor-confessdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CONFESSdata_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CONFESSdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/CONFESSdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-confessdata/bioconductor-confessdata_1.10.0_src_all.tar.gz" +) +MD5="3e44ef1d35b8701069ba3908770dbb1e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-confessdata/pre-unlink.sh b/recipes/bioconductor-confessdata/pre-unlink.sh new file mode 100644 index 0000000000000..15db66f08db44 --- /dev/null +++ b/recipes/bioconductor-confessdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CONFESSdata diff --git a/recipes/bioconductor-connectivitymap/meta.yaml b/recipes/bioconductor-connectivitymap/meta.yaml new file mode 100644 index 0000000000000..9d26bc50ebb58 --- /dev/null +++ b/recipes/bioconductor-connectivitymap/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "ConnectivityMap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff3bb449f67cd01953a13682b3496fff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The Broad Institute''s Connectivity Map (cmap02) is a "large reference catalogue of gene-expression data from cultured human cells perturbed with many chemicals and genetic reagents", containing more than 7000 gene expression profiles and 1300 small molecules.' + diff --git a/recipes/bioconductor-connectivitymap/post-link.sh b/recipes/bioconductor-connectivitymap/post-link.sh new file mode 100644 index 0000000000000..26df838ebd549 --- /dev/null +++ b/recipes/bioconductor-connectivitymap/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ConnectivityMap_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ConnectivityMap_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ConnectivityMap_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-connectivitymap/bioconductor-connectivitymap_1.18.0_src_all.tar.gz" +) +MD5="ff3bb449f67cd01953a13682b3496fff" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-connectivitymap/pre-unlink.sh b/recipes/bioconductor-connectivitymap/pre-unlink.sh new file mode 100644 index 0000000000000..5480847c70c85 --- /dev/null +++ b/recipes/bioconductor-connectivitymap/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ConnectivityMap diff --git a/recipes/bioconductor-consensus/build.sh b/recipes/bioconductor-consensus/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-consensus/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensus/meta.yaml b/recipes/bioconductor-consensus/meta.yaml new file mode 100644 index 0000000000000..e37579829adc3 --- /dev/null +++ b/recipes/bioconductor-consensus/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "consensus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 78e920b773a164d19e561122b9d53954 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, rmarkdown, BiocGenerics +requirements: + host: + - r-base + - r-gplots + - r-matrixstats + - r-rcolorbrewer + run: + - r-base + - r-gplots + - r-matrixstats + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'An implementation of the American Society for Testing and Materials (ASTM) Standard E691 for interlaboratory testing procedures, designed for cross-platform genomic measurements. Given three (3) or more genomic platforms or laboratory protocols, this package provides interlaboratory testing procedures giving per-locus comparisons for sensitivity and precision between platforms.' + diff --git a/recipes/bioconductor-consensusclusterplus/build.sh b/recipes/bioconductor-consensusclusterplus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-consensusclusterplus/build.sh +++ b/recipes/bioconductor-consensusclusterplus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensusclusterplus/meta.yaml b/recipes/bioconductor-consensusclusterplus/meta.yaml index 6e92bb502872a..b4226ed40597f 100644 --- a/recipes/bioconductor-consensusclusterplus/meta.yaml +++ b/recipes/bioconductor-consensusclusterplus/meta.yaml @@ -1,39 +1,45 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "ConsensusClusterPlus" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ce09181763cfcb03a650d3b3c378b6e84533efd37e5693786255ead94dcb7a52 + md5: e53f78c29f4dc2a0a9feaf93acb4c71f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-all >=1.22.0,<1.24.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-all >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster run: - - 'bioconductor-all >=1.22.0,<1.24.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-all >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL version 2' summary: 'algorithm for determining cluster count and membership by stability evidence in unsupervised analysis' extra: identifiers: - biotools:consensusclusterplus + parent_recipe: + name: bioconductor-consensusclusterplus + path: recipes/bioconductor-consensusclusterplus + version: 1.44.0 + diff --git a/recipes/bioconductor-consensusde/build.sh b/recipes/bioconductor-consensusde/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-consensusde/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensusde/meta.yaml b/recipes/bioconductor-consensusde/meta.yaml new file mode 100644 index 0000000000000..fde497af711db --- /dev/null +++ b/recipes/bioconductor-consensusde/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "consensusDE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11e5c9a0b5eb21efed6daa2b0dde82ac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-airway >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-ruvseq >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - r-base + - r-dendextend + - r-rcolorbrewer + run: + - 'bioconductor-airway >=1.2.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-ruvseq >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene >=3.2.0,<3.3.0' + - r-base + - r-dendextend + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package allows users to perform DE analysis using multiple algorithms. It seeks consensus from multiple methods. Currently it supports "Voom", "EdgeR" and "DESeq", but can be easily extended. It uses RUV-seq (optional) to remove batch effects.' + diff --git a/recipes/bioconductor-consensusov/build.sh b/recipes/bioconductor-consensusov/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-consensusov/build.sh +++ b/recipes/bioconductor-consensusov/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensusov/meta.yaml b/recipes/bioconductor-consensusov/meta.yaml index 886bce7b48afb..d20a9e4442095 100644 --- a/recipes/bioconductor-consensusov/meta.yaml +++ b/recipes/bioconductor-consensusov/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.1" %} {% set name = "consensusOV" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 487c6acf505fdcc2394a98ee88427fbbbb5a77ccd1f7d16f53763cc7d291cd5f + md5: bae7c5cf0c2d5174dcde8cba046e1222 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, ggplot2 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefu >=2.12.0,<2.14.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefu >=2.14.0,<2.15.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-gdata - r-matrixstats - r-randomforest run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefu >=2.12.0,<2.14.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefu >=2.14.0,<2.15.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-gdata - r-matrixstats @@ -39,8 +41,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements four major subtype classifiers for high-grade serous (HGS) ovarian cancer as described by Helland et al. (PLoS One, 2011), Bentink et al. (PLoS One, 2012), Verhaak et al. (J Clin Invest, 2013), and Konecny et al. (J Natl Cancer Inst, 2014). In addition, the package implements a consensus classifier, which consolidates and improves on the robustness of the proposed subtype classifiers, thereby providing reliable stratification of patients with HGS ovarian tumors of clearly defined subtype.' - +extra: + parent_recipe: + name: bioconductor-consensusov + path: recipes/bioconductor-consensusov + version: 1.2.0 diff --git a/recipes/bioconductor-consensusseeker/build.sh b/recipes/bioconductor-consensusseeker/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-consensusseeker/build.sh +++ b/recipes/bioconductor-consensusseeker/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-consensusseeker/meta.yaml b/recipes/bioconductor-consensusseeker/meta.yaml index cbe4cee1ad67c..bd96947d86300 100644 --- a/recipes/bioconductor-consensusseeker/meta.yaml +++ b/recipes/bioconductor-consensusseeker/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "consensusSeekeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 286721522fcec4124beb0f7b0c2830589109a68828019b43a904ca1c36b7805b + md5: 32baf724416cf72420acc402a030cc1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, ggplot2, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-stringr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package compares genomic positions and genomic ranges from multiple experiments to extract common regions. The size of the analyzed region is adjustable as well as the number of experiences in which a feature must be present in a potential region to tag this region as a consensus region.' extra: identifiers: - biotools:consensusseeker - doi:10.1515/sagmb-2014-0098 + parent_recipe: + name: bioconductor-consensusseeker + path: recipes/bioconductor-consensusseeker + version: 1.8.0 + diff --git a/recipes/bioconductor-contibait/build.sh b/recipes/bioconductor-contibait/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-contibait/build.sh +++ b/recipes/bioconductor-contibait/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-contibait/meta.yaml b/recipes/bioconductor-contibait/meta.yaml index 56173c2c6fbb1..2e6367748d3e6 100644 --- a/recipes/bioconductor-contibait/meta.yaml +++ b/recipes/bioconductor-contibait/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "contiBAIT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 58bf2ef2c66036bbd356257334ec557be6af06ed791c94986e907d857f2ce3e3 + md5: 8854ac11a9aaab81bf63b0f3ffee1168 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-bh >=1.51.0-3' - r-clue @@ -42,16 +43,16 @@ requirements: - r-reshape2 - r-tsp run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-bh >=1.51.0-3' - r-clue @@ -73,10 +74,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Using strand inheritance data from multiple single cells from the organism whose genome is to be assembled, contiBAIT can cluster unbridged contigs together into putative chromosomes, and order the contigs within those chromosomes.' extra: identifiers: - biotools:contibait - doi:10.1093/bioinformatics/btx281 + parent_recipe: + name: bioconductor-contibait + path: recipes/bioconductor-contibait + version: 1.8.0 + diff --git a/recipes/bioconductor-conumee/build.sh b/recipes/bioconductor-conumee/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-conumee/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-conumee/meta.yaml b/recipes/bioconductor-conumee/meta.yaml new file mode 100644 index 0000000000000..9ac8038f845f8 --- /dev/null +++ b/recipes/bioconductor-conumee/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.16.0" %} +{% set name = "conumee" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cbf7b1712e25b8433f543f3d9d6459a1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, minfiData, RCurl +requirements: + host: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + run: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains a set of processing and plotting methods for performing copy-number variation (CNV) analysis using Illumina 450k or EPIC methylation arrays.' + diff --git a/recipes/bioconductor-convert/build.sh b/recipes/bioconductor-convert/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-convert/build.sh +++ b/recipes/bioconductor-convert/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-convert/meta.yaml b/recipes/bioconductor-convert/meta.yaml index d4953f0a129d7..917c03eab128e 100644 --- a/recipes/bioconductor-convert/meta.yaml +++ b/recipes/bioconductor-convert/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "convert" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 344208d1cf513bcb9a66b8b34c51274faf24e05d03f06362c833adf4391ac62b + md5: 315f0cead1c62a2d4e898a1d7136c625 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Define coerce methods for microarray data objects.' extra: identifiers: - biotools:convert - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-convert + path: recipes/bioconductor-convert + version: 1.56.0 + diff --git a/recipes/bioconductor-copa/build.sh b/recipes/bioconductor-copa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-copa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-copa/meta.yaml b/recipes/bioconductor-copa/meta.yaml new file mode 100644 index 0000000000000..0cdcb2ce9d2fc --- /dev/null +++ b/recipes/bioconductor-copa/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.50.0" %} +{% set name = "copa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0b6d430c7136ee40abaae1d099d2dfd1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: colonCA +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'COPA is a method to find genes that undergo recurrent fusion in a given cancer type by finding pairs of genes that have mutually exclusive outlier profiles.' + diff --git a/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml new file mode 100644 index 0000000000000..58e238c3b4da5 --- /dev/null +++ b/recipes/bioconductor-copdsexualdimorphism.data/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "COPDSexualDimorphism.data" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4089a6b6e4d5537d8b1c4352800ab0a4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-2.1 + summary: 'Datasets to support COPDSexaulDimorphism Package.' + diff --git a/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh new file mode 100644 index 0000000000000..8546ee245a480 --- /dev/null +++ b/recipes/bioconductor-copdsexualdimorphism.data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="COPDSexualDimorphism.data_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COPDSexualDimorphism.data_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/COPDSexualDimorphism.data_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copdsexualdimorphism.data/bioconductor-copdsexualdimorphism.data_1.18.0_src_all.tar.gz" +) +MD5="4089a6b6e4d5537d8b1c4352800ab0a4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-copdsexualdimorphism.data/pre-unlink.sh b/recipes/bioconductor-copdsexualdimorphism.data/pre-unlink.sh new file mode 100644 index 0000000000000..2d59a53bfc0c5 --- /dev/null +++ b/recipes/bioconductor-copdsexualdimorphism.data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ COPDSexualDimorphism.data diff --git a/recipes/bioconductor-copyhelper/meta.yaml b/recipes/bioconductor-copyhelper/meta.yaml index a33dcae4461ca..f0eecafa07659 100644 --- a/recipes/bioconductor-copyhelper/meta.yaml +++ b/recipes/bioconductor-copyhelper/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "CopyhelpeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2927de1db24986129406c4d8e8699675dfb1b48b1c906e7bc4406670264494c7 + md5: d1141ae0fe9aa075e083042ededcafce build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This package contains the helper files that are required to run the Bioconductor package CopywriteR. It contains pre-assembled 1kb bin GC-content and mappability files for the reference genomes hg18, hg19, hg38, mm9 and mm10. In addition, it contains a blacklist filter to remove regions that display CNV. Files are stored as GRanges objects from the GenomicRanges Bioconductor package.' - +extra: + parent_recipe: + name: bioconductor-copyhelper + path: recipes/bioconductor-copyhelper + version: 1.12.0 diff --git a/recipes/bioconductor-copyhelper/post-link.sh b/recipes/bioconductor-copyhelper/post-link.sh index e4c9f44df41a3..c75091947f326 100644 --- a/recipes/bioconductor-copyhelper/post-link.sh +++ b/recipes/bioconductor-copyhelper/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="CopyhelpeR_1.12.0.tar.gz" +FN="CopyhelpeR_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/CopyhelpeR_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/CopyhelpeR_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CopyhelpeR_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyhelpeR_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyhelper/bioconductor-copyhelper_1.14.0_src_all.tar.gz" ) -MD5="5a1d068158d3fb73abaf6ca93ee994b0" +MD5="d1141ae0fe9aa075e083042ededcafce" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-copyneutralima/meta.yaml b/recipes/bioconductor-copyneutralima/meta.yaml new file mode 100644 index 0000000000000..fce9fd0f21316 --- /dev/null +++ b/recipes/bioconductor-copyneutralima/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "CopyNeutralIMA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 88e8d2b42e4512161e2c2a7fa95b6a5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle,knitr,rmarkdown,minfi,conumee,minfiData +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - 'r-rdpack >=0.8' + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - 'r-rdpack >=0.8' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides a set of genomic copy neutral samples hybridized using Illumina Methylation arrays (450k and EPIC).' + diff --git a/recipes/bioconductor-copyneutralima/post-link.sh b/recipes/bioconductor-copyneutralima/post-link.sh new file mode 100644 index 0000000000000..ee9106d0fa38a --- /dev/null +++ b/recipes/bioconductor-copyneutralima/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CopyNeutralIMA_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CopyNeutralIMA_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/CopyNeutralIMA_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-copyneutralima/bioconductor-copyneutralima_1.0.0_src_all.tar.gz" +) +MD5="88e8d2b42e4512161e2c2a7fa95b6a5b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-copyneutralima/pre-unlink.sh b/recipes/bioconductor-copyneutralima/pre-unlink.sh new file mode 100644 index 0000000000000..a54add6577cd3 --- /dev/null +++ b/recipes/bioconductor-copyneutralima/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CopyNeutralIMA diff --git a/recipes/bioconductor-copynumber/build.sh b/recipes/bioconductor-copynumber/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-copynumber/build.sh +++ b/recipes/bioconductor-copynumber/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-copynumber/meta.yaml b/recipes/bioconductor-copynumber/meta.yaml index f924933fd6a8c..a722ea4dde3be 100644 --- a/recipes/bioconductor-copynumber/meta.yaml +++ b/recipes/bioconductor-copynumber/meta.yaml @@ -1,41 +1,47 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "copynumber" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bad6db743ca26a2f12e2a538fb4b2e24bff291139223d4e3b8f0ea0b16b73679 + md5: d2ce25bf392279699524af3cf45cf4c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Penalized least squares regression is applied to fit piecewise constant curves to copy number data to locate genomic regions of constant copy number. Procedures are available for individual segmentation of each sample, joint segmentation of several samples and joint segmentation of the two data tracks from SNP-arrays. Several plotting functions are available for visualization of the data and the segmentation results.' extra: identifiers: - biotools:copynumber + parent_recipe: + name: bioconductor-copynumber + path: recipes/bioconductor-copynumber + version: 1.20.0 + diff --git a/recipes/bioconductor-copywriter/build.sh b/recipes/bioconductor-copywriter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-copywriter/build.sh +++ b/recipes/bioconductor-copywriter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-copywriter/meta.yaml b/recipes/bioconductor-copywriter/meta.yaml index 2e5895a0fce82..0150aa881f1e2 100644 --- a/recipes/bioconductor-copywriter/meta.yaml +++ b/recipes/bioconductor-copywriter/meta.yaml @@ -1,49 +1,51 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "CopywriteR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e383b2bdf215962f4792035e9aa1d891e05a6f2cec0047caa2ec0bb503e6fd2c + md5: a34d836b32a16c62c84c49b14030018b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, SCLCBam, snow requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-copyhelper >=1.12.0,<1.14.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-copyhelper >=1.14.0,<1.15.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-futile.logger - r-gtools - r-matrixstats run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-copyhelper >=1.12.0,<1.14.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-copyhelper >=1.14.0,<1.15.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-futile.logger @@ -53,10 +55,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'CopywriteR extracts DNA copy number information from targeted sequencing by utiizing off-target reads. It allows for extracting uniformly distributed copy number information, can be used without reference, and can be applied to sequencing data obtained from various techniques including chromatin immunoprecipitation and target enrichment on small gene panels. Thereby, CopywriteR constitutes a widely applicable alternative to available copy number detection tools.' extra: identifiers: - biotools:copywriter - doi:10.1186/s13059-015-0617-1 + parent_recipe: + name: bioconductor-copywriter + path: recipes/bioconductor-copywriter + version: 2.12.0 + diff --git a/recipes/bioconductor-cordon/build.sh b/recipes/bioconductor-cordon/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cordon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cordon/meta.yaml b/recipes/bioconductor-cordon/meta.yaml new file mode 100644 index 0000000000000..65ef8eb4acc7a --- /dev/null +++ b/recipes/bioconductor-cordon/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.1" %} +{% set name = "coRdon" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cce2223c43430259ba3291816ecd36ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-purrr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-purrr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tool for analysis of codon usage in various unannotated or KEGG/COG annotated DNA sequences. Calculates different measures of CU bias and CU-based predictors of gene expressivity, and performs gene set enrichment analysis for annotated sequences. Implements several methods for visualization of CU and enrichment analysis results.' + diff --git a/recipes/bioconductor-coregnet/build.sh b/recipes/bioconductor-coregnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coregnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coregnet/meta.yaml b/recipes/bioconductor-coregnet/meta.yaml new file mode 100644 index 0000000000000..f1a80d043534a --- /dev/null +++ b/recipes/bioconductor-coregnet/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.20.0" %} +{% set name = "CoRegNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9271a02c25c486a3becae3002e02590a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RColorBrewer, gplots, BiocStyle, knitr +requirements: + host: + - r-arules + - r-base + - r-igraph + - r-shiny + run: + - r-arules + - r-base + - r-igraph + - r-shiny + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides methods to identify active transcriptional programs. Methods and classes are provided to import or infer large scale co-regulatory network from transcriptomic data. The specificity of the encoded networks is to model Transcription Factor cooperation. External regulation evidences (TFBS, ChIP,...) can be integrated to assess the inferred network and refine it if necessary. Transcriptional activity of the regulators in the network can be estimated using an measure of their influence in a given sample. Finally, an interactive UI can be used to navigate through the network of cooperative regulators and to visualize their activity in a specific sample or subgroup sample. The proposed visualization tool can be used to integrate gene expression, transcriptional activity, copy number status, sample classification and a transcriptional network including co-regulation information.' + diff --git a/recipes/bioconductor-cormotif/build.sh b/recipes/bioconductor-cormotif/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cormotif/build.sh +++ b/recipes/bioconductor-cormotif/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cormotif/conda_build_config.yaml b/recipes/bioconductor-cormotif/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-cormotif/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-cormotif/meta.yaml b/recipes/bioconductor-cormotif/meta.yaml index 70d3c05b263c1..252eed210b4f1 100644 --- a/recipes/bioconductor-cormotif/meta.yaml +++ b/recipes/bioconductor-cormotif/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Cormotif" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ee273daa7997a0249f0a07dfe4317656adbfeee07152af7199d46e190c4066be + md5: 23da3810b5bd4632e8cec7e5a23d132f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'It fits correlation motif model to multiple studies to detect study specific differential expression patterns.' extra: identifiers: - biotools:cormotif + parent_recipe: + name: bioconductor-cormotif + path: recipes/bioconductor-cormotif + version: 1.26.0 + diff --git a/recipes/bioconductor-cormut/build.sh b/recipes/bioconductor-cormut/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cormut/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cormut/meta.yaml b/recipes/bioconductor-cormut/meta.yaml new file mode 100644 index 0000000000000..5682eb39dab7f --- /dev/null +++ b/recipes/bioconductor-cormut/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.24.0" %} +{% set name = "CorMut" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87d0c12fe94d44ee994cf211b377db63 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-igraph + - r-seqinr + run: + - r-base + - r-igraph + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'CorMut provides functions for computing kaks for individual sites or specific amino acids and detecting correlated mutations among them. Three methods are provided for detecting correlated mutations ,including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; Second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network. The reference sequence should be the first sequence of the sequence file, and does not allow the presence of gap.' + diff --git a/recipes/bioconductor-correp/build.sh b/recipes/bioconductor-correp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-correp/build.sh +++ b/recipes/bioconductor-correp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-correp/meta.yaml b/recipes/bioconductor-correp/meta.yaml index c3184599801bb..2b536fd208fa5 100644 --- a/recipes/bioconductor-correp/meta.yaml +++ b/recipes/bioconductor-correp/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "CORREP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e3b3e907709ff15c337e14444c7125f7b0ede1449fbc4587653afeb759a8da3e + md5: bb75ae6c927d9b6ab112864dad047cf5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: cluster, MASS requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Multivariate correlation estimation and statistical inference. See package vignette.' extra: identifiers: - biotools:correp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-correp + path: recipes/bioconductor-correp + version: 1.46.0 + diff --git a/recipes/bioconductor-coseq/build.sh b/recipes/bioconductor-coseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coseq/meta.yaml b/recipes/bioconductor-coseq/meta.yaml new file mode 100644 index 0000000000000..d1da376060d75 --- /dev/null +++ b/recipes/bioconductor-coseq/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.6.0" %} +{% set name = "coseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 82a886ded142822f3f84ef320ee3d51b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-htsfilter >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-capushe + - r-compositions + - r-corrplot + - r-e1071 + - 'r-ggplot2 >=2.1.0' + - 'r-htscluster >=2.0.8' + - r-mvtnorm + - r-rmixmod + - r-scales + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-htsfilter >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-capushe + - r-compositions + - r-corrplot + - r-e1071 + - 'r-ggplot2 >=2.1.0' + - 'r-htscluster >=2.0.8' + - r-mvtnorm + - r-rmixmod + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'Co-expression analysis for expression profiles arising from high-throughput sequencing data. Feature (e.g., gene) profiles are clustered using adapted transformations and mixture models or a K-means algorithm, and model selection criteria (to choose an appropriate number of clusters) are provided.' + diff --git a/recipes/bioconductor-cosmic.67/meta.yaml b/recipes/bioconductor-cosmic.67/meta.yaml new file mode 100644 index 0000000000000..bad388b85efda --- /dev/null +++ b/recipes/bioconductor-cosmic.67/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.18.0" %} +{% set name = "COSMIC.67" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db1bb894b11d6e1f9d2675e68bdf3291 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'COSMIC: Catalogue Of Somatic Mutations In Cancer, version 67 (2013-10-24)' + diff --git a/recipes/bioconductor-cosmic.67/post-link.sh b/recipes/bioconductor-cosmic.67/post-link.sh new file mode 100644 index 0000000000000..2505a2a1f7393 --- /dev/null +++ b/recipes/bioconductor-cosmic.67/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="COSMIC.67_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/COSMIC.67_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/COSMIC.67_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cosmic.67/bioconductor-cosmic.67_1.18.0_src_all.tar.gz" +) +MD5="db1bb894b11d6e1f9d2675e68bdf3291" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cosmic.67/pre-unlink.sh b/recipes/bioconductor-cosmic.67/pre-unlink.sh new file mode 100644 index 0000000000000..e16f8cda3d4b2 --- /dev/null +++ b/recipes/bioconductor-cosmic.67/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ COSMIC.67 diff --git a/recipes/bioconductor-cosmiq/build.sh b/recipes/bioconductor-cosmiq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cosmiq/build.sh +++ b/recipes/bioconductor-cosmiq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cosmiq/meta.yaml b/recipes/bioconductor-cosmiq/meta.yaml index 675a5aa9dbc36..c410e554fe1ea 100644 --- a/recipes/bioconductor-cosmiq/meta.yaml +++ b/recipes/bioconductor-cosmiq/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.13.0" %} +{% set version = "1.16.0" %} {% set name = "cosmiq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 76e57b7368920cef01e28bfeed4ddf25735f43e4b5e71f83170836575b568ac7 + md5: a0e2d99096bae3cf865b0301d8404b59 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-faahko >=1.20.0,<1.22.0' - - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-faahko >=1.22.0,<1.23.0' + - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-pracma - r-rcpp run: - - 'bioconductor-faahko >=1.20.0,<1.22.0' - - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-faahko >=1.22.0,<1.23.0' + - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-pracma - r-rcpp @@ -39,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'cosmiq is a tool for the preprocessing of liquid- or gas - chromatography mass spectrometry (LCMS/GCMS) data with a focus on metabolomics or lipidomics applications. To improve the detection of low abundant signals, cosmiq generates master maps of the mZ/RT space from all acquired runs before a peak detection algorithm is applied. The result is a more robust identification and quantification of low-intensity MS signals compared to conventional approaches where peak picking is performed in each LCMS/GCMS file separately. The cosmiq package builds on the xcmsSet object structure and can be therefore integrated well with the package xcms as an alternative preprocessing step.' extra: identifiers: - biotools:cosmiq - doi:10.5167/uzh-107947 + parent_recipe: + name: bioconductor-cosmiq + path: recipes/bioconductor-cosmiq + version: 1.13.0 + diff --git a/recipes/bioconductor-cosnet/build.sh b/recipes/bioconductor-cosnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cosnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cosnet/meta.yaml b/recipes/bioconductor-cosnet/meta.yaml new file mode 100644 index 0000000000000..42fdf99cee87c --- /dev/null +++ b/recipes/bioconductor-cosnet/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.16.0" %} +{% set name = "COSNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ca0dbf84990b9770b2179ff397e5c407 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: bionetdata, PerfMeas, RUnit, BiocGenerics +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Package that implements the COSNet classification algorithm. The algorithm predicts node labels in partially labeled graphs where few positives are available for the class being predicted.' + diff --git a/recipes/bioconductor-cottoncdf/meta.yaml b/recipes/bioconductor-cottoncdf/meta.yaml new file mode 100644 index 0000000000000..1d231e4e94f00 --- /dev/null +++ b/recipes/bioconductor-cottoncdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "cottoncdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b9d2a4b43235c6e531b78cca006e84b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Cotton.cdf file.' + diff --git a/recipes/bioconductor-cottoncdf/post-link.sh b/recipes/bioconductor-cottoncdf/post-link.sh new file mode 100644 index 0000000000000..ba38c815ebcf4 --- /dev/null +++ b/recipes/bioconductor-cottoncdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cottoncdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cottoncdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/cottoncdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cottoncdf/bioconductor-cottoncdf_2.18.0_src_all.tar.gz" +) +MD5="b9d2a4b43235c6e531b78cca006e84b2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cottoncdf/pre-unlink.sh b/recipes/bioconductor-cottoncdf/pre-unlink.sh new file mode 100644 index 0000000000000..850c5dede3d09 --- /dev/null +++ b/recipes/bioconductor-cottoncdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cottoncdf diff --git a/recipes/bioconductor-cottonprobe/meta.yaml b/recipes/bioconductor-cottonprobe/meta.yaml new file mode 100644 index 0000000000000..fea33b15b3432 --- /dev/null +++ b/recipes/bioconductor-cottonprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "cottonprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 032fa94876685820d94526fd56dd0b65 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Cotton\_probe\_tab.' + diff --git a/recipes/bioconductor-cottonprobe/post-link.sh b/recipes/bioconductor-cottonprobe/post-link.sh new file mode 100644 index 0000000000000..2e1b6131d4b85 --- /dev/null +++ b/recipes/bioconductor-cottonprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cottonprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cottonprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/cottonprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cottonprobe/bioconductor-cottonprobe_2.18.0_src_all.tar.gz" +) +MD5="032fa94876685820d94526fd56dd0b65" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cottonprobe/pre-unlink.sh b/recipes/bioconductor-cottonprobe/pre-unlink.sh new file mode 100644 index 0000000000000..668b6f6dde7c0 --- /dev/null +++ b/recipes/bioconductor-cottonprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cottonprobe diff --git a/recipes/bioconductor-countclust/build.sh b/recipes/bioconductor-countclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-countclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-countclust/meta.yaml b/recipes/bioconductor-countclust/meta.yaml new file mode 100644 index 0000000000000..1427daff1fe9b --- /dev/null +++ b/recipes/bioconductor-countclust/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.10.0" %} +{% set name = "CountClust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8ef00ccb97e6a6da9d98d496f901bb54 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, kableExtra, BiocStyle, Biobase, roxygen2, RColorBrewer, devtools, xtable +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-cowplot + - r-flexmix + - 'r-ggplot2 >=2.1.0' + - r-gtools + - r-maptpx + - r-picante + - 'r-plyr >=1.7.1' + - r-reshape2 + - r-slam + - r-squarem + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-cowplot + - r-flexmix + - 'r-ggplot2 >=2.1.0' + - r-gtools + - r-maptpx + - r-picante + - 'r-plyr >=1.7.1' + - r-reshape2 + - r-slam + - r-squarem +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Fits grade of membership models (GoM, also known as admixture models) to cluster RNA-seq gene expression count data, identifies characteristic genes driving cluster memberships, and provides a visual summary of the cluster memberships.' + diff --git a/recipes/bioconductor-countsimqc/build.sh b/recipes/bioconductor-countsimqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-countsimqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-countsimqc/meta.yaml b/recipes/bioconductor-countsimqc/meta.yaml new file mode 100644 index 0000000000000..7deacb599286a --- /dev/null +++ b/recipes/bioconductor-countsimqc/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "countsimQC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 57a8e42b86fec1cd161aa644697d7d37 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-catools + - r-dplyr + - r-dt + - r-ggplot2 + - r-randtests + - 'r-rmarkdown >=0.9.5' + - r-tidyr + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-catools + - r-dplyr + - r-dt + - r-ggplot2 + - r-randtests + - 'r-rmarkdown >=0.9.5' + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'countsimQC provides functionality to create a comprehensive report comparing a broad range of characteristics across a collection of count matrices. One important use case is the comparison of one or more synthetic count matrices to a real count matrix, possibly the one underlying the simulations. However, any collection of count matrices can be compared.' + diff --git a/recipes/bioconductor-coveb/build.sh b/recipes/bioconductor-coveb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coveb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coveb/meta.yaml b/recipes/bioconductor-coveb/meta.yaml new file mode 100644 index 0000000000000..65e875fd81be6 --- /dev/null +++ b/recipes/bioconductor-coveb/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.8.0" %} +{% set name = "covEB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11438b895b39f1dbcda0684a814ee9d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: curatedBladderData +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-gsl + - r-igraph + - r-laplacesdemon + - r-matrix + - r-mvtnorm + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-gsl + - r-igraph + - r-laplacesdemon + - r-matrix + - r-mvtnorm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Using bayesian methods to estimate correlation matrices assuming that they can be written and estimated as block diagonal matrices. These block diagonal matrices are determined using shrinkage parameters that values below this parameter to zero.' + diff --git a/recipes/bioconductor-coverageview/build.sh b/recipes/bioconductor-coverageview/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-coverageview/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-coverageview/meta.yaml b/recipes/bioconductor-coverageview/meta.yaml new file mode 100644 index 0000000000000..f614db3768ce7 --- /dev/null +++ b/recipes/bioconductor-coverageview/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.20.0" %} +{% set name = "CoverageView" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7022b9de2a05fe8e1f1da1ca1d7482b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides a framework for the visualization of genome coverage profiles. It can be used for ChIP-seq experiments, but it can be also used for genome-wide nucleosome positioning experiments or other experiment types where it is important to have a framework in order to inspect how the coverage distributed across the genome' + diff --git a/recipes/bioconductor-covrna/build.sh b/recipes/bioconductor-covrna/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-covrna/build.sh +++ b/recipes/bioconductor-covrna/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-covrna/meta.yaml b/recipes/bioconductor-covrna/meta.yaml index 96d14fb357596..11e68574e3cae 100644 --- a/recipes/bioconductor-covrna/meta.yaml +++ b/recipes/bioconductor-covrna/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "covRNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6dfee06f3b3722dfa39cac96574c073ca91e6b6ee494961eee2a669b05542da9 + md5: 808e8c797079d7a87f802b5d45935d73 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-ade4 - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-ade4 - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides the analysis methods fourthcorner and RLQ analysis for large-scale transcriptomic data.' extra: identifiers: - biotools:covrna - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-covrna + path: recipes/bioconductor-covrna + version: 1.6.0 + diff --git a/recipes/bioconductor-cpvsnp/build.sh b/recipes/bioconductor-cpvsnp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cpvsnp/build.sh +++ b/recipes/bioconductor-cpvsnp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cpvsnp/meta.yaml b/recipes/bioconductor-cpvsnp/meta.yaml index 045d362ef57ac..b60fb45e398be 100644 --- a/recipes/bioconductor-cpvsnp/meta.yaml +++ b/recipes/bioconductor-cpvsnp/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "cpvSNP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dd9d5369cc78395f7860b5ecb276c04e6f385bc437611e178cf84b486dcababb + md5: 398ce7f3fde5ae72b9a0c171902351b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, BiocGenerics, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-corpcor - r-ggplot2 - r-plyr run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-corpcor - r-ggplot2 @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Gene set analysis methods exist to combine SNP-level association p-values into gene sets, calculating a single association p-value for each gene set. This package implements two such methods that require only the calculated SNP p-values, the gene set(s) of interest, and a correlation matrix (if desired). One method (GLOSSI) requires independent SNPs and the other (VEGAS) can take into account correlation (LD) among the SNPs. Built-in plotting functions are available to help users visualize results.' extra: identifiers: - biotools:cpvsnp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-cpvsnp + path: recipes/bioconductor-cpvsnp + version: 1.12.0 + diff --git a/recipes/bioconductor-cqn/build.sh b/recipes/bioconductor-cqn/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cqn/build.sh +++ b/recipes/bioconductor-cqn/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cqn/meta.yaml b/recipes/bioconductor-cqn/meta.yaml index e408f1b58ad65..a662636ac6259 100644 --- a/recipes/bioconductor-cqn/meta.yaml +++ b/recipes/bioconductor-cqn/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "cqn" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d8ce94ce508dea2284fc121f00dba4ee64b2ddd65c1ef0f2309a65d7cf20db6f + md5: e9d700eb482ac9845651f0440db3ec7f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: scales, edgeR requirements: host: - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-mclust - r-nor1mix - r-quantreg run: - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-mclust - r-nor1mix @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.' extra: identifiers: - biotools:cqn + parent_recipe: + name: bioconductor-cqn + path: recipes/bioconductor-cqn + version: 1.26.0 + diff --git a/recipes/bioconductor-crcl18/meta.yaml b/recipes/bioconductor-crcl18/meta.yaml new file mode 100644 index 0000000000000..87b83983ee992 --- /dev/null +++ b/recipes/bioconductor-crcl18/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "CRCL18" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 552108f3a1772e108e845fea9ac04fa8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'colorectal cancer mRNA and miRNA on 18 cell lines' + diff --git a/recipes/bioconductor-crcl18/post-link.sh b/recipes/bioconductor-crcl18/post-link.sh new file mode 100644 index 0000000000000..329a00cc047ea --- /dev/null +++ b/recipes/bioconductor-crcl18/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="CRCL18_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/CRCL18_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/CRCL18_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-crcl18/bioconductor-crcl18_1.2.0_src_all.tar.gz" +) +MD5="552108f3a1772e108e845fea9ac04fa8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-crcl18/pre-unlink.sh b/recipes/bioconductor-crcl18/pre-unlink.sh new file mode 100644 index 0000000000000..6fb23ca74bfe8 --- /dev/null +++ b/recipes/bioconductor-crcl18/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ CRCL18 diff --git a/recipes/bioconductor-crimage/build.sh b/recipes/bioconductor-crimage/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-crimage/build.sh +++ b/recipes/bioconductor-crimage/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crimage/meta.yaml b/recipes/bioconductor-crimage/meta.yaml index f10163c9c7dc1..4c17c413de0f5 100644 --- a/recipes/bioconductor-crimage/meta.yaml +++ b/recipes/bioconductor-crimage/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "CRImage" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 945b1bd9a5287e961857412ac742b9c881161e4c4b235e67bac15767edcbd9dc + md5: fcab4dae1b32b2a00aedf7c509307ac9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-acgh >=1.58.0,<1.60.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' - r-base - r-e1071 - r-foreach - r-mass - r-sgeostat run: - - 'bioconductor-acgh >=1.58.0,<1.60.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' - r-base - r-e1071 - r-foreach @@ -39,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'CRImage provides functionality to process and analyze images, in particular to classify cells in biological images. Furthermore, in the context of tumor images, it provides functionality to calculate tumour cellularity.' extra: identifiers: - biotools:crimage - doi:10.1126/scitranslmed.3004330 + parent_recipe: + name: bioconductor-crimage + path: recipes/bioconductor-crimage + version: 1.28.0 + diff --git a/recipes/bioconductor-crisprseek/build.sh b/recipes/bioconductor-crisprseek/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-crisprseek/build.sh +++ b/recipes/bioconductor-crisprseek/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprseek/meta.yaml b/recipes/bioconductor-crisprseek/meta.yaml index 0303d6fd3dd36..83345e89aef74 100644 --- a/recipes/bioconductor-crisprseek/meta.yaml +++ b/recipes/bioconductor-crisprseek/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "CRISPRseek" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cc8e9cfdef9a66734b8207dbb38345a725bd4dc0b08399505b7bf64c2abc73b1 + md5: 73f09ccf2c434036da758ab88e0f280c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-hash - r-seqinr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-hash @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. If GeneRfold and GeneR are installed (http://bioconductor.case.edu/bioconductor/2.8/bioc/html/GeneRfold.html, http://bioc.ism.ac.jp/packages/2.8/bioc/html/GeneR.html), then the minimum free energy and bracket notation of secondary structure of gRNA and gRNA backbone constant region will be included in the summary file. This package leverages Biostrings and BSgenome packages.' + summary: 'The package includes functions to find potential guide RNAs for input target sequences, optionally filter guide RNAs without restriction enzyme cut site, or without paired guide RNAs, genome-wide search for off-targets, score, rank, fetch flank sequence and indicate whether the target and off-targets are located in exon region or not. Potential guide RNAs are annotated with total score of the top5 and topN off-targets, detailed topN mismatch sites, restriction enzyme cut sites, and paired guide RNAs. This package leverages Biostrings and BSgenome packages.' extra: identifiers: - biotools:crisprseek + parent_recipe: + name: bioconductor-crisprseek + path: recipes/bioconductor-crisprseek + version: 1.20.0 + diff --git a/recipes/bioconductor-crisprseekplus/build.sh b/recipes/bioconductor-crisprseekplus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-crisprseekplus/build.sh +++ b/recipes/bioconductor-crisprseekplus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprseekplus/conda_build_config.yaml b/recipes/bioconductor-crisprseekplus/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-crisprseekplus/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-crisprseekplus/meta.yaml b/recipes/bioconductor-crisprseekplus/meta.yaml index a99bf1d94d729..a7a6b265b2a9f 100644 --- a/recipes/bioconductor-crisprseekplus/meta.yaml +++ b/recipes/bioconductor-crisprseekplus/meta.yaml @@ -1,44 +1,46 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "crisprseekplus" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ef0a05e770b745512ace4e0b3c56aae299cde00372490ecc75fbf86d674608e0 + md5: 555d70d98d046f584dc4ec325ba9c6cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, rmarkdown, knitr, R.rsp requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-crisprseek >=1.20.0,<1.22.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-guideseq >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-crisprseek >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-guideseq >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dt - r-hash - r-shiny - r-shinyjs run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-crisprseek >=1.20.0,<1.22.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-guideseq >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-crisprseek >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-guideseq >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dt - r-hash - r-shiny @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Bioinformatics platform containing interface to work with offTargetAnalysis and compare2Sequences in the CRISPRseek package, and GUIDEseqAnalysis.' extra: identifiers: - biotools:crisprseekplus - doi:10.1371/journal.pone.0108424 + parent_recipe: + name: bioconductor-crisprseekplus + path: recipes/bioconductor-crisprseekplus + version: 1.6.0 + diff --git a/recipes/bioconductor-crisprvariants/build.sh b/recipes/bioconductor-crisprvariants/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-crisprvariants/build.sh +++ b/recipes/bioconductor-crisprvariants/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crisprvariants/conda_build_config.yaml b/recipes/bioconductor-crisprvariants/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-crisprvariants/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-crisprvariants/meta.yaml b/recipes/bioconductor-crisprvariants/meta.yaml index 7b58deaf33cde..3916b59316ce8 100644 --- a/recipes/bioconductor-crisprvariants/meta.yaml +++ b/recipes/bioconductor-crisprvariants/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "CrispRVariants" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 00e161bb5614820fbaad0753439b2453a8c96fa909ed918ff23da72abb22a332 + md5: 23ba6adc80afcdf68fb73bd81f648097 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, gdata, GenomicFeatures, knitr, rmarkdown, rtracklayer, sangerseqR, testthat, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-ggplot2 >=2.2.0' - r-gridextra @@ -49,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'CrispRVariants provides tools for analysing the results of a CRISPR-Cas9 mutagenesis sequencing experiment, or other sequencing experiments where variants within a given region are of interest. These tools allow users to localize variant allele combinations with respect to any genomic location (e.g. the Cas9 cut site), plot allele combinations and calculate mutation rates with flexible filtering of unrelated variants.' extra: identifiers: - biotools:crisprvariants + parent_recipe: + name: bioconductor-crisprvariants + path: recipes/bioconductor-crisprvariants + version: 1.8.0 + diff --git a/recipes/bioconductor-crlmm/build.sh b/recipes/bioconductor-crlmm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-crlmm/build.sh +++ b/recipes/bioconductor-crlmm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crlmm/conda_build_config.yaml b/recipes/bioconductor-crlmm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-crlmm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-crlmm/meta.yaml b/recipes/bioconductor-crlmm/meta.yaml index 329219b07dd8e..0a8b185874e25 100644 --- a/recipes/bioconductor-crlmm/meta.yaml +++ b/recipes/bioconductor-crlmm/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "crlmm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ce2821228fc573b1bc4dc36d783e74a9500601e13feb89cce877616d152e083a + md5: 0297a5176d679d97b5465292552b151b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: hapmapsnp6, genomewidesnp6Crlmm (>= 1.0.7), GGdata, snpStats, RUnit requirements: host: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-snpchip >=2.26.0,<2.28.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' - r-base - r-beanplot - r-ellipse @@ -37,14 +38,14 @@ requirements: - 'r-rcppeigen >=0.3.1.2.1' - r-vgam run: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-snpchip >=2.26.0,<2.28.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' - r-base - r-beanplot - r-ellipse @@ -62,9 +63,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Faster implementation of CRLMM specific to SNP 5.0 and 6.0 arrays, as well as a copy number tool specific to 5.0, 6.0, and Illumina platforms.' extra: identifiers: - biotools:crlmm + parent_recipe: + name: bioconductor-crlmm + path: recipes/bioconductor-crlmm + version: 1.38.0 + diff --git a/recipes/bioconductor-crossmeta/build.sh b/recipes/bioconductor-crossmeta/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-crossmeta/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-crossmeta/meta.yaml b/recipes/bioconductor-crossmeta/meta.yaml new file mode 100644 index 0000000000000..73c2ecebb7645 --- /dev/null +++ b/recipes/bioconductor-crossmeta/meta.yaml @@ -0,0 +1,91 @@ +{% set version = "1.8.0" %} +{% set name = "crossmeta" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8ca286bce5ef78116e67a41eea184ed2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, lydata, org.Hs.eg.db, testthat, ccdata +requirements: + host: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ccmap >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - 'r-biocmanager >=1.24.0' + - 'r-data.table >=1.10.4' + - 'r-doparallel >=1.0.10' + - 'r-dorng >=1.6' + - 'r-dt >=0.2' + - 'r-fdrtool >=1.2.15' + - 'r-foreach >=1.4.3' + - 'r-ggplot2 >=2.2.1' + - 'r-matrixstats >=0.51.0' + - 'r-metama >=3.1.2' + - 'r-metap >=0.8' + - 'r-miniui >=0.1.1' + - 'r-pander >=0.6.0' + - 'r-plotly >=4.5.6' + - 'r-rcolorbrewer >=1.1.2' + - 'r-rdrop2 >=0.7.0' + - 'r-reshape >=0.8.6' + - 'r-shiny >=1.0.0' + - 'r-stringr >=1.2.0' + run: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ccmap >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - 'r-biocmanager >=1.24.0' + - 'r-data.table >=1.10.4' + - 'r-doparallel >=1.0.10' + - 'r-dorng >=1.6' + - 'r-dt >=0.2' + - 'r-fdrtool >=1.2.15' + - 'r-foreach >=1.4.3' + - 'r-ggplot2 >=2.2.1' + - 'r-matrixstats >=0.51.0' + - 'r-metama >=3.1.2' + - 'r-metap >=0.8' + - 'r-miniui >=0.1.1' + - 'r-pander >=0.6.0' + - 'r-plotly >=4.5.6' + - 'r-rcolorbrewer >=1.1.2' + - 'r-rdrop2 >=0.7.0' + - 'r-reshape >=0.8.6' + - 'r-shiny >=1.0.0' + - 'r-stringr >=1.2.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Implements cross-platform and cross-species meta-analyses of Affymentrix, Illumina, and Agilent microarray data. This package automates common tasks such as downloading, normalizing, and annotating raw GEO data. The user then selects control and treatment samples in order to perform differential expression/pathway analyses for all comparisons. After analysing each contrast seperately, the user can select tissue sources for each contrast and specify any tissue sources that should be grouped for the subsequent meta-analyses. Finally, effect size and pathway meta-analyses can proceed and the results graphically explored.' + diff --git a/recipes/bioconductor-csar/build.sh b/recipes/bioconductor-csar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-csar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-csar/meta.yaml b/recipes/bioconductor-csar/meta.yaml new file mode 100644 index 0000000000000..b3059df2ba746 --- /dev/null +++ b/recipes/bioconductor-csar/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.34.0" %} +{% set name = "CSAR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cb843cd969ee7b70323486c565279993 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ShortRead, Biostrings +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Statistical tools for ChIP-seq data analysis. The package includes the statistical method described in Kaufmann et al. (2009) PLoS Biology: 7(4):e1000090. Briefly, Taking the average DNA fragment size subjected to sequencing into account, the software calculates genomic single-nucleotide read-enrichment values. After normalization, sample and control are compared using a test based on the Poisson distribution. Test statistic thresholds to control the false discovery rate are obtained through random permutation.' + diff --git a/recipes/bioconductor-csaw/build.sh b/recipes/bioconductor-csaw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-csaw/build.sh +++ b/recipes/bioconductor-csaw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-csaw/conda_build_config.yaml b/recipes/bioconductor-csaw/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-csaw/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-csaw/meta.yaml b/recipes/bioconductor-csaw/meta.yaml index 6675885ee89c7..74d7dbec4bfff 100644 --- a/recipes/bioconductor-csaw/meta.yaml +++ b/recipes/bioconductor-csaw/meta.yaml @@ -1,52 +1,56 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "csaw" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 718a6ce380ae8d7f72b1da2434705a459b373bb5fb1eb824823947949c6935ba + md5: a2e1154cfc380fba475e70c86339e18d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.knownGene, testthat +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-rcpp run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-rcpp build: @@ -57,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Detection of differentially bound regions in ChIP-seq data with sliding windows, with methods for normalization and proper FDR control.' extra: identifiers: - biotools:csaw + parent_recipe: + name: bioconductor-csaw + path: recipes/bioconductor-csaw + version: 1.14.1 + diff --git a/recipes/bioconductor-cssp/build.sh b/recipes/bioconductor-cssp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cssp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cssp/meta.yaml b/recipes/bioconductor-cssp/meta.yaml new file mode 100644 index 0000000000000..5d3eea5b8ba02 --- /dev/null +++ b/recipes/bioconductor-cssp/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "CSSP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 80255d123a4ba68f4b7bc8eafa0f30f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Power computation for ChIP-Seq data based on Bayesian estimation for local poisson counting process.' + diff --git a/recipes/bioconductor-ctc/build.sh b/recipes/bioconductor-ctc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ctc/build.sh +++ b/recipes/bioconductor-ctc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctc/meta.yaml b/recipes/bioconductor-ctc/meta.yaml index 0f5a66b82713b..946fc3ab61669 100644 --- a/recipes/bioconductor-ctc/meta.yaml +++ b/recipes/bioconductor-ctc/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ctc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 694e669972363fef4a07e0402c29a590e4854d1bded86aa3f9c3264b2abd4d69 + md5: fe42ef0d23d5e1861c71b74a423f17e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-amap @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Tools for export and import classification trees and clusters to other programs' extra: identifiers: - biotools:ctc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ctc + path: recipes/bioconductor-ctc + version: 1.54.0 + diff --git a/recipes/bioconductor-ctdquerier/build.sh b/recipes/bioconductor-ctdquerier/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ctdquerier/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctdquerier/meta.yaml b/recipes/bioconductor-ctdquerier/meta.yaml new file mode 100644 index 0000000000000..ecccae8ca9ed9 --- /dev/null +++ b/recipes/bioconductor-ctdquerier/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "CTDquerier" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 30fbafbd91f9c7191e26145edd756856 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr +requirements: + host: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-igraph + - r-rappdirs + - r-rcurl + - r-stringdist + - r-stringr + run: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-igraph + - r-rappdirs + - r-rcurl + - r-stringdist + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Package to retrieve and visualize data from the Comparative Toxicogenomics Database (http://ctdbase.org/). The downloaded data is formated as DataFrames for further downstream analyses.' + diff --git a/recipes/bioconductor-ctrap/build.sh b/recipes/bioconductor-ctrap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ctrap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctrap/meta.yaml b/recipes/bioconductor-ctrap/meta.yaml new file mode 100644 index 0000000000000..f32b6236c3fd9 --- /dev/null +++ b/recipes/bioconductor-ctrap/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.3" %} +{% set name = "cTRAP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: df4aabaf7896ba049296d92bd7885506 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, covr, biomaRt +requirements: + host: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-piano >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-base + - r-cowplot + - r-data.table + - r-ggplot2 + - r-httr + - r-pbapply + - r-plyr + - r-r.utils + - r-readr + run: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-piano >=1.22.0,<1.23.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-base + - r-cowplot + - r-data.table + - r-ggplot2 + - r-httr + - r-pbapply + - r-plyr + - r-r.utils + - r-readr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Compare differential gene expression results with those from known cellular perturbations (such as gene knock-down, overexpression or small molecules) derived from the Connectivity Map. Such analyses allow not only to infer the molecular causes of the observed difference in gene expression but also to identify small molecules that could drive or revert specific transcriptomic alterations.' + diff --git a/recipes/bioconductor-ctsge/build.sh b/recipes/bioconductor-ctsge/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ctsge/build.sh +++ b/recipes/bioconductor-ctsge/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ctsge/meta.yaml b/recipes/bioconductor-ctsge/meta.yaml index 44972efff7f72..74f0c84b81667 100644 --- a/recipes/bioconductor-ctsge/meta.yaml +++ b/recipes/bioconductor-ctsge/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "ctsGE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0460482b3575ca441698824da239d230295f71599df7502f6d6426cd37136afb + md5: 874c15078bf9b02310a3ba4695b44b1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, dplyr, DT, GEOquery, knitr, pander, rmarkdown, testthat requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ccapp - r-ggplot2 @@ -26,7 +28,7 @@ requirements: - r-shiny - r-stringr run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ccapp - r-ggplot2 @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Methodology for supervised clustering of potentially many predictor variables, such as genes etc., in time series datasets Provides functions that help the user assigning genes to predefined set of model profiles.' extra: identifiers: - biotools:ctsge - doi:10.1093/bioinformatics/btx116 + parent_recipe: + name: bioconductor-ctsge + path: recipes/bioconductor-ctsge + version: 1.6.1 + diff --git a/recipes/bioconductor-cummerbund/build.sh b/recipes/bioconductor-cummerbund/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cummerbund/build.sh +++ b/recipes/bioconductor-cummerbund/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cummerbund/meta.yaml b/recipes/bioconductor-cummerbund/meta.yaml index dbdd23afde242..8db061dc53887 100644 --- a/recipes/bioconductor-cummerbund/meta.yaml +++ b/recipes/bioconductor-cummerbund/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "cummeRbund" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: edc8d4c2e0b1cf6b8096ba69d84aecb083dea9a135a72d5b511d37ebb2e61596 + md5: a713a35d1c8f2a837d9c5a8ab86b8f72 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: cluster, plyr, NMFN, stringr, GenomicFeatures, GenomicRanges, rjson requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fastcluster - r-ggplot2 @@ -30,11 +32,11 @@ requirements: - r-reshape2 - r-rsqlite run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fastcluster - r-ggplot2 @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Allows for persistent storage, access, exploration, and manipulation of Cufflinks high-throughput sequencing data. In addition, provides numerous plotting functions for commonly used visualizations.' extra: identifiers: - biotools:cummerbund - doi:10.1038/nprot.2012.016 + parent_recipe: + name: bioconductor-cummerbund + path: recipes/bioconductor-cummerbund + version: 2.22.0 + diff --git a/recipes/bioconductor-curatedbladderdata/meta.yaml b/recipes/bioconductor-curatedbladderdata/meta.yaml new file mode 100644 index 0000000000000..4f2eec7eaadca --- /dev/null +++ b/recipes/bioconductor-curatedbladderdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "curatedBladderData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9626900fba87d603d8a0d7b068f3ce02 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, survival, xtable, sva, genefilter, logging +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The curatedBladderData package provides relevant functions and data for gene expression analysis in patients with bladder cancer.' + diff --git a/recipes/bioconductor-curatedbladderdata/post-link.sh b/recipes/bioconductor-curatedbladderdata/post-link.sh new file mode 100644 index 0000000000000..34b380fbcd462 --- /dev/null +++ b/recipes/bioconductor-curatedbladderdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedBladderData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedBladderData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedBladderData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedbladderdata/bioconductor-curatedbladderdata_1.18.0_src_all.tar.gz" +) +MD5="9626900fba87d603d8a0d7b068f3ce02" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedbladderdata/pre-unlink.sh b/recipes/bioconductor-curatedbladderdata/pre-unlink.sh new file mode 100644 index 0000000000000..cc76e604b3460 --- /dev/null +++ b/recipes/bioconductor-curatedbladderdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedBladderData diff --git a/recipes/bioconductor-curatedbreastdata/meta.yaml b/recipes/bioconductor-curatedbreastdata/meta.yaml new file mode 100644 index 0000000000000..22e3d229baad8 --- /dev/null +++ b/recipes/bioconductor-curatedbreastdata/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.10.0" %} +{% set name = "curatedBreastData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f331996cfe36abc88dbc84a8fde187c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-ggplot2 + - r-xml + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-ggplot2 + - r-xml + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Curated human breast cancer tissue S4 ExpresionSet datasets from over 16 clinical trials comprising over 2,000 patients. All datasets contain at least one type of outcomes variable and treatment information (minimum level: whether they had chemotherapy and whether they had hormonal therapy). Includes code to post-process these datasets.' + diff --git a/recipes/bioconductor-curatedbreastdata/post-link.sh b/recipes/bioconductor-curatedbreastdata/post-link.sh new file mode 100644 index 0000000000000..2ff59a64889aa --- /dev/null +++ b/recipes/bioconductor-curatedbreastdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedBreastData_2.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedBreastData_2.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedBreastData_2.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedbreastdata/bioconductor-curatedbreastdata_2.10.0_src_all.tar.gz" +) +MD5="f331996cfe36abc88dbc84a8fde187c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedbreastdata/pre-unlink.sh b/recipes/bioconductor-curatedbreastdata/pre-unlink.sh new file mode 100644 index 0000000000000..b6217451cf4a7 --- /dev/null +++ b/recipes/bioconductor-curatedbreastdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedBreastData diff --git a/recipes/bioconductor-curatedcrcdata/meta.yaml b/recipes/bioconductor-curatedcrcdata/meta.yaml new file mode 100644 index 0000000000000..3542d0d1fea45 --- /dev/null +++ b/recipes/bioconductor-curatedcrcdata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "2.14.0" %} +{% set name = "curatedCRCData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 930dbdba821daa1232beb01eee233d80 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-nlme + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-nlme + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The curatedCRC package provides relevant functions and data for gene expression analysis in patients with colorectal cancer.' + diff --git a/recipes/bioconductor-curatedcrcdata/post-link.sh b/recipes/bioconductor-curatedcrcdata/post-link.sh new file mode 100644 index 0000000000000..71f39b75f3357 --- /dev/null +++ b/recipes/bioconductor-curatedcrcdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedCRCData_2.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedCRCData_2.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedCRCData_2.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedcrcdata/bioconductor-curatedcrcdata_2.14.0_src_all.tar.gz" +) +MD5="930dbdba821daa1232beb01eee233d80" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedcrcdata/pre-unlink.sh b/recipes/bioconductor-curatedcrcdata/pre-unlink.sh new file mode 100644 index 0000000000000..1536601aeba40 --- /dev/null +++ b/recipes/bioconductor-curatedcrcdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedCRCData diff --git a/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml b/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-curatedmetagenomicdata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml index b44a073ec828d..5b3537252deb0 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/meta.yaml +++ b/recipes/bioconductor-curatedmetagenomicdata/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.3" %} {% set name = "curatedMetagenomicData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 873352867c5af358425f497c95e5a51834a73b808d28ab4319d9e5b1a5fa036a + md5: 647d57c43704bee51d7d54327e419cd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocManager, devtools, roxygen2, testthat, covr, knitr, rmarkdown, BiocCheck, BiocStyle, BiocParallel, readr, RISmed, ggplot2, metagenomeSeq, phyloseq, ape requirements: host: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-experimenthub >=1.6.1,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr - r-tidyr run: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-experimenthub >=1.6.1,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-dplyr >=0.5.0' - r-magrittr @@ -40,6 +42,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 - summary: ' The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites.' + summary: 'The curatedMetagenomicData package provides microbial taxonomic, functional, and gene marker abundance for samples collected from different bodysites.' +extra: + parent_recipe: + name: bioconductor-curatedmetagenomicdata + path: recipes/bioconductor-curatedmetagenomicdata + version: 1.10.2 + diff --git a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh index 406f8735b1e59..31be771a6b2cb 100644 --- a/recipes/bioconductor-curatedmetagenomicdata/post-link.sh +++ b/recipes/bioconductor-curatedmetagenomicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedMetagenomicData_1.10.2.tar.gz" +FN="curatedMetagenomicData_1.12.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/curatedMetagenomicData_1.10.2.tar.gz" - "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.10.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.10.2_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedMetagenomicData_1.12.3.tar.gz" + "https://bioarchive.galaxyproject.org/curatedMetagenomicData_1.12.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedmetagenomicdata/bioconductor-curatedmetagenomicdata_1.12.3_src_all.tar.gz" ) -MD5="36b9a395b479a4024fbf376e3009dc02" +MD5="647d57c43704bee51d7d54327e419cd4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-curatedovariandata/conda_build_config.yaml b/recipes/bioconductor-curatedovariandata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-curatedovariandata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-curatedovariandata/meta.yaml b/recipes/bioconductor-curatedovariandata/meta.yaml index 652fd76d63ed4..b80df52bbb3ad 100644 --- a/recipes/bioconductor-curatedovariandata/meta.yaml +++ b/recipes/bioconductor-curatedovariandata/meta.yaml @@ -1,35 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "curatedOvarianData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b7663661c156fd6b616562850c49fd98dddb7dd32f9a04ba7eb5abe87809f3d9 + md5: 7c3a22afa72323d96332d78df1478c8a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: survival, RUnit, metafor, genefilter, logging, sva, xtable, futile.logger, BiocStyle requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'The curatedOvarianData package provides data for gene expression analysis in patients with ovarian cancer.' +extra: + parent_recipe: + name: bioconductor-curatedovariandata + path: recipes/bioconductor-curatedovariandata + version: 1.18.0 + diff --git a/recipes/bioconductor-curatedovariandata/post-link.sh b/recipes/bioconductor-curatedovariandata/post-link.sh index e7a730f612358..65e509d207d67 100644 --- a/recipes/bioconductor-curatedovariandata/post-link.sh +++ b/recipes/bioconductor-curatedovariandata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="curatedOvarianData_1.18.0.tar.gz" +FN="curatedOvarianData_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/curatedOvarianData_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/curatedOvarianData_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedOvarianData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedOvarianData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedovariandata/bioconductor-curatedovariandata_1.20.0_src_all.tar.gz" ) -MD5="0fd49d3ff3764702e6324e8e03af2a0a" +MD5="7c3a22afa72323d96332d78df1478c8a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-curatedtcgadata/meta.yaml b/recipes/bioconductor-curatedtcgadata/meta.yaml new file mode 100644 index 0000000000000..a62774f47ddc9 --- /dev/null +++ b/recipes/bioconductor-curatedtcgadata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.4.0" %} +{% set name = "curatedTCGAData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2bb34b9c62fc697c3fff464396c08b91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, readr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides publicly available data from The Cancer Genome Atlas (TCGA) Bioconductor MultiAssayExperiment class objects. These objects integrate multiple assays (e.g. RNA-seq, copy number, mutation, microRNA, protein, and others) with clinical / pathological data. The MultiAssayExperiment class links assay barcodes with patient IDs, enabling harmonized subsetting of rows (features) and columns (patients / samples) across the entire experiment.' + diff --git a/recipes/bioconductor-curatedtcgadata/post-link.sh b/recipes/bioconductor-curatedtcgadata/post-link.sh new file mode 100644 index 0000000000000..65821a4340406 --- /dev/null +++ b/recipes/bioconductor-curatedtcgadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="curatedTCGAData_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/curatedTCGAData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/curatedTCGAData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-curatedtcgadata/bioconductor-curatedtcgadata_1.4.0_src_all.tar.gz" +) +MD5="2bb34b9c62fc697c3fff464396c08b91" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-curatedtcgadata/pre-unlink.sh b/recipes/bioconductor-curatedtcgadata/pre-unlink.sh new file mode 100644 index 0000000000000..b2a643f91dfa4 --- /dev/null +++ b/recipes/bioconductor-curatedtcgadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ curatedTCGAData diff --git a/recipes/bioconductor-customprodb/build.sh b/recipes/bioconductor-customprodb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-customprodb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-customprodb/meta.yaml b/recipes/bioconductor-customprodb/meta.yaml new file mode 100644 index 0000000000000..a975bd7f339b7 --- /dev/null +++ b/recipes/bioconductor-customprodb/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.22.0" %} +{% set name = "customProDB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 971e7cda62bc25dfa59f452ce73b1d09 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-ahocorasicktrie + - r-base + - r-dbi + - r-plyr + - r-rcurl + - r-rsqlite + - r-stringr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-ahocorasicktrie + - r-base + - r-dbi + - r-plyr + - r-rcurl + - r-rsqlite + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Database search is the most widely used approach for peptide and protein identification in mass spectrometry-based proteomics studies. Our previous study showed that sample-specific protein databases derived from RNA-Seq data can better approximate the real protein pools in the samples and thus improve protein identification. More importantly, single nucleotide variations, short insertion and deletions and novel junctions identified from RNA-Seq data make protein database more complete and sample-specific. Here, we report an R package customProDB that enables the easy generation of customized databases from RNA-Seq data for proteomics search. This work bridges genomics and proteomics studies and facilitates cross-omics data integration.' + diff --git a/recipes/bioconductor-cve/build.sh b/recipes/bioconductor-cve/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cve/build.sh +++ b/recipes/bioconductor-cve/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cve/meta.yaml b/recipes/bioconductor-cve/meta.yaml index 8c11ef9a582da..36c87775f82f6 100644 --- a/recipes/bioconductor-cve/meta.yaml +++ b/recipes/bioconductor-cve/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "CVE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ea637575e5524138da65c50e14b02e41873927bb3b916404cd8d514c694d8d22 + md5: b21a70bfa5c7401ffd91e3eb8be07d39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, RTCGAToolbox, testthat, BiocStyle requirements: host: - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - r-ape - r-base - r-ggplot2 @@ -27,9 +29,10 @@ requirements: - r-plyr - r-rcolorbrewer - r-shiny + - r-tidyverse - r-wgcna run: - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' - r-ape - r-base - r-ggplot2 @@ -38,15 +41,21 @@ requirements: - r-plyr - r-rcolorbrewer - r-shiny + - r-tidyverse - r-wgcna test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Shiny app for interactive variant prioritisation in precision oncology. The input file for CVE is the output file of the recently released Oncotator Variant Annotation tool summarising variant-centric information from 14 different publicly available resources relevant for cancer researches. Interactive priortisation in CVE is based on known germline and cancer variants, DNA repair genes and functional prediction scores. An optional feature of CVE is the exploration of the tumour-specific pathway context that is facilitated using co-expression modules generated from publicly available transcriptome data. Finally druggability of prioritised variants is assessed using the Drug Gene Interaction Database (DGIdb).' extra: identifiers: - biotools:cve - doi:10.1186/s12920-017-0261-6 + parent_recipe: + name: bioconductor-cve + path: recipes/bioconductor-cve + version: 1.6.0 + diff --git a/recipes/bioconductor-cycle/build.sh b/recipes/bioconductor-cycle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cycle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cycle/meta.yaml b/recipes/bioconductor-cycle/meta.yaml new file mode 100644 index 0000000000000..eff1f19f26bbe --- /dev/null +++ b/recipes/bioconductor-cycle/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.36.0" %} +{% set name = "cycle" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 20c0540915e76d5897c280c086256c36 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mfuzz >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mfuzz >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Package for assessing the statistical significance of periodic expression based on Fourier analysis and comparison with data generated by different background models' + diff --git a/recipes/bioconductor-cydar/build.sh b/recipes/bioconductor-cydar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cydar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cydar/meta.yaml b/recipes/bioconductor-cydar/meta.yaml new file mode 100644 index 0000000000000..2f26bba532060 --- /dev/null +++ b/recipes/bioconductor-cydar/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.6.0" %} +{% set name = "cydar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dd6fc3308e6af0aa4eb5a496c287f63d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ncdfFlow, testthat, knitr, edgeR, limma, glmnet, BiocStyle, flowStats +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rcpp + - r-shiny + - r-viridis + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rcpp + - r-shiny + - r-viridis + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Identifies differentially abundant populations between samples and groups in mass cytometry data. Provides methods for counting cells into hyperspheres, controlling the spatial false discovery rate, and visualizing changes in abundance in the high-dimensional marker space.' + diff --git a/recipes/bioconductor-cyp450cdf/meta.yaml b/recipes/bioconductor-cyp450cdf/meta.yaml new file mode 100644 index 0000000000000..956b267bd0954 --- /dev/null +++ b/recipes/bioconductor-cyp450cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "cyp450cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7923c4d24b7b654d0f59d52ed2258eb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the CYP450.CDF file.' + diff --git a/recipes/bioconductor-cyp450cdf/post-link.sh b/recipes/bioconductor-cyp450cdf/post-link.sh new file mode 100644 index 0000000000000..aaa49374be2eb --- /dev/null +++ b/recipes/bioconductor-cyp450cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="cyp450cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/cyp450cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/cyp450cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-cyp450cdf/bioconductor-cyp450cdf_2.18.0_src_all.tar.gz" +) +MD5="7923c4d24b7b654d0f59d52ed2258eb9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-cyp450cdf/pre-unlink.sh b/recipes/bioconductor-cyp450cdf/pre-unlink.sh new file mode 100644 index 0000000000000..cbb4023e0c416 --- /dev/null +++ b/recipes/bioconductor-cyp450cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ cyp450cdf diff --git a/recipes/bioconductor-cytodx/build.sh b/recipes/bioconductor-cytodx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytodx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytodx/meta.yaml b/recipes/bioconductor-cytodx/meta.yaml new file mode 100644 index 0000000000000..6f11d2af43d7c --- /dev/null +++ b/recipes/bioconductor-cytodx/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "CytoDx" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e27c398bc0ce56c5e2e2761ef520ce48 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-doparallel + - r-dplyr + - r-glmnet + - r-rpart + - r-rpart.plot + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-doparallel + - r-dplyr + - r-glmnet + - r-rpart + - r-rpart.plot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides functions that predict clinical outcomes using single cell data (such as flow cytometry data, RNA single cell sequencing data) without the requirement of cell gating or clustering.' + diff --git a/recipes/bioconductor-cytolib/build.sh b/recipes/bioconductor-cytolib/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-cytolib/build.sh +++ b/recipes/bioconductor-cytolib/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytolib/meta.yaml b/recipes/bioconductor-cytolib/meta.yaml index 2136b887eb320..593d2f9e8b16e 100644 --- a/recipes/bioconductor-cytolib/meta.yaml +++ b/recipes/bioconductor-cytolib/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "cytolib" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b348fb0dbe1b53484807e9a94fc14654afccdefab039ddd19037fa5cb94ca865 + md5: 4f085d7dc4cc1497651af1528af81d09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr +# SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' + - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' - r-base - 'r-bh >=1.62.0-1' run: - - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' + - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' - r-base - 'r-bh >=1.62.0-1' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides the core data structure and API to represent and interact with the gated cytometry data.' - +extra: + parent_recipe: + name: bioconductor-cytolib + path: recipes/bioconductor-cytolib + version: 1.2.0 diff --git a/recipes/bioconductor-cytoml/build.sh b/recipes/bioconductor-cytoml/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-cytoml/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-cytoml/meta.yaml b/recipes/bioconductor-cytoml/meta.yaml new file mode 100644 index 0000000000000..449aabe62609a --- /dev/null +++ b/recipes/bioconductor-cytoml/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.8.0" %} +{% set name = "CytoML" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a48283d851e9a8667be67d5c665c85f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, flowWorkspaceData (>= 2.11.1), knitr, parallel +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowutils >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ggcyto >=1.10.0,<1.11.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-opencyto >=1.20.0,<1.21.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-base64enc + - r-data.table + - r-jsonlite + - r-plyr + - r-xml + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowutils >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ggcyto >=1.10.0,<1.11.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-opencyto >=1.20.0,<1.21.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-base64enc + - r-data.table + - r-jsonlite + - r-plyr + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Uses platform-specific implemenations of the GatingML2.0 standard to exchange gated cytometry data with other software platforms.' + diff --git a/recipes/bioconductor-dada2/build.sh b/recipes/bioconductor-dada2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dada2/build.sh +++ b/recipes/bioconductor-dada2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dada2/meta.yaml b/recipes/bioconductor-dada2/meta.yaml index 34ad7daa6c6b9..beb4c3cb6586f 100644 --- a/recipes/bioconductor-dada2/meta.yaml +++ b/recipes/bioconductor-dada2/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "dada2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0444f3cbe52037a25d80052f081e2e7c4ad2167faab76d1b3d3f036186e3d824 + md5: 4ee982f882667aefb39624b5b71df387 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: GNU make requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' @@ -30,11 +32,11 @@ requirements: - 'r-rcppparallel >=4.3.0' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-data.table >=1.9.4' - 'r-ggplot2 >=2.1.0' @@ -49,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 - summary: 'The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and genus-species assignment by exact matching.' + summary: 'The dada2 package infers exact amplicon sequence variants (ASVs) from high-throughput amplicon sequencing data, replacing the coarser and less accurate OTU clustering approach. The dada2 pipeline takes as input demultiplexed fastq files, and outputs the sequence variants and their sample-wise abundances after removing substitution and chimera errors. Taxonomic classification is available via a native implementation of the RDP naive Bayesian classifier, and species-level assignment to 16S rRNA gene fragments by exact matching.' extra: identifiers: - biotools:dada2 + parent_recipe: + name: bioconductor-dada2 + path: recipes/bioconductor-dada2 + version: 1.8.0 + diff --git a/recipes/bioconductor-daglogo/build.sh b/recipes/bioconductor-daglogo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-daglogo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-daglogo/meta.yaml b/recipes/bioconductor-daglogo/meta.yaml new file mode 100644 index 0000000000000..a5775ecd8ae6c --- /dev/null +++ b/recipes/bioconductor-daglogo/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "dagLogo" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eb5d6fe6ff233fd79d7c1ed8fff34965 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: XML, BiocStyle, knitr, rmarkdown, testthat, UniProt.ws +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - r-base + - r-grimport + - r-pheatmap + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - r-base + - r-grimport + - r-pheatmap +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Visualize significant conserved amino acid sequence pattern in groups based on probability theory.' + diff --git a/recipes/bioconductor-dama/build.sh b/recipes/bioconductor-dama/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dama/build.sh +++ b/recipes/bioconductor-dama/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dama/meta.yaml b/recipes/bioconductor-dama/meta.yaml index 21354013ac775..445853cf45c4b 100644 --- a/recipes/bioconductor-dama/meta.yaml +++ b/recipes/bioconductor-dama/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "daMA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b202d97c77ea55125f56cd048a20a3e7c08a23f48d3c54ddcb17f501bdb92aff + md5: 51df11f7dc90a9ac4ab8f24e61584a0a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains functions for the efficient design of factorial two-colour microarray experiments and for the statistical analysis of factorial microarray data. Statistical details are described in Bretz et al. (2003, submitted)' extra: identifiers: - biotools:dama - doi:10.1016/j.csda.2004.08.014 + parent_recipe: + name: bioconductor-dama + path: recipes/bioconductor-dama + version: 1.52.0 + diff --git a/recipes/bioconductor-damirseq/build.sh b/recipes/bioconductor-damirseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-damirseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-damirseq/meta.yaml b/recipes/bioconductor-damirseq/meta.yaml new file mode 100644 index 0000000000000..6772db86b33d8 --- /dev/null +++ b/recipes/bioconductor-damirseq/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.6.1" %} +{% set name = "DaMiRseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f76e686c9519a275d45ed70899e87be8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-arm + - r-base + - r-caret + - r-corrplot + - r-e1071 + - r-factominer + - r-fselector + - r-ggplot2 + - r-hmisc + - r-ineq + - r-kknn + - r-lubridate + - r-mass + - r-pheatmap + - r-pls + - r-plsvarsel + - r-randomforest + - r-rcolorbrewer + - r-reshape2 + - r-rsnns + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-arm + - r-base + - r-caret + - r-corrplot + - r-e1071 + - r-factominer + - r-fselector + - r-ggplot2 + - r-hmisc + - r-ineq + - r-kknn + - r-lubridate + - r-mass + - r-pheatmap + - r-pls + - r-plsvarsel + - r-randomforest + - r-rcolorbrewer + - r-reshape2 + - r-rsnns +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The DaMiRseq package offers a tidy pipeline of data mining procedures to identify transcriptional biomarkers and exploit them for both binary and multi-class classification purposes. The package accepts any kind of data presented as a table of raw counts and allows including both continous and factorial variables that occur with the experimental setting. A series of functions enable the user to clean up the data by filtering genomic features and samples, to adjust data by identifying and removing the unwanted source of variation (i.e. batches and confounding factors) and to select the best predictors for modeling. Finally, a "stacking" ensemble learning technique is applied to build a robust classification model. Every step includes a checkpoint that the user may exploit to assess the effects of data management by looking at diagnostic plots, such as clustering and heatmaps, RLE boxplots, MDS or correlation plot.' + diff --git a/recipes/bioconductor-dapar/build.sh b/recipes/bioconductor-dapar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dapar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dapar/meta.yaml b/recipes/bioconductor-dapar/meta.yaml new file mode 100644 index 0000000000000..070d74a2d6c78 --- /dev/null +++ b/recipes/bioconductor-dapar/meta.yaml @@ -0,0 +1,109 @@ +{% set version = "1.14.2" %} +{% set name = "DAPAR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e846c78c32f5be0e021480a2c71c43c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, Biobase, testthat, BiocStyle +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-cairo + - 'r-cp4p >=0.3.5' + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-foreach + - r-ggplot2 + - r-gplots + - 'r-highcharter >=0.5.0' + - 'r-imp4p >=0.7' + - r-knitr + - r-lattice + - r-lme4 + - r-matrix + - r-norm + - r-openxlsx + - r-png + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tidyr + - r-tidyverse + - r-tmvtnorm + - r-vioplot + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-cairo + - 'r-cp4p >=0.3.5' + - r-doparallel + - r-dplyr + - r-factoextra + - r-factominer + - r-foreach + - r-ggplot2 + - r-gplots + - 'r-highcharter >=0.5.0' + - 'r-imp4p >=0.7' + - r-knitr + - r-lattice + - r-lme4 + - r-matrix + - r-norm + - r-openxlsx + - r-png + - r-rcolorbrewer + - r-readxl + - r-reshape2 + - r-scales + - r-stringr + - r-tidyr + - r-tidyverse + - r-tmvtnorm + - r-vioplot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains a collection of functions for the visualisation and the statistical analysis of proteomic data.' + diff --git a/recipes/bioconductor-dapardata/meta.yaml b/recipes/bioconductor-dapardata/meta.yaml new file mode 100644 index 0000000000000..961cc24649b34 --- /dev/null +++ b/recipes/bioconductor-dapardata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.12.1" %} +{% set name = "DAPARdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5db15dae7303ec5f823c84377aa5c12c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DAPAR, Prostar +requirements: + host: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + - r-knitr + run: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + - r-knitr + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Mass-spectrometry based UPS proteomics data sets from Ramus C, Hovasse A, Marcellin M, Hesse AM, Mouton-Barbosa E, Bouyssie D, Vaca S, Carapito C, Chaoui K, Bruley C, Garin J, Cianferani S, Ferro M, Dorssaeler AV, Burlet-Schiltz O, Schaeffer C, Coute Y, Gonzalez de Peredo A. Spiked proteomic standard dataset for testing label-free quantitative software and statistical methods. Data Brief. 2015 Dec 17;6:286-94 and Giai Gianetto, Q., Combes, F., Ramus, C., Bruley, C., Coute, Y., Burger, T. (2016). Calibration plot for proteomics: A graphical tool to visually check the assumptions underlying FDR control in quantitative experiments. Proteomics, 16(1), 29-32.' + diff --git a/recipes/bioconductor-dapardata/post-link.sh b/recipes/bioconductor-dapardata/post-link.sh new file mode 100644 index 0000000000000..0e24a67331a56 --- /dev/null +++ b/recipes/bioconductor-dapardata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DAPARdata_1.12.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DAPARdata_1.12.1.tar.gz" + "https://bioarchive.galaxyproject.org/DAPARdata_1.12.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dapardata/bioconductor-dapardata_1.12.1_src_all.tar.gz" +) +MD5="5db15dae7303ec5f823c84377aa5c12c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dapardata/pre-unlink.sh b/recipes/bioconductor-dapardata/pre-unlink.sh new file mode 100644 index 0000000000000..9b2172bea1d55 --- /dev/null +++ b/recipes/bioconductor-dapardata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DAPARdata diff --git a/recipes/bioconductor-dart/build.sh b/recipes/bioconductor-dart/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dart/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dart/meta.yaml b/recipes/bioconductor-dart/meta.yaml new file mode 100644 index 0000000000000..f714076b59c2e --- /dev/null +++ b/recipes/bioconductor-dart/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.30.0" %} +{% set name = "DART" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a2c0ddeb30154385e9b4672c8d137fac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: breastCancerVDX, breastCancerMAINZ, Biobase +requirements: + host: + - r-base + - 'r-igraph >=0.6.0' + run: + - r-base + - 'r-igraph >=0.6.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Denoising Algorithm based on Relevance network Topology (DART) is an algorithm designed to evaluate the consistency of prior information molecular signatures (e.g in-vitro perturbation expression signatures) in independent molecular data (e.g gene expression data sets). If consistent, a pruning network strategy is then used to infer the activation status of the molecular signature in individual samples.' + diff --git a/recipes/bioconductor-davidtiling/meta.yaml b/recipes/bioconductor-davidtiling/meta.yaml new file mode 100644 index 0000000000000..5b85384265c14 --- /dev/null +++ b/recipes/bioconductor-davidtiling/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.22.0" %} +{% set name = "davidTiling" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ace6b4becfd62c19a8b353de336d6ca6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package contains the data for the paper by L. David et al. in PNAS 2006 (PMID 16569694): 8 CEL files of Affymetrix genechips, an ExpressionSet object with the raw feature data, a probe annotation data structure for the chip and the yeast genome annotation (GFF file) that was used. In addition, some custom-written analysis functions are provided, as well as R scripts in the scripts directory.' + diff --git a/recipes/bioconductor-davidtiling/post-link.sh b/recipes/bioconductor-davidtiling/post-link.sh new file mode 100644 index 0000000000000..47cec70bdc6ff --- /dev/null +++ b/recipes/bioconductor-davidtiling/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="davidTiling_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/davidTiling_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/davidTiling_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-davidtiling/bioconductor-davidtiling_1.22.0_src_all.tar.gz" +) +MD5="ace6b4becfd62c19a8b353de336d6ca6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-davidtiling/pre-unlink.sh b/recipes/bioconductor-davidtiling/pre-unlink.sh new file mode 100644 index 0000000000000..58247b30d3e66 --- /dev/null +++ b/recipes/bioconductor-davidtiling/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ davidTiling diff --git a/recipes/bioconductor-dbchip/build.sh b/recipes/bioconductor-dbchip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dbchip/build.sh +++ b/recipes/bioconductor-dbchip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dbchip/meta.yaml b/recipes/bioconductor-dbchip/meta.yaml index a706e46279277..5dc0e15bdbbf6 100644 --- a/recipes/bioconductor-dbchip/meta.yaml +++ b/recipes/bioconductor-dbchip/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "DBChIP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1730dedbabacbeb22181dda8d9929e185a478721b7eb51204f8d2655f7c2c3c9 + md5: d2ca8f6a4e640074c6de45eba4db9a50 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ShortRead, BiocGenerics requirements: host: - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base run: - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'DBChIP detects differentially bound sharp binding sites across multiple conditions, with or without matching control samples.' - +extra: + parent_recipe: + name: bioconductor-dbchip + path: recipes/bioconductor-dbchip + version: 1.24.0 diff --git a/recipes/bioconductor-dcgsa/build.sh b/recipes/bioconductor-dcgsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dcgsa/build.sh +++ b/recipes/bioconductor-dcgsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dcgsa/meta.yaml b/recipes/bioconductor-dcgsa/meta.yaml index 0acb71ec61caa..0583ac96eaae9 100644 --- a/recipes/bioconductor-dcgsa/meta.yaml +++ b/recipes/bioconductor-dcgsa/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "dcGSA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3719cf082f6fb781bb157b156692cabb538e8ba101bdaccfc230c6b633d3b0a7 + md5: 7b32ffe9a7bcae85a38609f8a6afc06b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-matrix run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-matrix test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Distance-correlation based Gene Set Analysis for longitudinal gene expression profiles. In longitudinal studies, the gene expression profiles were collected at each visit from each subject and hence there are multiple measurements of the gene expression profiles for each subject. The dcGSA package could be used to assess the associations between gene sets and clinical outcomes of interest by fully taking advantage of the longitudinal nature of both the gene expression profiles and clinical outcomes.' extra: identifiers: - biotools:dcgsa - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dcgsa + path: recipes/bioconductor-dcgsa + version: 1.8.0 + diff --git a/recipes/bioconductor-dchiprep/build.sh b/recipes/bioconductor-dchiprep/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dchiprep/build.sh +++ b/recipes/bioconductor-dchiprep/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dchiprep/conda_build_config.yaml b/recipes/bioconductor-dchiprep/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-dchiprep/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-dchiprep/meta.yaml b/recipes/bioconductor-dchiprep/meta.yaml index f55d5b0bd57f4..15bccd72e5ae1 100644 --- a/recipes/bioconductor-dchiprep/meta.yaml +++ b/recipes/bioconductor-dchiprep/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DChIPRep" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8220ab43aa87cb6963cd69bc4680e6f21c9f9e022e0a9d32f6f9e52252dd67a9 + md5: 16c51ba26b30d3f5466e7aa8676a4441 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: mgcv, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-soggi >=1.12.0,<1.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-soggi >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-assertthat - r-base - r-fdrtool @@ -34,12 +36,12 @@ requirements: - r-smoothmest - r-tidyr run: - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-soggi >=1.12.0,<1.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-soggi >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-assertthat - r-base - r-fdrtool @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENCE' summary: 'The DChIPRep package implements a methodology to assess differences between chromatin modification profiles in replicated ChIP-Seq studies as described in Chabbert et. al - http://www.dx.doi.org/10.15252/msb.20145776. A detailed description of the method is given in the software paper at https://doi.org/10.7717/peerj.1981' extra: identifiers: - biotools:dchiprep + parent_recipe: + name: bioconductor-dchiprep + path: recipes/bioconductor-dchiprep + version: 1.10.0 + diff --git a/recipes/bioconductor-ddct/build.sh b/recipes/bioconductor-ddct/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ddct/build.sh +++ b/recipes/bioconductor-ddct/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ddct/meta.yaml b/recipes/bioconductor-ddct/meta.yaml index 01341c8b08727..ef3042a6e5d47 100644 --- a/recipes/bioconductor-ddct/meta.yaml +++ b/recipes/bioconductor-ddct/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "ddCt" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ad7eee57cd0e2e392d2d3f468ec1b050de62efc748bb6ee55105023d625f3805 + md5: a0d6affcd7f9fac5b22389a3657bba99 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' - r-xtable run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-lattice - 'r-rcolorbrewer >=0.1-3' @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The Delta-Delta-Ct (ddCt) Algorithm is an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. Compared to other approaches, it requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The ddCt package implements a pipeline to collect, analyse and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions.' extra: identifiers: - biotools:ddct - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ddct + path: recipes/bioconductor-ddct + version: 1.36.0 + diff --git a/recipes/bioconductor-ddpcrclust/build.sh b/recipes/bioconductor-ddpcrclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ddpcrclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ddpcrclust/meta.yaml b/recipes/bioconductor-ddpcrclust/meta.yaml new file mode 100644 index 0000000000000..d117ad01f0c49 --- /dev/null +++ b/recipes/bioconductor-ddpcrclust/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "ddPCRclust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cf65901cbc08efe813fa358b52244059 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowdensity >=1.16.0,<1.17.0' + - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' + - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - r-base + - r-clue + - r-ggplot2 + - r-openxlsx + - r-plotrix + - r-r.utils + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowdensity >=1.16.0,<1.17.0' + - 'bioconductor-flowpeaks >=1.28.0,<1.29.0' + - 'bioconductor-samspectral >=1.36.0,<1.37.0' + - r-base + - r-clue + - r-ggplot2 + - r-openxlsx + - r-plotrix + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The ddPCRclust algorithm can automatically quantify the CPDs of non-orthogonal ddPCR reactions with up to four targets. In order to determine the correct droplet count for each target, it is crucial to both identify all clusters and label them correctly based on their position. For more information on what data can be analyzed and how a template needs to be formatted, please check the vignette.' + diff --git a/recipes/bioconductor-debrowser/build.sh b/recipes/bioconductor-debrowser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-debrowser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-debrowser/meta.yaml b/recipes/bioconductor-debrowser/meta.yaml new file mode 100644 index 0000000000000..c284caf6679b8 --- /dev/null +++ b/recipes/bioconductor-debrowser/meta.yaml @@ -0,0 +1,107 @@ +{% set version = "1.10.4" %} +{% set name = "debrowser" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c5f863a0ba5f1df02036146e3e83fc04 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, rmarkdown, knitr, R.rsp +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-harman >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-colourpicker + - r-d3heatmap + - r-dt + - r-ggplot2 + - r-googleauthr + - r-gplots + - r-heatmaply + - r-igraph + - r-jsonlite + - r-plotly + - r-rcolorbrewer + - r-rcurl + - r-reshape2 + - r-shiny + - r-shinybs + - r-shinydashboard + - r-shinyjs + - r-stringi + - r-v8 + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-harman >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-colourpicker + - r-d3heatmap + - r-dt + - r-ggplot2 + - r-googleauthr + - r-gplots + - r-heatmaply + - r-igraph + - r-jsonlite + - r-plotly + - r-rcolorbrewer + - r-rcurl + - r-reshape2 + - r-shiny + - r-shinybs + - r-shinydashboard + - r-shinyjs + - r-stringi + - r-v8 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Bioinformatics platform containing interactive plots and tables for differential gene and region expression studies. Allows visualizing expression data much more deeply in an interactive and faster way. By changing the parameters, users can easily discover different parts of the data that like never have been done before. Manually creating and looking these plots takes time. With DEBrowser users can prepare plots without writing any code. Differential expression, PCA and clustering analysis are made on site and the results are shown in various plots such as scatter, bar, box, volcano, ma plots and Heatmaps.' + diff --git a/recipes/bioconductor-decipher/build.sh b/recipes/bioconductor-decipher/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-decipher/build.sh +++ b/recipes/bioconductor-decipher/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decipher/meta.yaml b/recipes/bioconductor-decipher/meta.yaml index af9c4a83d59ad..0f79433aa2080 100644 --- a/recipes/bioconductor-decipher/meta.yaml +++ b/recipes/bioconductor-decipher/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.8.1" %} +{% set version = "2.10.0" %} {% set name = "DECIPHER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8bfc5718de78dc4493a44555ea15513d183f9f6644ea9f563ab4a766eb02f1e7 + md5: c3d5e6617b7bcfae06453241cf97d1a2 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.35.12' - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-xvector + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-biostrings >=2.35.12' - - bioconductor-iranges - - bioconductor-s4vectors - - bioconductor-xvector + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dbi - 'r-rsqlite >=1.1' @@ -40,10 +40,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A toolset for deciphering and managing biological sequences.' - extra: identifiers: - biotools:DECIPHER + parent_recipe: + name: bioconductor-decipher + path: recipes/bioconductor-decipher + version: 2.8.1 + diff --git a/recipes/bioconductor-decomplexdisease/build.sh b/recipes/bioconductor-decomplexdisease/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-decomplexdisease/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decomplexdisease/meta.yaml b/recipes/bioconductor-decomplexdisease/meta.yaml new file mode 100644 index 0000000000000..97b0f5826df0c --- /dev/null +++ b/recipes/bioconductor-decomplexdisease/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.2.0" %} +{% set name = "DEComplexDisease" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8939bc37f0e9520bb74d734800f681d7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-rcpp >=0.12.7' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-rcpp >=0.12.7' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'It is designed to find the differential expressed genes (DEGs) for complex disease, which is characterized by the heterogeneous genomic expression profiles. Different from the established DEG analysis tools, it does not assume the patients of complex diseases to share the common DEGs. By applying a bi-clustering algorithm, DECD finds the DEGs shared by as many patients. In this way, DECD describes the DEGs of complex disease in a novel syntax, e.g. a gene list composed of 200 genes are differentially expressed in 30% percent of studied complex disease. Applying the DECD analysis results, users are possible to find the patients affected by the same mechanism based on the shared signatures.' + diff --git a/recipes/bioconductor-deconrnaseq/build.sh b/recipes/bioconductor-deconrnaseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-deconrnaseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deconrnaseq/meta.yaml b/recipes/bioconductor-deconrnaseq/meta.yaml new file mode 100644 index 0000000000000..5d5801ba60e7c --- /dev/null +++ b/recipes/bioconductor-deconrnaseq/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.24.0" %} +{% set name = "DeconRNASeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 22cb44d707c7ce74ce46d782949aaad7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - r-base + - r-ggplot2 + - r-limsolve + run: + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - r-base + - r-ggplot2 + - r-limsolve +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'DeconSeq is an R package for deconvolution of heterogeneous tissues based on mRNA-Seq data. It modeled expression levels from heterogeneous cell populations in mRNA-Seq as the weighted average of expression from different constituting cell types and predicted cell type proportions of single expression profiles.' + diff --git a/recipes/bioconductor-decontam/build.sh b/recipes/bioconductor-decontam/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-decontam/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-decontam/meta.yaml b/recipes/bioconductor-decontam/meta.yaml new file mode 100644 index 0000000000000..014bd0cbd3b66 --- /dev/null +++ b/recipes/bioconductor-decontam/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "decontam" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f1e2437a912018381ddcbe50b78825b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, phyloseq +requirements: + host: + - r-base + - 'r-ggplot2 >=2.1.0' + - 'r-reshape2 >=1.4.1' + run: + - r-base + - 'r-ggplot2 >=2.1.0' + - 'r-reshape2 >=1.4.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Simple statistical identification of contaminating sequence features in marker-gene or metagenomics data. Works on any kind of feature derived from environmental sequencing data (e.g. ASVs, OTUs, taxonomic groups, MAGs,...). Requires DNA quantitation data or sequenced negative control samples.' + diff --git a/recipes/bioconductor-deds/build.sh b/recipes/bioconductor-deds/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deds/build.sh +++ b/recipes/bioconductor-deds/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deds/meta.yaml b/recipes/bioconductor-deds/meta.yaml index 778578d918dd9..4db0b653381f3 100644 --- a/recipes/bioconductor-deds/meta.yaml +++ b/recipes/bioconductor-deds/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "DEDS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dc6dd316e1214f61bf58c9b6a14836726ed6f57a1c72b299687ec8f0b17bbc8b + md5: 520ca60c57d58412dd6eaede77dcd215 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This library contains functions that calculate various statistics of differential expression for microarray data, including t statistics, fold change, F statistics, SAM, moderated t and F statistics and B statistics. It also implements a new methodology called DEDS (Differential Expression via Distance Summary), which selects differentially expressed genes by integrating and summarizing a set of statistics using a weighted distance approach.' extra: identifiers: - biotools:deds - doi:10.1016/j.compbiomed.2013.12.002 + parent_recipe: + name: bioconductor-deds + path: recipes/bioconductor-deds + version: 1.54.0 + diff --git a/recipes/bioconductor-deepbluer/build.sh b/recipes/bioconductor-deepbluer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deepbluer/build.sh +++ b/recipes/bioconductor-deepbluer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deepbluer/meta.yaml b/recipes/bioconductor-deepbluer/meta.yaml index dbe5cc5d63e0b..38caee386f537 100644 --- a/recipes/bioconductor-deepbluer/meta.yaml +++ b/recipes/bioconductor-deepbluer/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "DeepBlueR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 459af8d672d68aa498b5babd16be29c91fe90cf00320421734dd7c7cdc850334 + md5: 34d71a046cc37a278f8f36fc41358513 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, LOLA, Gviz, gplots, ggplot2, tidyr, RColorBrewer, matrixStats requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-data.table - r-diffr @@ -35,9 +37,9 @@ requirements: - r-withr - r-xml run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-data.table - r-diffr @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'Accessing the DeepBlue Epigenetics Data Server through R.' extra: identifiers: - biotools:deepbluer + parent_recipe: + name: bioconductor-deepbluer + path: recipes/bioconductor-deepbluer + version: 1.6.0 + diff --git a/recipes/bioconductor-deepsnv/build.sh b/recipes/bioconductor-deepsnv/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deepsnv/build.sh +++ b/recipes/bioconductor-deepsnv/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deepsnv/meta.yaml b/recipes/bioconductor-deepsnv/meta.yaml index b79fbf2f734a9..265c7ecba8b96 100644 --- a/recipes/bioconductor-deepsnv/meta.yaml +++ b/recipes/bioconductor-deepsnv/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "deepSNV" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 55036b553920826aeead816e48a8760b756bca513de09a247521b36788aaa01d + md5: e75cbb2a6a32b486dd4f525de48d8f40 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RColorBrewer, knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-vgam run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-vgam build: @@ -44,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides provides quantitative variant callers for detecting subclonal mutations in ultra-deep (>=100x coverage) sequencing experiments. The deepSNV algorithm is used for a comparative setup with a control experiment of the same loci and uses a beta-binomial model and a likelihood ratio test to discriminate sequencing errors and subclonal SNVs. The shearwater algorithm computes a Bayes classifier based on a beta-binomial model for variant calling with multiple samples for precisely estimating model parameters - such as local error rates and dispersion - and prior knowledge, e.g. from variation data bases such as COSMIC.' extra: identifiers: - biotools:deepsnv + parent_recipe: + name: bioconductor-deepsnv + path: recipes/bioconductor-deepsnv + version: 1.26.1 + diff --git a/recipes/bioconductor-deformats/build.sh b/recipes/bioconductor-deformats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deformats/build.sh +++ b/recipes/bioconductor-deformats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deformats/meta.yaml b/recipes/bioconductor-deformats/meta.yaml index 115af25add325..0f83c2135e75d 100644 --- a/recipes/bioconductor-deformats/meta.yaml +++ b/recipes/bioconductor-deformats/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DEFormats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 29c1f463f5afda69be011c4d23549838c5f30571c3015d5a30d5b60c97115723 + md5: 69f526fa202b52de33804e15791a1243 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle (>= 1.8.0), knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table run: - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-checkmate - r-data.table @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Convert between different data formats used by differential gene expression analysis tools.' extra: identifiers: - biotools:deformats - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-deformats + path: recipes/bioconductor-deformats + version: 1.8.0 + diff --git a/recipes/bioconductor-degraph/build.sh b/recipes/bioconductor-degraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-degraph/build.sh +++ b/recipes/bioconductor-degraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-degraph/meta.yaml b/recipes/bioconductor-degraph/meta.yaml index e261c6255683f..a1e3bb072aff1 100644 --- a/recipes/bioconductor-degraph/meta.yaml +++ b/recipes/bioconductor-degraph/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DEGraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fd70e69c20e39e93ee0a53705191d9d9e94f1b6ac11ba373e15517c2fb9a6023 + md5: 51a9e855c83c270117e9cd3ed052d86e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: corpcor, fields, graph, KEGGgraph, lattice, marray, RBGL, rrcov, Rgraphviz, NCIgraph requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-ncigraph >=1.28.0,<1.30.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-ncigraph >=1.30.0,<1.31.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-lattice - r-mvtnorm @@ -30,11 +32,11 @@ requirements: - r-r.utils - r-rrcov run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-ncigraph >=1.28.0,<1.30.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-ncigraph >=1.30.0,<1.31.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-lattice - r-mvtnorm @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DEGraph implements recent hypothesis testing methods which directly assess whether a particular gene network is differentially expressed between two conditions. This is to be contrasted with the more classical two-step approaches which first test individual genes, then test gene sets for enrichment in differentially expressed genes. These recent methods take into account the topology of the network to yield more powerful detection procedures. DEGraph provides methods to easily test all KEGG pathways for differential expression on any gene expression data set and tools to visualize the results.' extra: identifiers: - biotools:degraph - doi:10.1214/11-AOAS528 + parent_recipe: + name: bioconductor-degraph + path: recipes/bioconductor-degraph + version: 1.32.0 + diff --git a/recipes/bioconductor-degreport/build.sh b/recipes/bioconductor-degreport/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-degreport/build.sh +++ b/recipes/bioconductor-degreport/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-degreport/meta.yaml b/recipes/bioconductor-degreport/meta.yaml index d50bd1444ef76..b69958bdfa00f 100644 --- a/recipes/bioconductor-degreport/meta.yaml +++ b/recipes/bioconductor-degreport/meta.yaml @@ -1,44 +1,49 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DEGreport" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9c837442bf21031bc88fb6fec9ef30abd01fcb56fa45ee6f39b62701b8ee89e5 + md5: fef844e701dc5fbd8755aa0b1069ba38 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, AnnotationDbi, limma, pheatmap, knitr, rmarkdown, statmod, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-broom - r-circlize - r-cluster - r-cowplot - r-dplyr + - r-ggdendro - r-ggplot2 - r-ggrepel - r-knitr + - r-lasso2 - r-logging - r-magrittr - r-nozzle.r1 - r-psych - - r-quantreg + - r-rcolorbrewer - r-reshape - r-rlang - r-scales @@ -46,27 +51,30 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-broom - r-circlize - r-cluster - r-cowplot - r-dplyr + - r-ggdendro - r-ggplot2 - r-ggrepel - r-knitr + - r-lasso2 - r-logging - r-magrittr - r-nozzle.r1 - r-psych - - r-quantreg + - r-rcolorbrewer - r-reshape - r-rlang - r-scales @@ -77,10 +85,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Creation of a HTML report of differential expression analyses of count data. It integrates some of the code mentioned in DESeq2 and edgeR vignettes, and report a ranked list of genes according to the fold changes mean and variability for each selected gene.' extra: identifiers: - biotools:degreport - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-degreport + path: recipes/bioconductor-degreport + version: 1.16.0 + diff --git a/recipes/bioconductor-degseq/build.sh b/recipes/bioconductor-degseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-degseq/build.sh +++ b/recipes/bioconductor-degseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-degseq/meta.yaml b/recipes/bioconductor-degseq/meta.yaml index 923a2bf646bf5..e4a46d257fa10 100644 --- a/recipes/bioconductor-degseq/meta.yaml +++ b/recipes/bioconductor-degseq/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.34.1" %} +{% set version = "1.36.1" %} {% set name = "DEGseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0512b751635a51e9123ebdcbc6bf1e1a6440524d06ecdc1efc6a93738f01ad18 + md5: b8923f545fdf7ddeece5e9abd038cc00 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base run: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base build: - {{ compiler('c') }} @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'DEGseq is an R package to identify differentially expressed genes from RNA-Seq data.' extra: identifiers: - biotools:degseq - doi:10.1093/bioinformatics/btp612 + parent_recipe: + name: bioconductor-degseq + path: recipes/bioconductor-degseq + version: 1.34.1 + diff --git a/recipes/bioconductor-delayedarray/build.sh b/recipes/bioconductor-delayedarray/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-delayedarray/build.sh +++ b/recipes/bioconductor-delayedarray/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-delayedarray/meta.yaml b/recipes/bioconductor-delayedarray/meta.yaml index 84020fb5ece73..a5627fc94e3e9 100644 --- a/recipes/bioconductor-delayedarray/meta.yaml +++ b/recipes/bioconductor-delayedarray/meta.yaml @@ -1,42 +1,50 @@ -{% set version = "0.6.6" %} +{% set version = "0.8.0" %} {% set name = "DelayedArray" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c25d2c41c18f37930ad94ccea9d18f1c2c45481cb0253456b48e0fac5d057766 + md5: f8365083bd320d946db08c9aa34c335c build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Matrix, HDF5Array, genefilter, SummarizedExperiment, airway, pryr, DelayedMatrixStats, knitr, BiocStyle, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrixstats + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Wrapping an array-like object (typically an on-disk object) in a DelayedArray object allows one to perform common array operations on it without loading the object in memory. In order to reduce memory usage and optimize performance, operations on the object are either delayed or executed using a block processing mechanism. Note that this also works on in-memory array-like objects like DataFrame objects (typically with Rle columns), Matrix objects, and ordinary arrays and data frames.' - +extra: + parent_recipe: + name: bioconductor-delayedarray + path: recipes/bioconductor-delayedarray + version: 0.6.6 diff --git a/recipes/bioconductor-delayedmatrixstats/build.sh b/recipes/bioconductor-delayedmatrixstats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-delayedmatrixstats/build.sh +++ b/recipes/bioconductor-delayedmatrixstats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-delayedmatrixstats/meta.yaml b/recipes/bioconductor-delayedmatrixstats/meta.yaml index 76fddf0acb794..b88ff00838d32 100644 --- a/recipes/bioconductor-delayedmatrixstats/meta.yaml +++ b/recipes/bioconductor-delayedmatrixstats/meta.yaml @@ -1,33 +1,39 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "DelayedMatrixStats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ef0c42d1fb2810202bb90500dd9eabdbfc02a79ea45d0eaff4774e41d7c5ab5 + md5: 7393b93bd0df9dfc1964e1d05f3e474b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, covr, BiocStyle, microbenchmark, profmem requirements: host: - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix - 'r-matrixstats >=0.53.1' run: - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix - 'r-matrixstats >=0.53.1' @@ -35,9 +41,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'A port of the ''matrixStats'' API for use with DelayedMatrix objects from the ''DelayedArray'' package. High-performing functions operating on rows and columns of DelayedMatrix objects, e.g. col / rowMedians(), col / rowRanks(), and col / rowSds(). Functions optimized per data type and for subsetted calculations such that both memory usage and processing time is minimized.' - - +extra: + parent_recipe: + name: bioconductor-delayedmatrixstats + path: recipes/bioconductor-delayedmatrixstats + version: 1.2.0 diff --git a/recipes/bioconductor-deltagseg/build.sh b/recipes/bioconductor-deltagseg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-deltagseg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deltagseg/meta.yaml b/recipes/bioconductor-deltagseg/meta.yaml new file mode 100644 index 0000000000000..ccc5e6859ded3 --- /dev/null +++ b/recipes/bioconductor-deltagseg/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.22.0" %} +{% set name = "deltaGseg" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fa281178cf227dc36cbc08c12954a7cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - r-base + - r-changepoint + - r-fbasics + - r-ggplot2 + - r-pvclust + - r-reshape + - r-scales + - r-tseries + - r-wavethresh + run: + - r-base + - r-changepoint + - r-fbasics + - r-ggplot2 + - r-pvclust + - r-reshape + - r-scales + - r-tseries + - r-wavethresh +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifying distinct subpopulations through multiscale time series analysis' + diff --git a/recipes/bioconductor-demand/build.sh b/recipes/bioconductor-demand/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-demand/build.sh +++ b/recipes/bioconductor-demand/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-demand/meta.yaml b/recipes/bioconductor-demand/meta.yaml index 5c26c8af2e28c..4ed10bb08cc15 100644 --- a/recipes/bioconductor-demand/meta.yaml +++ b/recipes/bioconductor-demand/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DeMAND" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 932af6daf6014d8ab650d900b2d0ed0eae2e1fff5d23041270395eed6d54bfc7 + md5: 7407289aa62fd7f774451b158ee89d6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'DEMAND predicts Drug MoA by interrogating a cell context specific regulatory network with a small number (N >= 6) of compound-induced gene expression signatures, to elucidate specific proteins whose interactions in the network is dysregulated by the compound.' extra: identifiers: - biotools:demand - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-demand + path: recipes/bioconductor-demand + version: 1.10.0 + diff --git a/recipes/bioconductor-dep/build.sh b/recipes/bioconductor-dep/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dep/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dep/meta.yaml b/recipes/bioconductor-dep/meta.yaml new file mode 100644 index 0000000000000..43132170452c7 --- /dev/null +++ b/recipes/bioconductor-dep/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "1.4.0" %} +{% set name = "DEP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://{{ name|lower }}ot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ea171465a54d5eadb6474de86bacf5cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, enrichR, knitr, BiocStyle +requirements: + host: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-assertthat + - r-base + - r-circlize + - r-cluster + - r-dplyr + - r-dt + - r-fdrtool + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-imputelcmd + - r-purrr + - r-rcolorbrewer + - r-readr + - r-rmarkdown + - r-shiny + - r-shinydashboard + - r-tibble + - r-tidyr + run: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-assertthat + - r-base + - r-circlize + - r-cluster + - r-dplyr + - r-dt + - r-fdrtool + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-imputelcmd + - r-purrr + - r-rcolorbrewer + - r-readr + - r-rmarkdown + - r-shiny + - r-shinydashboard + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides an integrated analysis workflow for robust and reproducible analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment. It requires tabular input (e.g. txt files) as generated by quantitative analysis softwares of raw mass spectrometry data, such as MaxQuant or IsobarQuant. Functions are provided for data preparation, filtering, variance normalization and imputation of missing values, as well as statistical testing of differentially enriched / expressed proteins. It also includes tools to check intermediate steps in the workflow, such as normalization and missing values imputation. Finally, visualization tools are provided to explore the results, including heatmap, volcano plot and barplot representations. For scientists with limited experience in R, the package also contains wrapper functions that entail the complete analysis workflow and generate a report. Even easier to use are the interactive Shiny apps that are provided by the package.' + diff --git a/recipes/bioconductor-deqms/build.sh b/recipes/bioconductor-deqms/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deqms/build.sh +++ b/recipes/bioconductor-deqms/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deqms/meta.yaml b/recipes/bioconductor-deqms/meta.yaml index 7c5d1da90baa3..1fa489bb792b1 100644 --- a/recipes/bioconductor-deqms/meta.yaml +++ b/recipes/bioconductor-deqms/meta.yaml @@ -12,18 +12,19 @@ source: - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' md5: 43415cf52b11a83771f6eb5b308cce83 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + noarch: generic # Suggests: BiocStyle,knitr,rmarkdown,plyr,matrixStats,reshape2,farms,RColorBrewer,utils,ggrepel,pheatmap,ExperimentHub requirements: host: - - 'bioconductor-limma >=3.34.0,<3.40.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 run: - - 'bioconductor-limma >=3.34.0,<3.40.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 test: @@ -33,4 +34,9 @@ about: home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'DEqMS is developped on top of Limma. However, Limma assumes same prior variance for all genes. In proteomics, the accuracy of protein abundance estimates varies by the number of peptides/PSMs quantified in both label-free and labelled data. Proteins quantification by multiple peptides or PSMs are more accurate. DEqMS package is able to estimate different prior variances for proteins quantified by different number of PSMs/peptides, therefore acchieving better accuracy. The package can be applied to analyze both label-free and labelled proteomics data.' +extra: + parent_recipe: + name: bioconductor-deqms + path: recipes/bioconductor-deqms + version: 1.0.0 diff --git a/recipes/bioconductor-derfinder/build.sh b/recipes/bioconductor-derfinder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-derfinder/build.sh +++ b/recipes/bioconductor-derfinder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-derfinder/meta.yaml b/recipes/bioconductor-derfinder/meta.yaml index af3228b812d69..b00d40d9a819f 100644 --- a/recipes/bioconductor-derfinder/meta.yaml +++ b/recipes/bioconductor-derfinder/meta.yaml @@ -1,69 +1,72 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "derfinder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2a9311b86a201ae0b7953733420f2f1175c578c3f98d7a776be3bec21c24f837 + md5: 7899d9344b5d359f2fb65d88a8bd3bfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle (>= 2.5.19), biovizBase, sessioninfo, derfinderData (>= 0.99.0), derfinderPlot, DESeq2, ggplot2, knitcitations (>= 1.0.1), knitr (>= 1.6), limma, RefManageR, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-bumphunter >=1.22.0,<1.24.0' - - 'bioconductor-derfinderhelper >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-derfinderhelper >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-bumphunter >=1.22.0,<1.24.0' - - 'bioconductor-derfinderhelper >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-derfinderhelper >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'This package provides functions for annotation-agnostic differential - expression analysis of RNA-seq data. Two implementations of the DER Finder - approach are included in this package (1) single base-level F-statistics - and (2) DER identification at the expressed regions-level. The DER Finder - approach can also be used to identify differentially bounded ChIP-seq peaks.' + summary: 'This package provides functions for annotation-agnostic differential expression analysis of RNA-seq data. Two implementations of the DER Finder approach are included in this package: (1) single base-level F-statistics and (2) DER identification at the expressed regions-level. The DER Finder approach can also be used to identify differentially bounded ChIP-seq peaks.' extra: identifiers: - biotools:derfinder + parent_recipe: + name: bioconductor-derfinder + path: recipes/bioconductor-derfinder + version: 1.14.0 + diff --git a/recipes/bioconductor-derfinderdata/meta.yaml b/recipes/bioconductor-derfinderdata/meta.yaml new file mode 100644 index 0000000000000..b230e5f4c069f --- /dev/null +++ b/recipes/bioconductor-derfinderdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.0.0" %} +{% set name = "derfinderData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a33f63fe0dc553cdb09434a7b243535b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), knitrBootstrap (>= 0.9.0), RefManageR, rmarkdown (>= 0.3.3), +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Processed 22 samples from BrainSpan keeping only the information for chromosome 21. Data is stored in the BigWig format and is used for examples in other packages.' + diff --git a/recipes/bioconductor-derfinderdata/post-link.sh b/recipes/bioconductor-derfinderdata/post-link.sh new file mode 100644 index 0000000000000..307c7cbc43023 --- /dev/null +++ b/recipes/bioconductor-derfinderdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="derfinderData_2.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/derfinderData_2.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/derfinderData_2.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-derfinderdata/bioconductor-derfinderdata_2.0.0_src_all.tar.gz" +) +MD5="a33f63fe0dc553cdb09434a7b243535b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-derfinderdata/pre-unlink.sh b/recipes/bioconductor-derfinderdata/pre-unlink.sh new file mode 100644 index 0000000000000..6b6f273a3abcd --- /dev/null +++ b/recipes/bioconductor-derfinderdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ derfinderData diff --git a/recipes/bioconductor-derfinderhelper/build.sh b/recipes/bioconductor-derfinderhelper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-derfinderhelper/build.sh +++ b/recipes/bioconductor-derfinderhelper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-derfinderhelper/meta.yaml b/recipes/bioconductor-derfinderhelper/meta.yaml index e32dbc5f84218..967400cf19f37 100644 --- a/recipes/bioconductor-derfinderhelper/meta.yaml +++ b/recipes/bioconductor-derfinderhelper/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "derfinderHelper" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 25eda535a4442aa581aa6ae28a98584d43ac0a948f86269f31be82910b8ee475 + md5: 0aa279c6fed199400564d6cdc3f1ffd3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), rmarkdown (>= 0.3.3), testthat requirements: host: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix run: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Helper package for speeding up the derfinder package when using multiple cores.' extra: identifiers: - biotools:derfinderhelper + parent_recipe: + name: bioconductor-derfinderhelper + path: recipes/bioconductor-derfinderhelper + version: 1.14.0 + diff --git a/recipes/bioconductor-derfinderplot/build.sh b/recipes/bioconductor-derfinderplot/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-derfinderplot/build.sh +++ b/recipes/bioconductor-derfinderplot/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-derfinderplot/conda_build_config.yaml b/recipes/bioconductor-derfinderplot/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-derfinderplot/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-derfinderplot/meta.yaml b/recipes/bioconductor-derfinderplot/meta.yaml index a2ec90694cb52..41ff4b9e98809 100644 --- a/recipes/bioconductor-derfinderplot/meta.yaml +++ b/recipes/bioconductor-derfinderplot/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "derfinderPlot" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 59bc73fcb16331910b0cecaa8ff418d31afad9bd093c850a166e8e597beed8f8 + md5: fb39127239320c43ca5180870017ecb2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biovizBase (>= 1.27.2), bumphunter (>= 1.7.6), derfinderData (>= 0.99.0), sessioninfo, knitcitations (>= 1.0.1), knitr (>= 1.6), BiocStyle (>= 2.5.19), org.Hs.eg.db, rmarkdown (>= 0.3.3), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-derfinder >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-plyr @@ -34,14 +36,14 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-derfinder >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-plyr @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides plotting functions for results from the derfinder package.' extra: identifiers: - biotools:derfinderplot + parent_recipe: + name: bioconductor-derfinderplot + path: recipes/bioconductor-derfinderplot + version: 1.14.0 + diff --git a/recipes/bioconductor-descan2/build.sh b/recipes/bioconductor-descan2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-descan2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-descan2/meta.yaml b/recipes/bioconductor-descan2/meta.yaml new file mode 100644 index 0000000000000..9f2d9bc293004 --- /dev/null +++ b/recipes/bioconductor-descan2/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.2.0" %} +{% set name = "DEScan2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6d6d1d534831bb5fefe9a82eedec0af4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, testthat, edgeR, limma, EDASeq, RUVSeq, RColorBrewer, statmod +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-glue + - r-plyr + - 'r-rcpp >=0.12.13' + - r-rcpparmadillo + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-glue + - r-plyr + - 'r-rcpp >=0.12.13' + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Integrated peak and differential caller, specifically designed for broad epigenomic signals.' + diff --git a/recipes/bioconductor-deseq/build.sh b/recipes/bioconductor-deseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deseq/build.sh +++ b/recipes/bioconductor-deseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deseq/meta.yaml b/recipes/bioconductor-deseq/meta.yaml index 83acb09e9a992..6387485ed9709 100644 --- a/recipes/bioconductor-deseq/meta.yaml +++ b/recipes/bioconductor-deseq/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "DESeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d5d29792e1ecdd29dd63b04eac4c0937eba68504a5f3227c3702b8a827e27d7a + md5: 594feee53e87602603b3a8124cd8500a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: pasilla (>= 0.2.10), vsn, gplots requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - r-base - r-lattice - r-locfit - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' - r-base - r-lattice - r-locfit @@ -44,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution' extra: identifiers: - biotools:deseq + parent_recipe: + name: bioconductor-deseq + path: recipes/bioconductor-deseq + version: 1.32.0 + diff --git a/recipes/bioconductor-deseq2/build.sh b/recipes/bioconductor-deseq2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-deseq2/build.sh +++ b/recipes/bioconductor-deseq2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-deseq2/meta.yaml b/recipes/bioconductor-deseq2/meta.yaml index 820855ff60a7a..0593f604374b3 100644 --- a/recipes/bioconductor-deseq2/meta.yaml +++ b/recipes/bioconductor-deseq2/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "DESeq2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 33e214e9f9f9bb5d6c0dacdd0d4a8ba4857ce0277f09a192ab35a940d67556f2 + md5: b7cf6da541d28dcd9abe09425dc43447 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, vsn, pheatmap, RColorBrewer, IHW, apeglm, ashr, tximport, tximportData, readr, pbapply, airway, pasilla (>= 0.2.10) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-hmisc @@ -34,15 +35,15 @@ requirements: - 'r-rcpp >=0.11.0' - r-rcpparmadillo run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-hmisc @@ -57,10 +58,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.' extra: identifiers: - biotools:deseq2 - doi:10.1186/s13059-014-0550-8 + parent_recipe: + name: bioconductor-deseq2 + path: recipes/bioconductor-deseq2 + version: 1.20.0 + diff --git a/recipes/bioconductor-desingle/build.sh b/recipes/bioconductor-desingle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-desingle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-desingle/meta.yaml b/recipes/bioconductor-desingle/meta.yaml new file mode 100644 index 0000000000000..a19f0d67ba751 --- /dev/null +++ b/recipes/bioconductor-desingle/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.1" %} +{% set name = "DEsingle" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8d446c9bd3e760ae2c67426a1911e42c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, SingleCellExperiment +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - 'r-bbmle >=1.0.18' + - 'r-gamlss >=4.4-0' + - 'r-mass >=7.3-45' + - 'r-matrix >=1.2-14' + - 'r-maxlik >=1.3-4' + - 'r-pscl >=1.4.9' + - 'r-vgam >=1.0-2' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - 'r-bbmle >=1.0.18' + - 'r-gamlss >=4.4-0' + - 'r-mass >=7.3-45' + - 'r-matrix >=1.2-14' + - 'r-maxlik >=1.3-4' + - 'r-pscl >=1.4.9' + - 'r-vgam >=1.0-2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'DEsingle is an R package for differential expression (DE) analysis of single-cell RNA-seq (scRNA-seq) data. It defines and detects 3 types of differentially expressed genes between two groups of single cells, with regard to different expression status (DEs), differential expression abundance (DEa), and general differential expression (DEg). DEsingle employs Zero-Inflated Negative Binomial model to estimate the proportion of real and dropout zeros and to define and detect the 3 types of DE genes. Results showed that DEsingle outperforms existing methods for scRNA-seq DE analysis, and can reveal different types of DE genes that are enriched in different biological functions.' + diff --git a/recipes/bioconductor-desousa2013/meta.yaml b/recipes/bioconductor-desousa2013/meta.yaml new file mode 100644 index 0000000000000..ff91541e59185 --- /dev/null +++ b/recipes/bioconductor-desousa2013/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.18.0" %} +{% set name = "DeSousa2013" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6059d057fb2eb7d4b64896680da57226 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-frma >=1.34.0,<1.35.0' + - 'bioconductor-frmatools >=1.34.0,<1.35.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-cluster + - r-gplots + - r-pamr + - r-rgl + - r-rocr + - r-survival + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-frma >=1.34.0,<1.35.0' + - 'bioconductor-frmatools >=1.34.0,<1.35.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2frmavecs >=1.5.0,<1.6.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-cluster + - r-gplots + - r-pamr + - r-rgl + - r-rocr + - r-survival + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package reproduces the main pipeline to analyze the AMC-AJCCII-90 microarray data set in De Sousa et al. accepted by Nature Medicine in 2013.' + diff --git a/recipes/bioconductor-desousa2013/post-link.sh b/recipes/bioconductor-desousa2013/post-link.sh new file mode 100644 index 0000000000000..b810f8a5a3215 --- /dev/null +++ b/recipes/bioconductor-desousa2013/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DeSousa2013_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DeSousa2013_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/DeSousa2013_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-desousa2013/bioconductor-desousa2013_1.18.0_src_all.tar.gz" +) +MD5="6059d057fb2eb7d4b64896680da57226" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-desousa2013/pre-unlink.sh b/recipes/bioconductor-desousa2013/pre-unlink.sh new file mode 100644 index 0000000000000..ee9523c495598 --- /dev/null +++ b/recipes/bioconductor-desousa2013/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DeSousa2013 diff --git a/recipes/bioconductor-destiny/build.sh b/recipes/bioconductor-destiny/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-destiny/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-destiny/meta.yaml b/recipes/bioconductor-destiny/meta.yaml new file mode 100644 index 0000000000000..f99c18f5df3c6 --- /dev/null +++ b/recipes/bioconductor-destiny/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "2.12.0" %} +{% set name = "destiny" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ac5c9847de79461d53d1ad996f155d19 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: nbconvertR, testthat, FNN, tidyr, SingleCellExperiment +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggthemes + - r-igraph + - r-matrix + - r-proxy + - 'r-rcpp >=0.10.3' + - r-rcppeigen + - r-scales + - r-scatterplot3d + - r-smoother + - r-vim + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggthemes + - r-igraph + - r-matrix + - r-proxy + - 'r-rcpp >=0.10.3' + - r-rcppeigen + - r-scales + - r-scatterplot3d + - r-smoother + - r-vim + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'Create and plot diffusion maps.' + diff --git a/recipes/bioconductor-desubs/build.sh b/recipes/bioconductor-desubs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-desubs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-desubs/meta.yaml b/recipes/bioconductor-desubs/meta.yaml new file mode 100644 index 0000000000000..8e96ce40c22f2 --- /dev/null +++ b/recipes/bioconductor-desubs/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.8.1" %} +{% set name = "DEsubs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 90cc0ee693e5b17182604558c98ab38a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +requirements: + host: + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-circlize + - r-ggplot2 + - r-igraph + - r-jsonlite + - r-locfit + - r-matrix + - r-nbpseq + - r-pheatmap + run: + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-circlize + - r-ggplot2 + - r-igraph + - r-jsonlite + - r-locfit + - r-matrix + - r-nbpseq + - r-pheatmap +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'DEsubs is a network-based systems biology package that extracts disease-perturbed subpathways within a pathway network as recorded by RNA-seq experiments. It contains an extensive and customizable framework covering a broad range of operation modes at all stages of the subpathway analysis, enabling a case-specific approach. The operation modes refer to the pathway network construction and processing, the subpathway extraction, visualization and enrichment analysis with regard to various biological and pharmacological features. Its capabilities render it a tool-guide for both the modeler and experimentalist for the identification of more robust systems-level biomarkers for complex diseases.' + diff --git a/recipes/bioconductor-dexseq/build.sh b/recipes/bioconductor-dexseq/build.sh index e5264766ba3a0..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dexseq/build.sh +++ b/recipes/bioconductor-dexseq/build.sh @@ -1,12 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . -python_scripts=$PREFIX/lib/R/library/DEXSeq/python_scripts -sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_count.py -sed -i.bak '1s|^|#!/usr/bin/env python\'$'\n|g' $python_scripts/dexseq_prepare_annotation.py -chmod +x $python_scripts/dexseq_count.py -chmod +x $python_scripts/dexseq_prepare_annotation.py -mkdir -p $PREFIX/bin -ln -s $python_scripts/dexseq_count.py $PREFIX/bin/dexseq_count.py -ln -s $python_scripts/dexseq_prepare_annotation.py $PREFIX/bin/dexseq_prepare_annotation.py +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexseq/meta.yaml b/recipes/bioconductor-dexseq/meta.yaml index 41631be4ebe99..f75c6f302c7c3 100644 --- a/recipes/bioconductor-dexseq/meta.yaml +++ b/recipes/bioconductor-dexseq/meta.yaml @@ -1,78 +1,74 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "DEXSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e1e9026c07fc26e1eaee06a0dd63d2f765bcd711f350fdb2a2236ad65b1d0bd7 - + md5: 0852b22f25f3a3be615c118a2d0de719 build: - noarch: python - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ - + noarch: generic +# Suggests: GenomicFeatures (>= 1.13.29), pasilla (>= 0.2.22), parathyroidSE, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-hwriter - r-rcolorbrewer - r-statmod - r-stringr - - python <3 - - 'htseq >=0.6.1,<0.10.0' # dexseq_count.py performes an overly simplistic version check - test: commands: - '$R -e "library(''{{ name }}'')"' - - dexseq_count.py --help - - dexseq_prepare_annotation.py --help - about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package is focused on finding differential exon usage using RNA-seq exon counts between samples with different experimental designs. It provides functions that allows the user to make the necessary statistical tests based on a model that uses the negative binomial distribution to estimate the variance between biological replicates and generalized linear models for testing. The package also provides functions for the visualization and exploration of the results.' - extra: identifiers: - biotools:dexseq + parent_recipe: + name: bioconductor-dexseq + path: recipes/bioconductor-dexseq + version: 1.26.0 + diff --git a/recipes/bioconductor-dexus/build.sh b/recipes/bioconductor-dexus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dexus/build.sh +++ b/recipes/bioconductor-dexus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dexus/meta.yaml b/recipes/bioconductor-dexus/meta.yaml index b52dbaf9616f1..8e3ca4f1388f8 100644 --- a/recipes/bioconductor-dexus/meta.yaml +++ b/recipes/bioconductor-dexus/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "dexus" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 06d27f602a1bed95b7b14481901db2b5b78e04c357a2739a8fb9ca1dff324bb3 + md5: 72b9ed1be02b21ef3d12818a050f63ec build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, statmod, DESeq, RColorBrewer requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base build: - {{ compiler('c') }} @@ -31,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'DEXUS identifies differentially expressed genes in RNA-Seq data under all possible study designs such as studies without replicates, without sample groups, and with unknown conditions. DEXUS works also for known conditions, for example for RNA-Seq data with two or multiple conditions. RNA-Seq read count data can be provided both by the S4 class Count Data Set and by read count matrices. Differentially expressed transcripts can be visualized by heatmaps, in which unknown conditions, replicates, and samples groups are also indicated. This software is fast since the core algorithm is written in C. For very large data sets, a parallel version of DEXUS is provided in this package. DEXUS is a statistical model that is selected in a Bayesian framework by an EM algorithm. DEXUS does not need replicates to detect differentially expressed transcripts, since the replicates (or conditions) are estimated by the EM method for each transcript. The method provides an informative/non-informative value to extract differentially expressed transcripts at a desired significance level or power.' extra: identifiers: - biotools:dexus + parent_recipe: + name: bioconductor-dexus + path: recipes/bioconductor-dexus + version: 1.20.0 + diff --git a/recipes/bioconductor-dfp/build.sh b/recipes/bioconductor-dfp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dfp/build.sh +++ b/recipes/bioconductor-dfp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dfp/meta.yaml b/recipes/bioconductor-dfp/meta.yaml index f44bb1c7e66f5..3cce5dad5f13a 100644 --- a/recipes/bioconductor-dfp/meta.yaml +++ b/recipes/bioconductor-dfp/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "DFP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd8b0d9abb19314173743430d6c47ea3d21f2d142733d96a33c3529bac51eb8f + md5: 12981b09b4c4c8d2738eb7d9ae20e399 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a supervised technique able to identify differentially expressed genes, based on the construction of \emph{Fuzzy Patterns} (FPs). The Fuzzy Patterns are built by means of applying 3 Membership Functions to discretized gene expression values.' extra: identifiers: - biotools:dfp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dfp + path: recipes/bioconductor-dfp + version: 1.38.0 + diff --git a/recipes/bioconductor-diffbind/build.sh b/recipes/bioconductor-diffbind/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-diffbind/build.sh +++ b/recipes/bioconductor-diffbind/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffbind/conda_build_config.yaml b/recipes/bioconductor-diffbind/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-diffbind/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-diffbind/meta.yaml b/recipes/bioconductor-diffbind/meta.yaml index 3683be1c17e62..7ef8945940d99 100644 --- a/recipes/bioconductor-diffbind/meta.yaml +++ b/recipes/bioconductor-diffbind/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "DiffBind" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 50478712ff5b0fe9dd47a9879ddde81a611a1dcf117e84c7634c8cd3fef230f0 + md5: cebf717d82d269302bb10819892d6b6e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: DESeq, BiocStyle, testthat requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-systempiper >=1.14.0,<1.16.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-systempiper >=1.16.0,<1.17.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-amap - r-base - r-dplyr @@ -41,18 +42,18 @@ requirements: - r-rcolorbrewer - r-rcpp run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-systempiper >=1.14.0,<1.16.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-systempiper >=1.16.0,<1.17.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-amap - r-base - r-dplyr @@ -71,9 +72,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.' extra: identifiers: - biotools:diffbind + parent_recipe: + name: bioconductor-diffbind + path: recipes/bioconductor-diffbind + version: 2.8.0 + diff --git a/recipes/bioconductor-diffcoexp/build.sh b/recipes/bioconductor-diffcoexp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-diffcoexp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffcoexp/meta.yaml b/recipes/bioconductor-diffcoexp/meta.yaml new file mode 100644 index 0000000000000..9049dd7c39c24 --- /dev/null +++ b/recipes/bioconductor-diffcoexp/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "diffcoexp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 84d4b05956389705839485018b5aa33c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-diffcorr + - r-igraph + - r-psych + - r-wgcna + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-diffcorr + - r-igraph + - r-psych + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>2)' + summary: 'A tool for the identification of differentially coexpressed links (DCLs) and differentially coexpressed genes (DCGs). DCLs are gene pairs with significantly different correlation coefficients under two conditions. DCGs are genes with significantly more DCLs than by chance.' + diff --git a/recipes/bioconductor-diffcyt/build.sh b/recipes/bioconductor-diffcyt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-diffcyt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffcyt/meta.yaml b/recipes/bioconductor-diffcyt/meta.yaml new file mode 100644 index 0000000000000..6263374d93a9f --- /dev/null +++ b/recipes/bioconductor-diffcyt/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.0" %} +{% set name = "diffcyt" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 148190e2f1cdea2b7a9e713bdbaf4d0a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, HDCytoData, CATALYST +requirements: + host: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-dplyr + - r-lme4 + - r-magrittr + - r-multcomp + - r-reshape2 + - r-tidyr + run: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-dplyr + - r-lme4 + - r-magrittr + - r-multcomp + - r-reshape2 + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on (i) high-resolution clustering and (ii) empirical Bayes moderated tests adapted from transcriptomics.' + diff --git a/recipes/bioconductor-diffgeneanalysis/build.sh b/recipes/bioconductor-diffgeneanalysis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-diffgeneanalysis/build.sh +++ b/recipes/bioconductor-diffgeneanalysis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffgeneanalysis/meta.yaml b/recipes/bioconductor-diffgeneanalysis/meta.yaml index e7121679e2049..d7db5cb7f4ea1 100644 --- a/recipes/bioconductor-diffgeneanalysis/meta.yaml +++ b/recipes/bioconductor-diffgeneanalysis/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "diffGeneAnalysis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 41cb78d5a2afaa71a324598ed8fcca613fd71c88f97b8dd2598d286123d4979d + md5: 506fc6d4eb0b4d2d23cee89b0f19c704 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Analyze microarray data' extra: identifiers: - biotools:diffgeneanalysis - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-diffgeneanalysis + path: recipes/bioconductor-diffgeneanalysis + version: 1.62.0 + diff --git a/recipes/bioconductor-diffhic/build.sh b/recipes/bioconductor-diffhic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-diffhic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffhic/meta.yaml b/recipes/bioconductor-diffhic/meta.yaml new file mode 100644 index 0000000000000..532ad782ad190 --- /dev/null +++ b/recipes/bioconductor-diffhic/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.14.0" %} +{% set name = "diffHic" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3a4a022ba4b42c3c84d13a12a2e3e79 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BSgenome.Ecoli.NCBI.20080805, Matrix, testthat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-locfit + - r-rcpp + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-locfit + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Detects differential interactions across biological conditions in a Hi-C experiment. Methods are provided for read alignment and data pre-processing into interaction counts. Statistical analysis is based on edgeR and supports normalization and filtering. Several visualization options are also available.' + diff --git a/recipes/bioconductor-difflogo/build.sh b/recipes/bioconductor-difflogo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-difflogo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-difflogo/meta.yaml b/recipes/bioconductor-difflogo/meta.yaml new file mode 100644 index 0000000000000..7011e42c6038d --- /dev/null +++ b/recipes/bioconductor-difflogo/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.6.0" %} +{% set name = "DiffLogo" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7135a21ee77702fa93080a7076f9d314 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, seqLogo, MotifDb +requirements: + host: + - r-base + - r-cba + run: + - r-base + - r-cba +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'DiffLogo is an easy-to-use tool to visualize motif differences.' + diff --git a/recipes/bioconductor-diffloop/build.sh b/recipes/bioconductor-diffloop/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-diffloop/build.sh +++ b/recipes/bioconductor-diffloop/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffloop/meta.yaml b/recipes/bioconductor-diffloop/meta.yaml index bbe0fd37af806..0fdf4551e19a0 100644 --- a/recipes/bioconductor-diffloop/meta.yaml +++ b/recipes/bioconductor-diffloop/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "diffloop" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9aa3941c0740a604c427570611a9fd9defc9475170ba707af0de57ee64557bf9 + md5: a5f0e706ebe5ef31bbea8c497fe7ad90 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DESeq2, diffloopdata, ggrepel, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-sushi >=1.18.0,<1.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sushi >=1.20.0,<1.21.0' - r-base - r-data.table - r-dplyr @@ -41,16 +43,16 @@ requirements: - r-reshape2 - r-statmod run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-sushi >=1.18.0,<1.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sushi >=1.20.0,<1.21.0' - r-base - r-data.table - r-dplyr @@ -67,10 +69,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'A suite of tools for subsetting, visualizing, annotating, and statistically analyzing the results of one or more ChIA-PET experiments or other assays that infer chromatin loops.' extra: identifiers: - biotools:diffloop - doi:10.1101/087338 + parent_recipe: + name: bioconductor-diffloop + path: recipes/bioconductor-diffloop + version: 1.8.0 + diff --git a/recipes/bioconductor-diffloopdata/meta.yaml b/recipes/bioconductor-diffloopdata/meta.yaml new file mode 100644 index 0000000000000..ef719cfa797e0 --- /dev/null +++ b/recipes/bioconductor-diffloopdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "diffloopdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 157263c6bb6d391cab4e51e575e014c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'ChIA-PET example datasets and additional data for use with the diffloop package.' + diff --git a/recipes/bioconductor-diffloopdata/post-link.sh b/recipes/bioconductor-diffloopdata/post-link.sh new file mode 100644 index 0000000000000..f6d2241193456 --- /dev/null +++ b/recipes/bioconductor-diffloopdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="diffloopdata_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/diffloopdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/diffloopdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-diffloopdata/bioconductor-diffloopdata_1.10.0_src_all.tar.gz" +) +MD5="157263c6bb6d391cab4e51e575e014c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-diffloopdata/pre-unlink.sh b/recipes/bioconductor-diffloopdata/pre-unlink.sh new file mode 100644 index 0000000000000..028fcbdb03cae --- /dev/null +++ b/recipes/bioconductor-diffloopdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ diffloopdata diff --git a/recipes/bioconductor-diffustats/build.sh b/recipes/bioconductor-diffustats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-diffustats/build.sh +++ b/recipes/bioconductor-diffustats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diffustats/meta.yaml b/recipes/bioconductor-diffustats/meta.yaml index 22bb914de41ba..a1835e37667e8 100644 --- a/recipes/bioconductor-diffustats/meta.yaml +++ b/recipes/bioconductor-diffustats/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "0.104.0" %} +{% set version = "1.2.0" %} {% set name = "diffuStats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 82b116d961ffb346635336e18ae1ea646457f757ca0e994cd1b2e07277b0baf0 + md5: 98921980a28a6e7ce21bf8b1d83eb6f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, ggplot2, ggsci, igraphdata, BiocStyle, reshape2 +# SystemRequirements: GNU make requirements: host: - r-base @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Label propagation approaches are a widely used procedure in computational biology for giving context to molecular entities using network data. Node labels, which can derive from gene expression, genome-wide association studies, protein domains or metabolomics profiling, are propagated to their neighbours in the network, effectively smoothing the scores through prior annotated knowledge and prioritising novel candidates. The R package diffuStats contains a collection of diffusion kernels and scoring approaches that facilitates their computation and benchmarking.' extra: identifiers: - biotools:diffuStats - doi:10.1093/bioinformatics/btx632 + parent_recipe: + name: bioconductor-diffustats + path: recipes/bioconductor-diffustats + version: 0.104.0 + diff --git a/recipes/bioconductor-diggit/build.sh b/recipes/bioconductor-diggit/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-diggit/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-diggit/meta.yaml b/recipes/bioconductor-diggit/meta.yaml new file mode 100644 index 0000000000000..4ad0366109eda --- /dev/null +++ b/recipes/bioconductor-diggit/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.14.0" %} +{% set name = "diggit" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a21bdc5d8e8cbb24df4dd989df2d1450 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: diggitdata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-ks + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-ks +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Inference of Genetic Variants Driving Cellullar Phenotypes by the DIGGIT algorithm' + diff --git a/recipes/bioconductor-diggitdata/meta.yaml b/recipes/bioconductor-diggitdata/meta.yaml new file mode 100644 index 0000000000000..30a740dfbbcd6 --- /dev/null +++ b/recipes/bioconductor-diggitdata/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.14.0" %} +{% set name = "diggitdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5129f39e50ca1fa38fe4e56ef691e868 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package provides expression profile and CNV data for glioblastoma from TCGA, and transcriptional and post-translational regulatory networks assembled with the ARACNe and MINDy algorithms, respectively.' + diff --git a/recipes/bioconductor-diggitdata/post-link.sh b/recipes/bioconductor-diggitdata/post-link.sh new file mode 100644 index 0000000000000..60356cb2acbb5 --- /dev/null +++ b/recipes/bioconductor-diggitdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="diggitdata_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/diggitdata_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/diggitdata_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-diggitdata/bioconductor-diggitdata_1.14.0_src_all.tar.gz" +) +MD5="5129f39e50ca1fa38fe4e56ef691e868" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-diggitdata/pre-unlink.sh b/recipes/bioconductor-diggitdata/pre-unlink.sh new file mode 100644 index 0000000000000..f380adc600957 --- /dev/null +++ b/recipes/bioconductor-diggitdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ diggitdata diff --git a/recipes/bioconductor-director/build.sh b/recipes/bioconductor-director/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-director/build.sh +++ b/recipes/bioconductor-director/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-director/meta.yaml b/recipes/bioconductor-director/meta.yaml index 18d2f5893ab1e..6426cf6c1e66e 100644 --- a/recipes/bioconductor-director/meta.yaml +++ b/recipes/bioconductor-director/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "Director" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 95b739eeb2ab5864dafa4b557ca25214dc205b365003981221ec9c2ca50cd368 + md5: 2f4bce6a06d8920880b28603880e9284 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Director is an R package designed to streamline the visualization of molecular effects in regulatory cascades. It utilizes the R package htmltools and a modified Sankey plugin of the JavaScript library D3 to provide a fast and easy, browser-enabled solution to discovering potentially interesting downstream effects of regulatory and/or co-expressed molecules. The diagrams are robust, interactive, and packaged as highly-portable HTML files that eliminate the need for third-party software to view. This enables a straightforward approach for scientists to interpret the data produced, and bioinformatics developers an alternative means to present relevant data.' extra: identifiers: - biotools:director - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-director + path: recipes/bioconductor-director + version: 1.6.0 + diff --git a/recipes/bioconductor-dirichletmultinomial/build.sh b/recipes/bioconductor-dirichletmultinomial/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dirichletmultinomial/build.sh +++ b/recipes/bioconductor-dirichletmultinomial/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dirichletmultinomial/meta.yaml b/recipes/bioconductor-dirichletmultinomial/meta.yaml index 6f51b6b8feaa2..08ad1aa871e8f 100644 --- a/recipes/bioconductor-dirichletmultinomial/meta.yaml +++ b/recipes/bioconductor-dirichletmultinomial/meta.yaml @@ -1,45 +1,50 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "DirichletMultinomial" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da7972706c671159b08b5891949b57e909ce8c614d2d5b34253682b402ba9e6d + md5: 33446ccce8a6f3064843a4686a64a7a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: lattice, parallel, MASS, RColorBrewer, xtable +# SystemRequirements: gsl requirements: - build: - - {{ compiler('c') }} - - make host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - openblas run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - openblas + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Dirichlet-multinomial mixture models can be used to describe variability in microbial metagenomic data. This package is an interface to code originally made available by Holmes, Harris, and Quince, 2012, PLoS ONE 7(2): 1-15, as discussed further in the man page for this package, ?DirichletMultinomial.' extra: identifiers: - biotools:dirichletmultinomial - doi:10.1371/journal.pone.0030126 + parent_recipe: + name: bioconductor-dirichletmultinomial + path: recipes/bioconductor-dirichletmultinomial + version: 1.22.0 + diff --git a/recipes/bioconductor-discordant/build.sh b/recipes/bioconductor-discordant/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-discordant/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-discordant/meta.yaml b/recipes/bioconductor-discordant/meta.yaml new file mode 100644 index 0000000000000..d08e6ba4b3721 --- /dev/null +++ b/recipes/bioconductor-discordant/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.6.0" %} +{% set name = "discordant" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 78d8beeab11c13dad6347719051af554 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-biwt + - r-gtools + - r-mass + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-biwt + - r-gtools + - r-mass + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Discordant is a method to determine differential correlation of molecular feature pairs from -omics data using mixture models. Algorithm is explained further in Siska et al.' + diff --git a/recipes/bioconductor-dks/build.sh b/recipes/bioconductor-dks/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dks/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dks/meta.yaml b/recipes/bioconductor-dks/meta.yaml new file mode 100644 index 0000000000000..f1e889d6fc430 --- /dev/null +++ b/recipes/bioconductor-dks/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.28.0" %} +{% set name = "dks" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5ef3fc109a885dd0a57afc15b4e1892e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-cubature + run: + - r-base + - r-cubature +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'The dks package consists of a set of diagnostic functions for multiple testing methods. The functions can be used to determine if the p-values produced by a multiple testing procedure are correct. These functions are designed to be applied to simulated data. The functions require the entire set of p-values from multiple simulated studies, so that the joint distribution can be evaluated.' + diff --git a/recipes/bioconductor-dlbcl/meta.yaml b/recipes/bioconductor-dlbcl/meta.yaml new file mode 100644 index 0000000000000..609f552281a8c --- /dev/null +++ b/recipes/bioconductor-dlbcl/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.22.0" %} +{% set name = "DLBCL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a031da595f9e721bc23ff580d3fa5bd4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package provides additional expression data on diffuse large B-cell lymphomas for the BioNet package.' + diff --git a/recipes/bioconductor-dlbcl/post-link.sh b/recipes/bioconductor-dlbcl/post-link.sh new file mode 100644 index 0000000000000..609338118d811 --- /dev/null +++ b/recipes/bioconductor-dlbcl/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DLBCL_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DLBCL_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/DLBCL_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dlbcl/bioconductor-dlbcl_1.22.0_src_all.tar.gz" +) +MD5="a031da595f9e721bc23ff580d3fa5bd4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dlbcl/pre-unlink.sh b/recipes/bioconductor-dlbcl/pre-unlink.sh new file mode 100644 index 0000000000000..ba7ada26f5706 --- /dev/null +++ b/recipes/bioconductor-dlbcl/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DLBCL diff --git a/recipes/bioconductor-dmchmm/build.sh b/recipes/bioconductor-dmchmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dmchmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmchmm/meta.yaml b/recipes/bioconductor-dmchmm/meta.yaml new file mode 100644 index 0000000000000..a7a21f2aad802 --- /dev/null +++ b/recipes/bioconductor-dmchmm/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.0" %} +{% set name = "DMCHMM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 18d395ae88598cefb95eefe00606bef5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-calibrate + - r-fdrtool + - r-multcomp + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-calibrate + - r-fdrtool + - r-multcomp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A pipeline for identifying differentially methylated CpG sites using Hidden Markov Model in bisulfite sequencing data.' + diff --git a/recipes/bioconductor-dmelsgi/meta.yaml b/recipes/bioconductor-dmelsgi/meta.yaml new file mode 100644 index 0000000000000..a6675415f275d --- /dev/null +++ b/recipes/bioconductor-dmelsgi/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.14.0" %} +{% set name = "DmelSGI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9eda48b2f405f9995dcd517916961e93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, EBImage, RColorBrewer, RNAinteractMAPK, RSVGTipsDevice, cgdsr, hwriter, xtable, beeswarm +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-abind + - r-base + - r-gplots + - r-igraph + - r-knitr + - r-tsp + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-abind + - r-base + - r-gplots + - r-igraph + - r-knitr + - r-tsp + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package contains the experimental data and documented source code of the manuscript "Fischer et al., A Map of Directional Genetic Interactions in a Metazoan Cell, eLife, 2015, in Press.". The vignette code generates all figures in the paper.' + diff --git a/recipes/bioconductor-dmelsgi/post-link.sh b/recipes/bioconductor-dmelsgi/post-link.sh new file mode 100644 index 0000000000000..dc1582005a955 --- /dev/null +++ b/recipes/bioconductor-dmelsgi/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DmelSGI_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DmelSGI_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/DmelSGI_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dmelsgi/bioconductor-dmelsgi_1.14.0_src_all.tar.gz" +) +MD5="9eda48b2f405f9995dcd517916961e93" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dmelsgi/pre-unlink.sh b/recipes/bioconductor-dmelsgi/pre-unlink.sh new file mode 100644 index 0000000000000..f7e46b407b08d --- /dev/null +++ b/recipes/bioconductor-dmelsgi/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DmelSGI diff --git a/recipes/bioconductor-dmrcaller/build.sh b/recipes/bioconductor-dmrcaller/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dmrcaller/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmrcaller/meta.yaml b/recipes/bioconductor-dmrcaller/meta.yaml new file mode 100644 index 0000000000000..eb05d65f55b04 --- /dev/null +++ b/recipes/bioconductor-dmrcaller/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.14.0" %} +{% set name = "DMRcaller" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ce092dcceace356aa8cc520295eb8fea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-betareg + - r-rcpp + - r-rcpproll + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-betareg + - r-rcpp + - r-rcpproll + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Uses Bisulfite sequencing data in two conditions and identifies differentially methylated regions between the conditions in CG and non-CG context. The input is the CX report files produced by Bismark and the output is a list of DMRs stored as GRanges objects.' + diff --git a/recipes/bioconductor-dmrcate/build.sh b/recipes/bioconductor-dmrcate/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dmrcate/build.sh +++ b/recipes/bioconductor-dmrcate/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmrcate/meta.yaml b/recipes/bioconductor-dmrcate/meta.yaml index ded67f87b14ca..bf304769dab11 100644 --- a/recipes/bioconductor-dmrcate/meta.yaml +++ b/recipes/bioconductor-dmrcate/meta.yaml @@ -1,53 +1,60 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DMRcate" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aaa612d617c617b313aa6ffa4ef80c33efe3c5dcc36f573cc02442d18bfab04a + md5: 4bfe58dbc6445926f73996a187c6aa1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics, IlluminaHumanMethylation450kanno.ilmn12.hg19, IlluminaHumanMethylationEPICanno.ilm10b4.hg19 requirements: host: - - 'bioconductor-dmrcatedata >=1.16.0,<1.18.0' - - 'bioconductor-dss >=2.28.0,<2.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-missmethyl >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-dmrcatedata >=1.18.0,<1.19.0' + - 'bioconductor-dss >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-plyr run: - - 'bioconductor-dmrcatedata >=1.16.0,<1.18.0' - - 'bioconductor-dss >=2.28.0,<2.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-missmethyl >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-dmrcatedata >=1.18.0,<1.19.0' + - 'bioconductor-dss >=2.30.0,<2.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-plyr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'De novo identification and extraction of differentially methylated regions (DMRs) from the human genome using Whole Genome Bisulphite Sequencing (WGBS) and Illumina Infinium Array (450K and EPIC) data. Provides functionality for filtering probes possibly confounded by SNPs and cross-hybridisation. Includes GRanges generation and plotting functions.' extra: identifiers: - biotools:dmrcate + parent_recipe: + name: bioconductor-dmrcate + path: recipes/bioconductor-dmrcate + version: 1.16.0 + diff --git a/recipes/bioconductor-dmrcatedata/meta.yaml b/recipes/bioconductor-dmrcatedata/meta.yaml index 710399ea52776..9a779a868a7cc 100644 --- a/recipes/bioconductor-dmrcatedata/meta.yaml +++ b/recipes/bioconductor-dmrcatedata/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DMRcatedata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aeb119417a23374f8d39e0a86b914258455c1446ff3f5b930eea1d18b378b701 + md5: b929cb1b0888f6cbd0e41219b3807b84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'This package contains 8 data objects supporting functionality and examples of the Bioconductor package DMRcate.' - +extra: + parent_recipe: + name: bioconductor-dmrcatedata + path: recipes/bioconductor-dmrcatedata + version: 1.16.0 diff --git a/recipes/bioconductor-dmrcatedata/post-link.sh b/recipes/bioconductor-dmrcatedata/post-link.sh index af9780e1d5bd9..87b74409ac6b8 100644 --- a/recipes/bioconductor-dmrcatedata/post-link.sh +++ b/recipes/bioconductor-dmrcatedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DMRcatedata_1.16.0.tar.gz" +FN="DMRcatedata_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/DMRcatedata_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/DMRcatedata_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DMRcatedata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/DMRcatedata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dmrcatedata/bioconductor-dmrcatedata_1.18.0_src_all.tar.gz" ) -MD5="9ab81fc10aecb5a0ee56ecd7374c093e" +MD5="b929cb1b0888f6cbd0e41219b3807b84" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-dmrforpairs/build.sh b/recipes/bioconductor-dmrforpairs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dmrforpairs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmrforpairs/meta.yaml b/recipes/bioconductor-dmrforpairs/meta.yaml new file mode 100644 index 0000000000000..e2edc4b3970e0 --- /dev/null +++ b/recipes/bioconductor-dmrforpairs/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.18.0" %} +{% set name = "DMRforPairs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f972e67a117c8be0dc1cc2fcf831ab7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - r-base + - 'r-r2html >=2.2.1' + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - r-base + - 'r-r2html >=2.2.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'DMRforPairs (formerly DMR2+) allows researchers to compare n>=2 unique samples with regard to their methylation profile. The (pairwise) comparison of n unique single samples distinguishes DMRforPairs from other existing pipelines as these often compare groups of samples in either single CpG locus or region based analysis. DMRforPairs defines regions of interest as genomic ranges with sufficient probes located in close proximity to each other. Probes in one region are optionally annotated to the same functional class(es). Differential methylation is evaluated by comparing the methylation values within each region between individual samples and (if the difference is sufficiently large), testing this difference formally for statistical significance.' + diff --git a/recipes/bioconductor-dmrscan/build.sh b/recipes/bioconductor-dmrscan/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dmrscan/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmrscan/meta.yaml b/recipes/bioconductor-dmrscan/meta.yaml new file mode 100644 index 0000000000000..60552464d5e8a --- /dev/null +++ b/recipes/bioconductor-dmrscan/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.8.0" %} +{% set name = "DMRScan" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0e746f249607060c44d9f4591fc72a1d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-mass + - r-matrix + - r-mvtnorm + - r-rcpproll + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-mass + - r-matrix + - r-mvtnorm + - r-rcpproll +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package detects significant differentially methylated regions (for both qualitative and quantitative traits), using a scan statistic with underlying Poisson heuristics. The scan statistic will depend on a sequence of window sizes (# of CpGs within each window) and on a threshold for each window size. This threshold can be calculated by three different means: i) analytically using Siegmund et.al (2012) solution (preferred), ii) an important sampling as suggested by Zhang (2008), and a iii) full MCMC modeling of the data, choosing between a number of different options for modeling the dependency between each CpG.' + diff --git a/recipes/bioconductor-dmrseq/build.sh b/recipes/bioconductor-dmrseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dmrseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dmrseq/meta.yaml b/recipes/bioconductor-dmrseq/meta.yaml new file mode 100644 index 0000000000000..e01b30c46942c --- /dev/null +++ b/recipes/bioconductor-dmrseq/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.2.1" %} +{% set name = "dmrseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e388d10623aea75e8909ccc6ef875fa5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotatr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-nlme + - r-outliers + - r-rcolorbrewer + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotatr >=1.8.0,<1.9.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-locfit + - r-matrixstats + - r-nlme + - r-outliers + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package implements an approach for scanning the genome to detect and perform accurate inference on differentially methylated regions from Whole Genome Bisulfite Sequencing data. The method is based on comparing detected regions to a pooled null distribution, that can be implemented even when as few as two samples per population are available. Region-level statistics are obtained by fitting a generalized least squares (GLS) regression model with a nested autoregressive correlated error structure for the effect of interest on transformed methylation proportions.' + diff --git a/recipes/bioconductor-dnabarcodes/build.sh b/recipes/bioconductor-dnabarcodes/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dnabarcodes/build.sh +++ b/recipes/bioconductor-dnabarcodes/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dnabarcodes/meta.yaml b/recipes/bioconductor-dnabarcodes/meta.yaml index 61ad5970eceae..2aaf8fe3fd0f0 100644 --- a/recipes/bioconductor-dnabarcodes/meta.yaml +++ b/recipes/bioconductor-dnabarcodes/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "DNABarcodes" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bdac77417ac37bc37dec8e3aa88bc9ada67a4a2c2a2b8ea1b8f7e409dc511676 + md5: 7c3ceda6d5afa1322c928dab20a28f74 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, BiocStyle, rmarkdown requirements: host: - r-base @@ -35,9 +36,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package offers a function to create DNA barcode sets capable of correcting insertion, deletion, and substitution errors. Existing barcodes can be analysed regarding their minimal, maximal and average distances between barcodes. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode.' extra: identifiers: - biotools:dnabarcodes + parent_recipe: + name: bioconductor-dnabarcodes + path: recipes/bioconductor-dnabarcodes + version: 1.10.0 + diff --git a/recipes/bioconductor-dnacopy/build.sh b/recipes/bioconductor-dnacopy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dnacopy/build.sh +++ b/recipes/bioconductor-dnacopy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dnacopy/meta.yaml b/recipes/bioconductor-dnacopy/meta.yaml index 79b0a5d3d2e61..f7e24d9bcfe42 100644 --- a/recipes/bioconductor-dnacopy/meta.yaml +++ b/recipes/bioconductor-dnacopy/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "DNAcopy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 163510992ff6e204c75da992434b08129fec043f66d4c79ec8c0f8c26a850e0e + md5: 184fc2c7f242fcfe49504ad1e135f34f build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Implements the circular binary segmentation (CBS) algorithm to segment DNA copy number data and identify genomic regions with abnormal copy number.' extra: identifiers: - biotools:dnacopy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dnacopy + path: recipes/bioconductor-dnacopy + version: 1.54.0 + diff --git a/recipes/bioconductor-dnashaper/build.sh b/recipes/bioconductor-dnashaper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dnashaper/build.sh +++ b/recipes/bioconductor-dnashaper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dnashaper/meta.yaml b/recipes/bioconductor-dnashaper/meta.yaml index d8fcaf3456511..1317fd25f9211 100644 --- a/recipes/bioconductor-dnashaper/meta.yaml +++ b/recipes/bioconductor-dnashaper/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DNAshapeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3ce868aa1189c396f1a20822fef9ca1768bddfaf1467e17d9a5a79bed3fa2fbc + md5: d0da206934c751b45cc8606a22dbeb6d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: AnnotationHub, knitr, rmarkdown, testthat, BSgenome.Scerevisiae.UCSC.sacCer3, BSgenome.Hsapiens.UCSC.hg19, caret requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-fields - 'r-rcpp >=0.12.1' run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-fields - 'r-rcpp >=0.12.1' @@ -37,9 +38,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'DNAhapeR is an R/BioConductor package for ultra-fast, high-throughput predictions of DNA shape features. The package allows to predict, visualize and encode DNA shape features for statistical learning.' extra: identifiers: - biotools:dnashaper + parent_recipe: + name: bioconductor-dnashaper + path: recipes/bioconductor-dnashaper + version: 1.8.0 + diff --git a/recipes/bioconductor-do.db/meta.yaml b/recipes/bioconductor-do.db/meta.yaml index e8b505e99a533..4b4b452f717c3 100644 --- a/recipes/bioconductor-do.db/meta.yaml +++ b/recipes/bioconductor-do.db/meta.yaml @@ -1,35 +1,40 @@ {% set version = "2.9" %} {% set name = "DO.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 762bcb9b5188274fd81d82f785cf2846a5acc61fad55e2ff8ec1502282c27881 + md5: 63dda6d46d2fe40c52a2e79260a7fb9d build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Disease Ontology assembled using data from DO' - +extra: + parent_recipe: + name: bioconductor-do.db + path: recipes/bioconductor-do.db + version: 2.9 diff --git a/recipes/bioconductor-do.db/post-link.sh b/recipes/bioconductor-do.db/post-link.sh index 2a87d86b99b54..3b3a029afa379 100644 --- a/recipes/bioconductor-do.db/post-link.sh +++ b/recipes/bioconductor-do.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="DO.db_2.9.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/DO.db_2.9.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/DO.db_2.9.tar.gz" "https://bioarchive.galaxyproject.org/DO.db_2.9.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-do.db/bioconductor-do.db_2.9_src_all.tar.gz" diff --git a/recipes/bioconductor-dominoeffect/build.sh b/recipes/bioconductor-dominoeffect/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dominoeffect/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dominoeffect/meta.yaml b/recipes/bioconductor-dominoeffect/meta.yaml new file mode 100644 index 0000000000000..1983744ade8c2 --- /dev/null +++ b/recipes/bioconductor-dominoeffect/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "DominoEffect" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 59b6b6a049d56b6407e31fa9f5a1c0f2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-data.table + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-data.table +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'The functions support identification and annotation of hotspot residues in proteins. These are individual amino acids that accumulate mutations at a much higher rate than their surrounding regions.' + diff --git a/recipes/bioconductor-donapllp2013/meta.yaml b/recipes/bioconductor-donapllp2013/meta.yaml new file mode 100644 index 0000000000000..eaf0805c0896e --- /dev/null +++ b/recipes/bioconductor-donapllp2013/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "DonaPLLP2013" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5a228295986fdfe1ad44a66ca2f1d947 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-base + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An experiment data package associated with the publication Dona et al. (2013). Package contains runnable vignettes showing an example image segmentation for one posterior lateral line primordium, and also the data table and code used to analyze tissue-scale lifetime-ratio statistics.' + diff --git a/recipes/bioconductor-donapllp2013/post-link.sh b/recipes/bioconductor-donapllp2013/post-link.sh new file mode 100644 index 0000000000000..67cbeb1413547 --- /dev/null +++ b/recipes/bioconductor-donapllp2013/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DonaPLLP2013_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DonaPLLP2013_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/DonaPLLP2013_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-donapllp2013/bioconductor-donapllp2013_1.20.0_src_all.tar.gz" +) +MD5="5a228295986fdfe1ad44a66ca2f1d947" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-donapllp2013/pre-unlink.sh b/recipes/bioconductor-donapllp2013/pre-unlink.sh new file mode 100644 index 0000000000000..bfeed34057947 --- /dev/null +++ b/recipes/bioconductor-donapllp2013/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DonaPLLP2013 diff --git a/recipes/bioconductor-doppelgangr/build.sh b/recipes/bioconductor-doppelgangr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-doppelgangr/build.sh +++ b/recipes/bioconductor-doppelgangr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-doppelgangr/meta.yaml b/recipes/bioconductor-doppelgangr/meta.yaml index bb11543e3796d..e1cd2503c88ad 100644 --- a/recipes/bioconductor-doppelgangr/meta.yaml +++ b/recipes/bioconductor-doppelgangr/meta.yaml @@ -1,35 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "doppelgangR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8a74bd7904a0ec830ad5f48dc17aee2e8c7433e33bb64a20a02a25ab6a14ea6a + md5: bc4ebb38cd72cff6db041e767b38385b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, curatedOvarianData, ROCR, pROC, RUnit, simulatorZ, proxy requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-digest - r-mnormt run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-digest - r-mnormt @@ -37,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'The main function is doppelgangR(), which takes as minimal input a list of ExpressionSet object, and searches all list pairs for duplicated samples. The search is based on the genomic data (exprs(eset)), phenotype/clinical data (pData(eset)), and "smoking guns" - supposedly unique identifiers found in pData(eset).' extra: identifiers: - biotools:doppelgangr - doi:10.1093/jnci/djw146 + parent_recipe: + name: bioconductor-doppelgangr + path: recipes/bioconductor-doppelgangr + version: 1.8.0 + diff --git a/recipes/bioconductor-doqtl/build.sh b/recipes/bioconductor-doqtl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-doqtl/build.sh +++ b/recipes/bioconductor-doqtl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-doqtl/meta.yaml b/recipes/bioconductor-doqtl/meta.yaml index 0a3ae09f40b52..df479a1f46808 100644 --- a/recipes/bioconductor-doqtl/meta.yaml +++ b/recipes/bioconductor-doqtl/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.16.2" %} +{% set version = "1.18.0" %} {% set name = "DOQTL" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a44668e9af9dfea9d82e85ba2e83d6034e526b6fc95ab60612f4ae8aeae08fe1 + md5: 8b15a6d126d98936877e94434c13b3b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: MUGAExampleData requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationtools >=1.54.0,<1.56.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationtools >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-corpcor - r-doparallel @@ -42,17 +43,17 @@ requirements: - r-runit - r-xml run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationtools >=1.54.0,<1.56.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationtools >=1.56.0,<1.57.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-corpcor - r-doparallel @@ -72,9 +73,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DOQTL is a quantitative trait locus (QTL) mapping pipeline designed for Diversity Outbred mice and other multi-parent outbred populations. The package reads in data from genotyping arrays and perform haplotype reconstruction using a hidden Markov model (HMM). The haplotype probabilities from the HMM are then used to perform linkage mapping. When founder sequences are available, DOQTL can use the haplotype reconstructions to impute the founder sequences onto DO genomes and perform association mapping.' extra: identifiers: - biotools:doqtl + parent_recipe: + name: bioconductor-doqtl + path: recipes/bioconductor-doqtl + version: 1.16.2 + diff --git a/recipes/bioconductor-doscheda/build.sh b/recipes/bioconductor-doscheda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-doscheda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-doscheda/meta.yaml b/recipes/bioconductor-doscheda/meta.yaml new file mode 100644 index 0000000000000..b27ddce5d445b --- /dev/null +++ b/recipes/bioconductor-doscheda/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.4.0" %} +{% set name = "Doscheda" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f10e02e1255d3fc585c0710e482d75e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-calibrate + - r-corrgram + - r-d3heatmap + - r-drc + - r-dt + - r-ggplot2 + - r-gridextra + - r-httr + - r-jsonlite + - r-matrixstats + - r-prodlim + - r-readxl + - r-reshape2 + - r-shiny + - r-shinydashboard + - r-stringr + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-calibrate + - r-corrgram + - r-d3heatmap + - r-drc + - r-dt + - r-ggplot2 + - r-gridextra + - r-httr + - r-jsonlite + - r-matrixstats + - r-prodlim + - r-readxl + - r-reshape2 + - r-shiny + - r-shinydashboard + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Doscheda focuses on quantitative chemoproteomics used to determine protein interaction profiles of small molecules from whole cell or tissue lysates using Mass Spectrometry data. The package provides a shiny application to run the pipeline, several visualisations and a downloadable report of an experiment.' + diff --git a/recipes/bioconductor-dose/build.sh b/recipes/bioconductor-dose/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dose/build.sh +++ b/recipes/bioconductor-dose/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dose/meta.yaml b/recipes/bioconductor-dose/meta.yaml index fe8a7e52e4727..86aa6afc2e424 100644 --- a/recipes/bioconductor-dose/meta.yaml +++ b/recipes/bioconductor-dose/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "3.6.1" %} +{% set version = "3.8.0" %} {% set name = "DOSE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b38aa2e548912f8ec2e471841e83346d240ff5dd1d6c2620d2fe209ca8cc9df + md5: a179a5c31428292643cadb40577409f7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-do.db >=2.9,<2.11.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-do.db 2.9' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-do.db >=2.9,<2.11.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-do.db 2.9' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-reshape2 @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively for measuring semantic similarities among DO terms and gene products. Enrichment analyses including hypergeometric model and gene set enrichment analysis are also implemented for discovering disease associations of high-throughput biological data.' extra: identifiers: - biotools:dose + parent_recipe: + name: bioconductor-dose + path: recipes/bioconductor-dose + version: 3.6.1 + diff --git a/recipes/bioconductor-drawproteins/build.sh b/recipes/bioconductor-drawproteins/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-drawproteins/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drawproteins/meta.yaml b/recipes/bioconductor-drawproteins/meta.yaml new file mode 100644 index 0000000000000..5b9d438daa076 --- /dev/null +++ b/recipes/bioconductor-drawproteins/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "drawProteins" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 206c89be262e17a9c1f9611aa69272c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: covr, testthat, knitr, rmarkdown, BiocStyle +requirements: + host: + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-readr + - r-stringr + run: + - r-base + - r-dplyr + - r-ggplot2 + - r-httr + - r-readr + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package draws protein schematics from Uniprot API output. From the JSON returned by the GET command, it creates a dataframe from the Uniprot Features API. This dataframe can then be used by geoms based on ggplot2 and base R to draw protein schematics.' + diff --git a/recipes/bioconductor-dream4/meta.yaml b/recipes/bioconductor-dream4/meta.yaml new file mode 100644 index 0000000000000..4e6bf3a212cdf --- /dev/null +++ b/recipes/bioconductor-dream4/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "DREAM4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 47e37f3d98279f6f1f1e5dfa1198f1b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, networkBMA +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Simulated expression data for five 10-node, and five 100-node networks, with associated data (including solutions) from the 2009 DREAM4 challenge.' + diff --git a/recipes/bioconductor-dream4/post-link.sh b/recipes/bioconductor-dream4/post-link.sh new file mode 100644 index 0000000000000..8b276626a350f --- /dev/null +++ b/recipes/bioconductor-dream4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DREAM4_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DREAM4_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/DREAM4_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dream4/bioconductor-dream4_1.18.0_src_all.tar.gz" +) +MD5="47e37f3d98279f6f1f1e5dfa1198f1b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dream4/pre-unlink.sh b/recipes/bioconductor-dream4/pre-unlink.sh new file mode 100644 index 0000000000000..2390d6e7257c0 --- /dev/null +++ b/recipes/bioconductor-dream4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DREAM4 diff --git a/recipes/bioconductor-dresscheck/meta.yaml b/recipes/bioconductor-dresscheck/meta.yaml new file mode 100644 index 0000000000000..e7ad67cf00c18 --- /dev/null +++ b/recipes/bioconductor-dresscheck/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "0.20.0" %} +{% set name = "dressCheck" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dad61d2a1cfae86bc1f1b9f132291ae6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: survival, chron +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'data and software for checking Dressman JCO 25(5) 2007' + diff --git a/recipes/bioconductor-dresscheck/post-link.sh b/recipes/bioconductor-dresscheck/post-link.sh new file mode 100644 index 0000000000000..e30625c962d74 --- /dev/null +++ b/recipes/bioconductor-dresscheck/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="dressCheck_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dressCheck_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/dressCheck_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dresscheck/bioconductor-dresscheck_0.20.0_src_all.tar.gz" +) +MD5="dad61d2a1cfae86bc1f1b9f132291ae6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dresscheck/pre-unlink.sh b/recipes/bioconductor-dresscheck/pre-unlink.sh new file mode 100644 index 0000000000000..030453c9e79fc --- /dev/null +++ b/recipes/bioconductor-dresscheck/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ dressCheck diff --git a/recipes/bioconductor-drimseq/build.sh b/recipes/bioconductor-drimseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-drimseq/build.sh +++ b/recipes/bioconductor-drimseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drimseq/meta.yaml b/recipes/bioconductor-drimseq/meta.yaml index 8929577128c11..887a639e2a881 100644 --- a/recipes/bioconductor-drimseq/meta.yaml +++ b/recipes/bioconductor-drimseq/meta.yaml @@ -1,42 +1,44 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "DRIMSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 336b05fcd2047fb41185437373557d3719e18b76bbf9bf0aade043f5473576d8 + md5: 1f674b2ade74a9c629045f01def425ff build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: PasillaTranscriptExpr, GeuvadisTranscriptExpr, grid, BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-mass - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-mass @@ -45,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package provides two frameworks. One for the differential transcript usage analysis between different conditions and one for the tuQTL analysis. Both are based on modeling the counts of genomic features (i.e., transcripts) with the Dirichlet-multinomial distribution. The package also makes available functions for visualization and exploration of the data and results.' extra: identifiers: - biotools:drimseq + parent_recipe: + name: bioconductor-drimseq + path: recipes/bioconductor-drimseq + version: 1.8.0 + diff --git a/recipes/bioconductor-drivernet/build.sh b/recipes/bioconductor-drivernet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-drivernet/build.sh +++ b/recipes/bioconductor-drivernet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drivernet/meta.yaml b/recipes/bioconductor-drivernet/meta.yaml index 10ecef010cb53..2324d3eef717e 100644 --- a/recipes/bioconductor-drivernet/meta.yaml +++ b/recipes/bioconductor-drivernet/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "DriverNet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 95c7c3ab5eb4f3b4837542fd58d2a8d7e9e7bd39df355482b1c139be8d622d55 + md5: 0a220e7958f082c4c716ee19f77f735a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'DriverNet is a package to predict functional important driver genes in cancer by integrating genome data (mutation and copy number variation data) and transcriptome data (gene expression data). The different kinds of data are combined by an influence graph, which is a gene-gene interaction network deduced from pathway data. A greedy algorithm is used to find the possible driver genes, which may mutated in a larger number of patients and these mutations will push the gene expression values of the connected genes to some extreme values.' extra: identifiers: - biotools:drivernet - doi:10.1186/gb-2012-13-12-r124 + parent_recipe: + name: bioconductor-drivernet + path: recipes/bioconductor-drivernet + version: 1.20.0 + diff --git a/recipes/bioconductor-dropletutils/build.sh b/recipes/bioconductor-dropletutils/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dropletutils/build.sh +++ b/recipes/bioconductor-dropletutils/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dropletutils/conda_build_config.yaml b/recipes/bioconductor-dropletutils/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-dropletutils/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-dropletutils/meta.yaml b/recipes/bioconductor-dropletutils/meta.yaml index 96949e202fdfe..51a89bce5c178 100644 --- a/recipes/bioconductor-dropletutils/meta.yaml +++ b/recipes/bioconductor-dropletutils/meta.yaml @@ -1,54 +1,48 @@ -{% set version = "1.0.3" %} +{% set version = "1.2.1" %} {% set name = "DropletUtils" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 63eb07ea6a35a6b52b8990209ce9b0cec5960ecee70e940dd689f2b9a08412ef + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 756b633ad77b92d78bd632eaa02c14ba build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, beachmat, knitr, BiocStyle, rmarkdown +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-genomeinfodb >=1.16.0' - - 'bioconductor-genomeinfodbdata >=1.1.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - r-base - - r-dplyr - r-matrix - - 'r-rcpp >=0.12.14' + - r-rcpp run: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-genomeinfodb >=1.16.0' - - 'bioconductor-genomeinfodbdata >=1.1.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' - r-base - r-matrix - - r-plyr - - 'r-rcpp >=0.12.14' + - r-rcpp build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -57,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'Utilities for Handling Single-Cell Droplet Data.' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides a number of utility functions for handling single-cell (RNA-seq) data from droplet technologies such as 10X Genomics. This includes data loading, identification of cells from empty droplets, removal of barcode-swapped pseudo-cells, and downsampling of the count matrix.' extra: identifiers: - biotools:DropletUtils + parent_recipe: + name: bioconductor-dropletutils + path: recipes/bioconductor-dropletutils + version: 1.0.3 + diff --git a/recipes/bioconductor-drosgenome1.db/meta.yaml b/recipes/bioconductor-drosgenome1.db/meta.yaml new file mode 100644 index 0000000000000..5a4c4edca09ec --- /dev/null +++ b/recipes/bioconductor-drosgenome1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "drosgenome1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 44bc6356bc04226cba8cb2f3544c4688 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Drosophila Genome Array annotation data (chip drosgenome1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-drosgenome1.db/post-link.sh b/recipes/bioconductor-drosgenome1.db/post-link.sh new file mode 100644 index 0000000000000..6e304888a1b8d --- /dev/null +++ b/recipes/bioconductor-drosgenome1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosgenome1.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/drosgenome1.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1.db/bioconductor-drosgenome1.db_3.2.3_src_all.tar.gz" +) +MD5="44bc6356bc04226cba8cb2f3544c4688" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosgenome1.db/pre-unlink.sh b/recipes/bioconductor-drosgenome1.db/pre-unlink.sh new file mode 100644 index 0000000000000..5d0a504daf133 --- /dev/null +++ b/recipes/bioconductor-drosgenome1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosgenome1.db diff --git a/recipes/bioconductor-drosgenome1cdf/meta.yaml b/recipes/bioconductor-drosgenome1cdf/meta.yaml new file mode 100644 index 0000000000000..18a9b42b4d25b --- /dev/null +++ b/recipes/bioconductor-drosgenome1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "drosgenome1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e12983f2148c10ef1faa50f810b6eee3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the DrosGenome1.CDF file.' + diff --git a/recipes/bioconductor-drosgenome1cdf/post-link.sh b/recipes/bioconductor-drosgenome1cdf/post-link.sh new file mode 100644 index 0000000000000..7e717a0fa859a --- /dev/null +++ b/recipes/bioconductor-drosgenome1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosgenome1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/drosgenome1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1cdf/bioconductor-drosgenome1cdf_2.18.0_src_all.tar.gz" +) +MD5="e12983f2148c10ef1faa50f810b6eee3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosgenome1cdf/pre-unlink.sh b/recipes/bioconductor-drosgenome1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..8d320b02b30cc --- /dev/null +++ b/recipes/bioconductor-drosgenome1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosgenome1cdf diff --git a/recipes/bioconductor-drosgenome1probe/meta.yaml b/recipes/bioconductor-drosgenome1probe/meta.yaml new file mode 100644 index 0000000000000..769246245c50a --- /dev/null +++ b/recipes/bioconductor-drosgenome1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "drosgenome1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1f12abdfeee65e8a6554f57507d86fb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was DrosGenome1\_probe\_tab.' + diff --git a/recipes/bioconductor-drosgenome1probe/post-link.sh b/recipes/bioconductor-drosgenome1probe/post-link.sh new file mode 100644 index 0000000000000..c28b5005a2559 --- /dev/null +++ b/recipes/bioconductor-drosgenome1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosgenome1probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosgenome1probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/drosgenome1probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosgenome1probe/bioconductor-drosgenome1probe_2.18.0_src_all.tar.gz" +) +MD5="1f12abdfeee65e8a6554f57507d86fb3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosgenome1probe/pre-unlink.sh b/recipes/bioconductor-drosgenome1probe/pre-unlink.sh new file mode 100644 index 0000000000000..7993c575d11de --- /dev/null +++ b/recipes/bioconductor-drosgenome1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosgenome1probe diff --git a/recipes/bioconductor-drosophila2.db/meta.yaml b/recipes/bioconductor-drosophila2.db/meta.yaml new file mode 100644 index 0000000000000..4d0c88424ce60 --- /dev/null +++ b/recipes/bioconductor-drosophila2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "drosophila2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 04a372eff398f79691216ed9fcc34bc8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Drosophila Genome 2.0 Array annotation data (chip drosophila2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-drosophila2.db/post-link.sh b/recipes/bioconductor-drosophila2.db/post-link.sh new file mode 100644 index 0000000000000..da47bcf20ed7b --- /dev/null +++ b/recipes/bioconductor-drosophila2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosophila2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/drosophila2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2.db/bioconductor-drosophila2.db_3.2.3_src_all.tar.gz" +) +MD5="04a372eff398f79691216ed9fcc34bc8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosophila2.db/pre-unlink.sh b/recipes/bioconductor-drosophila2.db/pre-unlink.sh new file mode 100644 index 0000000000000..efac30fdc91f8 --- /dev/null +++ b/recipes/bioconductor-drosophila2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosophila2.db diff --git a/recipes/bioconductor-drosophila2cdf/meta.yaml b/recipes/bioconductor-drosophila2cdf/meta.yaml new file mode 100644 index 0000000000000..cd31fe0d27b4e --- /dev/null +++ b/recipes/bioconductor-drosophila2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "drosophila2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3323e723c133ff2b6188e22bebf3e20a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Drosophila_2.cdf file.' + diff --git a/recipes/bioconductor-drosophila2cdf/post-link.sh b/recipes/bioconductor-drosophila2cdf/post-link.sh new file mode 100644 index 0000000000000..e8e6163f5f5fb --- /dev/null +++ b/recipes/bioconductor-drosophila2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosophila2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/drosophila2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2cdf/bioconductor-drosophila2cdf_2.18.0_src_all.tar.gz" +) +MD5="3323e723c133ff2b6188e22bebf3e20a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosophila2cdf/pre-unlink.sh b/recipes/bioconductor-drosophila2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..d1afd8501f189 --- /dev/null +++ b/recipes/bioconductor-drosophila2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosophila2cdf diff --git a/recipes/bioconductor-drosophila2probe/meta.yaml b/recipes/bioconductor-drosophila2probe/meta.yaml new file mode 100644 index 0000000000000..892260d8a7543 --- /dev/null +++ b/recipes/bioconductor-drosophila2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "drosophila2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ba0251902ea0a5f0db61105bdcdc3530 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Drosophila\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-drosophila2probe/post-link.sh b/recipes/bioconductor-drosophila2probe/post-link.sh new file mode 100644 index 0000000000000..36dc692f4d401 --- /dev/null +++ b/recipes/bioconductor-drosophila2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="drosophila2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/drosophila2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/drosophila2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drosophila2probe/bioconductor-drosophila2probe_2.18.0_src_all.tar.gz" +) +MD5="ba0251902ea0a5f0db61105bdcdc3530" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-drosophila2probe/pre-unlink.sh b/recipes/bioconductor-drosophila2probe/pre-unlink.sh new file mode 100644 index 0000000000000..f6378d7294f43 --- /dev/null +++ b/recipes/bioconductor-drosophila2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ drosophila2probe diff --git a/recipes/bioconductor-drugvsdisease/build.sh b/recipes/bioconductor-drugvsdisease/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-drugvsdisease/build.sh +++ b/recipes/bioconductor-drugvsdisease/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-drugvsdisease/conda_build_config.yaml b/recipes/bioconductor-drugvsdisease/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-drugvsdisease/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-drugvsdisease/meta.yaml b/recipes/bioconductor-drugvsdisease/meta.yaml index b393e73ff0ce7..94b245c620b1c 100644 --- a/recipes/bioconductor-drugvsdisease/meta.yaml +++ b/recipes/bioconductor-drugvsdisease/meta.yaml @@ -1,53 +1,54 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "DrugVsDisease" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd1554211afe42f7f75549bdc331ff8a80a26d52acf4e4e3afde1d328f0c2d38 + md5: d792eb60bfc4b9a515f66d1987bde570 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-arrayexpress >=1.40.0,<1.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-cmap2data >=1.16.0,<1.18.0' - - 'bioconductor-drugvsdiseasedata >=1.16.0,<1.18.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133a2.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-arrayexpress >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-cmap2data >=1.18.0,<1.19.0' + - 'bioconductor-drugvsdiseasedata >=1.18.0,<1.19.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133a2.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-runit - r-xtable run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-arrayexpress >=1.40.0,<1.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-cmap2data >=1.16.0,<1.18.0' - - 'bioconductor-drugvsdiseasedata >=1.16.0,<1.18.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133a2.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-arrayexpress >=1.42.0,<1.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-cmap2data >=1.18.0,<1.19.0' + - 'bioconductor-drugvsdiseasedata >=1.18.0,<1.19.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133a2.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-runit - r-xtable @@ -55,10 +56,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package generates ranked lists of differential gene expression for either disease or drug profiles. Input data can be downloaded from Array Express or GEO, or from local CEL files. Ranked lists of differential expression and associated p-values are calculated using Limma. Enrichment scores (Subramanian et al. PNAS 2005) are calculated to a reference set of default drug or disease profiles, or a set of custom data supplied by the user. Network visualisation of significant scores are output in Cytoscape format.' extra: identifiers: - biotools:drugvsdisease - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-drugvsdisease + path: recipes/bioconductor-drugvsdisease + version: 2.22.0 + diff --git a/recipes/bioconductor-drugvsdiseasedata/meta.yaml b/recipes/bioconductor-drugvsdiseasedata/meta.yaml index b69986483ab11..d9ac51ec2ddb9 100644 --- a/recipes/bioconductor-drugvsdiseasedata/meta.yaml +++ b/recipes/bioconductor-drugvsdiseasedata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "DrugVsDiseasedata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 24f6371b471a2478dab6d1c0a4ddf227f2074e5f6d06571b1f7a1d4173a984f3 + md5: e6cddb699ec1351eda47cbb3fb40e705 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data package which provides default disease expression profiles, clusters and annotation information for use with the DrugVsDisease package.' - +extra: + parent_recipe: + name: bioconductor-drugvsdiseasedata + path: recipes/bioconductor-drugvsdiseasedata + version: 1.16.0 diff --git a/recipes/bioconductor-drugvsdiseasedata/post-link.sh b/recipes/bioconductor-drugvsdiseasedata/post-link.sh index d464527fba155..b41469b0541d2 100644 --- a/recipes/bioconductor-drugvsdiseasedata/post-link.sh +++ b/recipes/bioconductor-drugvsdiseasedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="DrugVsDiseasedata_1.16.0.tar.gz" +FN="DrugVsDiseasedata_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/DrugVsDiseasedata_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DrugVsDiseasedata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/DrugVsDiseasedata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-drugvsdiseasedata/bioconductor-drugvsdiseasedata_1.18.0_src_all.tar.gz" ) -MD5="3cc03987897e80f8eb7ddfc821ed1ac1" +MD5="e6cddb699ec1351eda47cbb3fb40e705" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-dsimer/build.sh b/recipes/bioconductor-dsimer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dsimer/build.sh +++ b/recipes/bioconductor-dsimer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dsimer/meta.yaml b/recipes/bioconductor-dsimer/meta.yaml index 92f353b96566f..53bddefd9c9cd 100644 --- a/recipes/bioconductor-dsimer/meta.yaml +++ b/recipes/bioconductor-dsimer/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "dSimer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6775ba21090a335eaeed343f75c997c94222a0f80514af09c019de1d1e959179 + md5: 6f09cfd76372e623ef50b24ad7bd076f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' - 'r-rcpp >=0.11.3' - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-ggplot2 - 'r-igraph >=1.0.1' @@ -43,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'dSimer is an R package which provides computation of nine methods for measuring disease-disease similarity, including a standard cosine similarity measure and eight function-based methods. The disease similarity matrix obtained from these nine methods can be visualized through heatmap and network. Biological data widely used in disease-disease associations study are also provided by dSimer.' extra: identifiers: - biotools:dsimer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dsimer + path: recipes/bioconductor-dsimer + version: 1.6.0 + diff --git a/recipes/bioconductor-dsqtl/meta.yaml b/recipes/bioconductor-dsqtl/meta.yaml new file mode 100644 index 0000000000000..1131c45ab0f25 --- /dev/null +++ b/recipes/bioconductor-dsqtl/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.20.0" %} +{% set name = "dsQTL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 077dd1342d0cc842c44937a61e90ea10 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GGtools, rtracklayer +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'dsQTL, excerpt from Degner et al. 2012 Nature letter on DNA variants associated with DnaseI hypersensitivity' + diff --git a/recipes/bioconductor-dsqtl/post-link.sh b/recipes/bioconductor-dsqtl/post-link.sh new file mode 100644 index 0000000000000..478a0c3dfaa70 --- /dev/null +++ b/recipes/bioconductor-dsqtl/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="dsQTL_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dsQTL_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/dsQTL_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dsqtl/bioconductor-dsqtl_0.20.0_src_all.tar.gz" +) +MD5="077dd1342d0cc842c44937a61e90ea10" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dsqtl/pre-unlink.sh b/recipes/bioconductor-dsqtl/pre-unlink.sh new file mode 100644 index 0000000000000..1831a1e48af57 --- /dev/null +++ b/recipes/bioconductor-dsqtl/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ dsQTL diff --git a/recipes/bioconductor-dss/build.sh b/recipes/bioconductor-dss/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dss/build.sh +++ b/recipes/bioconductor-dss/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dss/meta.yaml b/recipes/bioconductor-dss/meta.yaml index 87a4da0f5f85e..e2d24b560941a 100644 --- a/recipes/bioconductor-dss/meta.yaml +++ b/recipes/bioconductor-dss/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "DSS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ae607b625c4451e6c7b91be226e6daeb5207ba97290812a989846298d80fa291 + md5: 6ea15f25bbe6c4c2afb12976d575cefc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bsseq >=1.16.1,<1.18.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bsseq >=1.16.1,<1.18.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' - r-base build: - {{ compiler('c') }} @@ -34,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'DSS is an R library performing differntial analysis for count-based sequencing data. It detectes differentially expressed genes (DEGs) from RNA-seq, and differentially methylated loci or regions (DML/DMRs) from bisulfite sequencing (BS-seq). The core of DSS is a new dispersion shrinkage method for estimating the dispersion parameter from Gamma-Poisson or Beta-Binomial distributions.' extra: identifiers: - biotools:dss + parent_recipe: + name: bioconductor-dss + path: recipes/bioconductor-dss + version: 2.28.0 + diff --git a/recipes/bioconductor-dta/build.sh b/recipes/bioconductor-dta/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dta/build.sh +++ b/recipes/bioconductor-dta/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dta/meta.yaml b/recipes/bioconductor-dta/meta.yaml index 67a58ac37129b..d005d1a0c4739 100644 --- a/recipes/bioconductor-dta/meta.yaml +++ b/recipes/bioconductor-dta/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "DTA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5bdf6c45717e63d88bbfaa48975b00b983d54d9815c5ca24c7de656670e1c2c4 + md5: 7af46c4b3ca3d98a4c9398b0d68a1c71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Dynamic Transcriptome Analysis (DTA) can monitor the cellular response to perturbations with higher sensitivity and temporal resolution than standard transcriptomics. The package implements the underlying kinetic modeling approach capable of the precise determination of synthesis- and decay rates from individual microarray or RNAseq measurements.' extra: identifiers: - biotools:dta - doi:10.1093/bioinformatics/bts052 + parent_recipe: + name: bioconductor-dta + path: recipes/bioconductor-dta + version: 2.26.0 + diff --git a/recipes/bioconductor-dualks/build.sh b/recipes/bioconductor-dualks/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-dualks/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dualks/meta.yaml b/recipes/bioconductor-dualks/meta.yaml new file mode 100644 index 0000000000000..fc347a269569f --- /dev/null +++ b/recipes/bioconductor-dualks/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.42.0" %} +{% set name = "dualKS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aef440fc9d6a7971b3ca41a51f7368c1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'This package implements a Kolmogorov Smirnov rank-sum based algorithm for training (i.e. discriminant analysis--identification of genes that discriminate between classes) and classification of gene expression data sets. One of the chief strengths of this approach is that it is amenable to the "multiclass" problem. That is, it can discriminate between more than 2 classes.' + diff --git a/recipes/bioconductor-duoclustering2018/meta.yaml b/recipes/bioconductor-duoclustering2018/meta.yaml new file mode 100644 index 0000000000000..f34f0280f267e --- /dev/null +++ b/recipes/bioconductor-duoclustering2018/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "DuoClustering2018" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 533a6230137770c646ced387a5ecd4fd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, iSEE, scater, SingleCellExperiment, SummarizedExperiment, plyr +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggthemes + - r-magrittr + - r-mclust + - r-purrr + - r-reshape2 + - r-tidyr + - r-viridis + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-ggthemes + - r-magrittr + - r-mclust + - r-purrr + - r-reshape2 + - r-tidyr + - r-viridis + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Preprocessed experimental and simulated scRNA-seq data sets used for evaluation of clustering methods for scRNA-seq data in Duò et al (2018). Also contains results from applying several clustering methods to each of the data sets, and functions for plotting method performance.' + diff --git a/recipes/bioconductor-duoclustering2018/post-link.sh b/recipes/bioconductor-duoclustering2018/post-link.sh new file mode 100644 index 0000000000000..38d8d1d122004 --- /dev/null +++ b/recipes/bioconductor-duoclustering2018/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DuoClustering2018_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DuoClustering2018_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/DuoClustering2018_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-duoclustering2018/bioconductor-duoclustering2018_1.0.0_src_all.tar.gz" +) +MD5="533a6230137770c646ced387a5ecd4fd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-duoclustering2018/pre-unlink.sh b/recipes/bioconductor-duoclustering2018/pre-unlink.sh new file mode 100644 index 0000000000000..06a9de2258ed4 --- /dev/null +++ b/recipes/bioconductor-duoclustering2018/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DuoClustering2018 diff --git a/recipes/bioconductor-dupchecker/build.sh b/recipes/bioconductor-dupchecker/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dupchecker/build.sh +++ b/recipes/bioconductor-dupchecker/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dupchecker/meta.yaml b/recipes/bioconductor-dupchecker/meta.yaml index dbf7b66579f74..7d7480fc03dcc 100644 --- a/recipes/bioconductor-dupchecker/meta.yaml +++ b/recipes/bioconductor-dupchecker/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "DupChecker" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e668197c0e0c4d560de03365a28e7bcbd7ca17a112e78596e2df95879054e13e + md5: c5867bb93e37d69cb72527f796de4e0f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -29,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: ' Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates would make study results questionable. We developed a Bioconductor package DupChecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.' + summary: 'Meta-analysis has become a popular approach for high-throughput genomic data analysis because it often can significantly increase power to detect biological signals or patterns in datasets. However, when using public-available databases for meta-analysis, duplication of samples is an often encountered problem, especially for gene expression data. Not removing duplicates would make study results questionable. We developed a Bioconductor package DupChecker that efficiently identifies duplicated samples by generating MD5 fingerprints for raw data.' extra: identifiers: - biotools:dupchecker + parent_recipe: + name: bioconductor-dupchecker + path: recipes/bioconductor-dupchecker + version: 1.18.0 + diff --git a/recipes/bioconductor-dupradar/build.sh b/recipes/bioconductor-dupradar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dupradar/build.sh +++ b/recipes/bioconductor-dupradar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dupradar/meta.yaml b/recipes/bioconductor-dupradar/meta.yaml index 317339bce97e4..2ae14b483e7b0 100644 --- a/recipes/bioconductor-dupradar/meta.yaml +++ b/recipes/bioconductor-dupradar/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.1" %} {% set name = "dupRadar" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e845aa9c135b741990e27a307fbb834ffacdd350ae5254920fa816f5145099ac + md5: 58ff3f96c44230db7e9483621a213421 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, AnnotationHub requirements: host: - - 'bioconductor-rsubread >=1.30.8,<1.32.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' - r-base run: - - 'bioconductor-rsubread >=1.30.8,<1.32.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Duplication rate quality control for RNA-Seq datasets.' extra: identifiers: - biotools:dupradar + parent_recipe: + name: bioconductor-dupradar + path: recipes/bioconductor-dupradar + version: 1.10.0 + diff --git a/recipes/bioconductor-dvddata/meta.yaml b/recipes/bioconductor-dvddata/meta.yaml new file mode 100644 index 0000000000000..24c6da4746cd9 --- /dev/null +++ b/recipes/bioconductor-dvddata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "DvDdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c2b58da21a872a2757fb6928e7fd155e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Data package which provides default drug and disease expression profiles for the DvD package.' + diff --git a/recipes/bioconductor-dvddata/post-link.sh b/recipes/bioconductor-dvddata/post-link.sh new file mode 100644 index 0000000000000..37956bd966240 --- /dev/null +++ b/recipes/bioconductor-dvddata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="DvDdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/DvDdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/DvDdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dvddata/bioconductor-dvddata_1.18.0_src_all.tar.gz" +) +MD5="c2b58da21a872a2757fb6928e7fd155e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dvddata/pre-unlink.sh b/recipes/bioconductor-dvddata/pre-unlink.sh new file mode 100644 index 0000000000000..d98462c261f97 --- /dev/null +++ b/recipes/bioconductor-dvddata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ DvDdata diff --git a/recipes/bioconductor-dyebias/build.sh b/recipes/bioconductor-dyebias/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dyebias/build.sh +++ b/recipes/bioconductor-dyebias/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dyebias/meta.yaml b/recipes/bioconductor-dyebias/meta.yaml index 9aee4da8a9595..869ecc22af231 100644 --- a/recipes/bioconductor-dyebias/meta.yaml +++ b/recipes/bioconductor-dyebias/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "dyebias" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 68ea39bc0ae6d4f8693a1ac8473559e4a7498f403d657085c51da3688412151e + md5: a5c7c84939a73cac498807188f7c8ee8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma, convert, GEOquery, dyebiasexamples, methods requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Many two-colour hybridizations suffer from a dye bias that is both gene-specific and slide-specific. The former depends on the content of the nucleotide used for labeling; the latter depends on the labeling percentage. The slide-dependency was hitherto not recognized, and made addressing the artefact impossible. Given a reasonable number of dye-swapped pairs of hybridizations, or of same vs. same hybridizations, both the gene- and slide-biases can be estimated and corrected using the GASSCO method (Margaritis et al., Mol. Sys. Biol. 5:266 (2009), doi:10.1038/msb.2009.21)' extra: identifiers: - biotools:dyebias + parent_recipe: + name: bioconductor-dyebias + path: recipes/bioconductor-dyebias + version: 1.40.0 + diff --git a/recipes/bioconductor-dyebiasexamples/meta.yaml b/recipes/bioconductor-dyebiasexamples/meta.yaml new file mode 100644 index 0000000000000..b7124dec80ee2 --- /dev/null +++ b/recipes/bioconductor-dyebiasexamples/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.22.0" %} +{% set name = "dyebiasexamples" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 21da0022921c7f6e6eeb997e1bc56fa4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: dyebias, convert, Biobase +requirements: + host: + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Data for the dyebias package, consisting of 4 self-self hybrizations of self-spotted yeast slides, as well as data from Array Express accession E-MTAB-32' + diff --git a/recipes/bioconductor-dyebiasexamples/post-link.sh b/recipes/bioconductor-dyebiasexamples/post-link.sh new file mode 100644 index 0000000000000..18a14ea13d57f --- /dev/null +++ b/recipes/bioconductor-dyebiasexamples/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="dyebiasexamples_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/dyebiasexamples_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/dyebiasexamples_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-dyebiasexamples/bioconductor-dyebiasexamples_1.22.0_src_all.tar.gz" +) +MD5="21da0022921c7f6e6eeb997e1bc56fa4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-dyebiasexamples/pre-unlink.sh b/recipes/bioconductor-dyebiasexamples/pre-unlink.sh new file mode 100644 index 0000000000000..87598d363162a --- /dev/null +++ b/recipes/bioconductor-dyebiasexamples/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ dyebiasexamples diff --git a/recipes/bioconductor-dyndoc/build.sh b/recipes/bioconductor-dyndoc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-dyndoc/build.sh +++ b/recipes/bioconductor-dyndoc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-dyndoc/meta.yaml b/recipes/bioconductor-dyndoc/meta.yaml index 986b176048adb..2d41257170297 100644 --- a/recipes/bioconductor-dyndoc/meta.yaml +++ b/recipes/bioconductor-dyndoc/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "DynDoc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78572bbef190ba20cfa7c9a23f62570aebe35b73e83e18c590875c6fc49c4dd2 + md5: 9ab4d310071f59bab69bad2f75c152e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of functions to create and interact with dynamic documents and vignettes.' extra: identifiers: - biotools:dyndoc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-dyndoc + path: recipes/bioconductor-dyndoc + version: 1.58.0 + diff --git a/recipes/bioconductor-easyqpcr/build.sh b/recipes/bioconductor-easyqpcr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-easyqpcr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-easyqpcr/meta.yaml b/recipes/bioconductor-easyqpcr/meta.yaml new file mode 100644 index 0000000000000..1092840651022 --- /dev/null +++ b/recipes/bioconductor-easyqpcr/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.24.0" %} +{% set name = "EasyqpcR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 858ce6239d7775d581f9dd188ea167df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SLqPCR, qpcrNorm, qpcR, knitr +requirements: + host: + - r-base + - r-gwidgetsrgtk2 + - r-matrixstats + - r-plotrix + - r-plyr + run: + - r-base + - r-gwidgetsrgtk2 + - r-matrixstats + - r-plotrix + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package is based on the qBase algorithms published by Hellemans et al. in 2007. The EasyqpcR package allows you to import easily qPCR data files as described in the vignette. Thereafter, you can calculate amplification efficiencies, relative quantities and their standard errors, normalization factors based on the best reference genes choosen (using the SLqPCR package), and then the normalized relative quantities, the NRQs scaled to your control and their standard errors. This package has been created for low-throughput qPCR data analysis.' + diff --git a/recipes/bioconductor-easyrnaseq/build.sh b/recipes/bioconductor-easyrnaseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-easyrnaseq/build.sh +++ b/recipes/bioconductor-easyrnaseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-easyrnaseq/meta.yaml b/recipes/bioconductor-easyrnaseq/meta.yaml index 606cfc2a8fcc6..72add9461662a 100644 --- a/recipes/bioconductor-easyrnaseq/meta.yaml +++ b/recipes/bioconductor-easyrnaseq/meta.yaml @@ -1,59 +1,61 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.2" %} {% set name = "easyRNASeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 08fda441093ae8770cab7e4378fdcf6b5823e3689b9bbf5121acc0c6201d25c0 + md5: e2daba492e062c9fae75030c5b3e280c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle (>= 2.7.8), BSgenome (>= 1.39.0), BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.4.0), curl, knitr, rmarkdown, RUnit (>= 0.4.31) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-locfit - 'r-lsd >=3.0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-locfit - 'r-lsd >=3.0' @@ -61,9 +63,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.' extra: identifiers: - biotools:easyrnaseq + parent_recipe: + name: bioconductor-easyrnaseq + path: recipes/bioconductor-easyrnaseq + version: 2.16.0 + diff --git a/recipes/bioconductor-eatonetalchipseq/meta.yaml b/recipes/bioconductor-eatonetalchipseq/meta.yaml new file mode 100644 index 0000000000000..5611c93590f7b --- /dev/null +++ b/recipes/bioconductor-eatonetalchipseq/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.20.0" %} +{% set name = "EatonEtAlChIPseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4733fad7f34d353e3dbe267587fe2198 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'Artistic 2.0' + summary: 'ChIP-seq analysis subset from "Conserved nucleosome positioning defines replication origins" (PMID 20351051)' + diff --git a/recipes/bioconductor-eatonetalchipseq/post-link.sh b/recipes/bioconductor-eatonetalchipseq/post-link.sh new file mode 100644 index 0000000000000..65f5f40833c67 --- /dev/null +++ b/recipes/bioconductor-eatonetalchipseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EatonEtAlChIPseq_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/EatonEtAlChIPseq_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/EatonEtAlChIPseq_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-eatonetalchipseq/bioconductor-eatonetalchipseq_0.20.0_src_all.tar.gz" +) +MD5="4733fad7f34d353e3dbe267587fe2198" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-eatonetalchipseq/pre-unlink.sh b/recipes/bioconductor-eatonetalchipseq/pre-unlink.sh new file mode 100644 index 0000000000000..5a7fe8651df48 --- /dev/null +++ b/recipes/bioconductor-eatonetalchipseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EatonEtAlChIPseq diff --git a/recipes/bioconductor-ebarrays/build.sh b/recipes/bioconductor-ebarrays/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ebarrays/build.sh +++ b/recipes/bioconductor-ebarrays/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebarrays/meta.yaml b/recipes/bioconductor-ebarrays/meta.yaml index c9f1e3e19f3f2..c2e84bb53a995 100644 --- a/recipes/bioconductor-ebarrays/meta.yaml +++ b/recipes/bioconductor-ebarrays/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "EBarrays" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7e3ff110be38d9276adfb7e331eabf84d77282156a1d26df8b49b686aedaae1 + md5: 4a42f6740313e671fbd0433896b6f227 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster - r-lattice run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster - r-lattice @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'EBarrays provides tools for the analysis of replicated/unreplicated microarray data.' extra: identifiers: - biotools:ebarrays - doi:10.1111/j.1541-0420.2006.00611.x + parent_recipe: + name: bioconductor-ebarrays + path: recipes/bioconductor-ebarrays + version: 2.44.0 + diff --git a/recipes/bioconductor-ebcoexpress/build.sh b/recipes/bioconductor-ebcoexpress/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ebcoexpress/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebcoexpress/meta.yaml b/recipes/bioconductor-ebcoexpress/meta.yaml new file mode 100644 index 0000000000000..bea9508059c84 --- /dev/null +++ b/recipes/bioconductor-ebcoexpress/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.26.0" %} +{% set name = "EBcoexpress" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 391a4f44e4fc3c4578121104a30877c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: graph, igraph, colorspace +requirements: + host: + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - r-base + - r-mclust + - r-minqa + run: + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - r-base + - r-mclust + - r-minqa + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'An Empirical Bayesian Approach to Differential Co-Expression Analysis at the Gene-Pair Level' + diff --git a/recipes/bioconductor-ebimage/build.sh b/recipes/bioconductor-ebimage/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ebimage/build.sh +++ b/recipes/bioconductor-ebimage/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebimage/meta.yaml b/recipes/bioconductor-ebimage/meta.yaml index 24511d0f2d276..175b332c7c580 100644 --- a/recipes/bioconductor-ebimage/meta.yaml +++ b/recipes/bioconductor-ebimage/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "4.22.1" %} +{% set version = "4.24.0" %} {% set name = "EBImage" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 497bb6a34edc39023339173c92d65ed4f558c6ab7eaa00459cc9684d612a5755 + md5: 3ddadf0e47dfe26013b10378dee62c55 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, digest, knitr, rmarkdown, shiny requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' @@ -30,7 +31,7 @@ requirements: - r-rcurl - r-tiff run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-abind - r-base - 'r-fftwtools >=0.9-7' @@ -49,9 +50,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'EBImage provides general purpose functionality for image processing and analysis. In the context of (high-throughput) microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and facilitates the use of other tools in the R environment for signal processing, statistical modeling, machine learning and visualization with image data.' extra: identifiers: - biotools:ebimage + parent_recipe: + name: bioconductor-ebimage + path: recipes/bioconductor-ebimage + version: 4.22.1 + diff --git a/recipes/bioconductor-ebsea/build.sh b/recipes/bioconductor-ebsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ebsea/build.sh +++ b/recipes/bioconductor-ebsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebsea/meta.yaml b/recipes/bioconductor-ebsea/meta.yaml index f2ba8c88c7adb..6ac1071f188b7 100644 --- a/recipes/bioconductor-ebsea/meta.yaml +++ b/recipes/bioconductor-ebsea/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "EBSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 22f601ca51ef5365f8f0a9dcd830c66aed9d847bc29f3bb2590bdadc7763f5c5 + md5: 6e9147314c2308892969992ca042ddec build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-plyr run: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-plyr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Calculates differential expression of genes based on exon counts of genes obtained from RNA-seq sequencing data.' extra: identifiers: - biotools:ebsea - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ebsea + path: recipes/bioconductor-ebsea + version: 1.8.0 + diff --git a/recipes/bioconductor-ebseq/build.sh b/recipes/bioconductor-ebseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ebseq/build.sh +++ b/recipes/bioconductor-ebseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebseq/meta.yaml b/recipes/bioconductor-ebseq/meta.yaml index 82e0879550416..bce5d98a7f5da 100644 --- a/recipes/bioconductor-ebseq/meta.yaml +++ b/recipes/bioconductor-ebseq/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "EBSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b39642a70e606d85ca5d17716fd48aa82e5459f85d44af592e9050eeb2fd5cd + md5: 15c6daeab2e0404935286858c33d080a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Differential Expression analysis at both gene and isoform level using RNA-seq data' extra: identifiers: - biotools:ebseq - doi:10.1093/bioinformatics/btt087 + parent_recipe: + name: bioconductor-ebseq + path: recipes/bioconductor-ebseq + version: 1.20.0 + diff --git a/recipes/bioconductor-ebseqhmm/build.sh b/recipes/bioconductor-ebseqhmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ebseqhmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ebseqhmm/meta.yaml b/recipes/bioconductor-ebseqhmm/meta.yaml new file mode 100644 index 0000000000000..9eb61a39c9beb --- /dev/null +++ b/recipes/bioconductor-ebseqhmm/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.16.0" %} +{% set name = "EBSeqHMM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e0c3433208791faa359e4343ed4ebe32 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - r-base + run: + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The EBSeqHMM package implements an auto-regressive hidden Markov model for statistical analysis in ordered RNA-seq experiments (e.g. time course or spatial course data). The EBSeqHMM package provides functions to identify genes and isoforms that have non-constant expression profile over the time points/positions, and cluster them into expression paths.' + diff --git a/recipes/bioconductor-ecoli2.db/meta.yaml b/recipes/bioconductor-ecoli2.db/meta.yaml new file mode 100644 index 0000000000000..bc547a1055123 --- /dev/null +++ b/recipes/bioconductor-ecoli2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "ecoli2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1fe0877a59b63453df6667944818e66b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.eck12.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.eck12.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix E. coli Genome 2.0 Array annotation data (chip ecoli2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ecoli2.db/post-link.sh b/recipes/bioconductor-ecoli2.db/post-link.sh new file mode 100644 index 0000000000000..4967e375ba169 --- /dev/null +++ b/recipes/bioconductor-ecoli2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoli2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/ecoli2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2.db/bioconductor-ecoli2.db_3.2.3_src_all.tar.gz" +) +MD5="1fe0877a59b63453df6667944818e66b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoli2.db/pre-unlink.sh b/recipes/bioconductor-ecoli2.db/pre-unlink.sh new file mode 100644 index 0000000000000..26e3da1f7090a --- /dev/null +++ b/recipes/bioconductor-ecoli2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoli2.db diff --git a/recipes/bioconductor-ecoli2cdf/meta.yaml b/recipes/bioconductor-ecoli2cdf/meta.yaml new file mode 100644 index 0000000000000..8d571c1663050 --- /dev/null +++ b/recipes/bioconductor-ecoli2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecoli2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b5cd1f05322ce494132ff649de9806c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the E_coli_2.cdf file.' + diff --git a/recipes/bioconductor-ecoli2cdf/post-link.sh b/recipes/bioconductor-ecoli2cdf/post-link.sh new file mode 100644 index 0000000000000..9856100a0a7ee --- /dev/null +++ b/recipes/bioconductor-ecoli2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoli2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoli2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2cdf/bioconductor-ecoli2cdf_2.18.0_src_all.tar.gz" +) +MD5="b5cd1f05322ce494132ff649de9806c6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoli2cdf/pre-unlink.sh b/recipes/bioconductor-ecoli2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..7a2dc60df38fa --- /dev/null +++ b/recipes/bioconductor-ecoli2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoli2cdf diff --git a/recipes/bioconductor-ecoli2probe/meta.yaml b/recipes/bioconductor-ecoli2probe/meta.yaml new file mode 100644 index 0000000000000..43c6be8e89252 --- /dev/null +++ b/recipes/bioconductor-ecoli2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecoli2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 061fcb782ee9da3aa5108881677a4531 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-ecoli2probe/post-link.sh b/recipes/bioconductor-ecoli2probe/post-link.sh new file mode 100644 index 0000000000000..8cb5aee73b4d9 --- /dev/null +++ b/recipes/bioconductor-ecoli2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoli2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoli2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoli2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoli2probe/bioconductor-ecoli2probe_2.18.0_src_all.tar.gz" +) +MD5="061fcb782ee9da3aa5108881677a4531" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoli2probe/pre-unlink.sh b/recipes/bioconductor-ecoli2probe/pre-unlink.sh new file mode 100644 index 0000000000000..2a90186a43ec0 --- /dev/null +++ b/recipes/bioconductor-ecoli2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoli2probe diff --git a/recipes/bioconductor-ecoliasv2cdf/meta.yaml b/recipes/bioconductor-ecoliasv2cdf/meta.yaml new file mode 100644 index 0000000000000..9109458b8c483 --- /dev/null +++ b/recipes/bioconductor-ecoliasv2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecoliasv2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d7771ca1648b26a6af5bfb7582c6c778 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ecoli_ASv2.CDF file.' + diff --git a/recipes/bioconductor-ecoliasv2cdf/post-link.sh b/recipes/bioconductor-ecoliasv2cdf/post-link.sh new file mode 100644 index 0000000000000..6cf2684b2b8f3 --- /dev/null +++ b/recipes/bioconductor-ecoliasv2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliasv2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliasv2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliasv2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2cdf/bioconductor-ecoliasv2cdf_2.18.0_src_all.tar.gz" +) +MD5="d7771ca1648b26a6af5bfb7582c6c778" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoliasv2cdf/pre-unlink.sh b/recipes/bioconductor-ecoliasv2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..057730173fb7a --- /dev/null +++ b/recipes/bioconductor-ecoliasv2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliasv2cdf diff --git a/recipes/bioconductor-ecoliasv2probe/meta.yaml b/recipes/bioconductor-ecoliasv2probe/meta.yaml new file mode 100644 index 0000000000000..c4b1411afdc3f --- /dev/null +++ b/recipes/bioconductor-ecoliasv2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecoliasv2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b3e4332266184576279c3a478f286dc9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_Asv2\_probe\_tab.' + diff --git a/recipes/bioconductor-ecoliasv2probe/post-link.sh b/recipes/bioconductor-ecoliasv2probe/post-link.sh new file mode 100644 index 0000000000000..384c866f1d197 --- /dev/null +++ b/recipes/bioconductor-ecoliasv2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliasv2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliasv2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliasv2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliasv2probe/bioconductor-ecoliasv2probe_2.18.0_src_all.tar.gz" +) +MD5="b3e4332266184576279c3a478f286dc9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoliasv2probe/pre-unlink.sh b/recipes/bioconductor-ecoliasv2probe/pre-unlink.sh new file mode 100644 index 0000000000000..33f40baa7f317 --- /dev/null +++ b/recipes/bioconductor-ecoliasv2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliasv2probe diff --git a/recipes/bioconductor-ecolicdf/meta.yaml b/recipes/bioconductor-ecolicdf/meta.yaml new file mode 100644 index 0000000000000..dcaf486e91e36 --- /dev/null +++ b/recipes/bioconductor-ecolicdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecolicdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4e664c1ac41a8ab68ef22f8a889b916c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ecoli.CDF file.' + diff --git a/recipes/bioconductor-ecolicdf/post-link.sh b/recipes/bioconductor-ecolicdf/post-link.sh new file mode 100644 index 0000000000000..73410dba35bcb --- /dev/null +++ b/recipes/bioconductor-ecolicdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecolicdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecolicdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecolicdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolicdf/bioconductor-ecolicdf_2.18.0_src_all.tar.gz" +) +MD5="4e664c1ac41a8ab68ef22f8a889b916c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecolicdf/pre-unlink.sh b/recipes/bioconductor-ecolicdf/pre-unlink.sh new file mode 100644 index 0000000000000..123e4943d8296 --- /dev/null +++ b/recipes/bioconductor-ecolicdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecolicdf diff --git a/recipes/bioconductor-ecolik12.db0/meta.yaml b/recipes/bioconductor-ecolik12.db0/meta.yaml new file mode 100644 index 0000000000000..0125036171024 --- /dev/null +++ b/recipes/bioconductor-ecolik12.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "ecoliK12.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d2ee48a340d6222a8e78582748849d42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for E coli K12 Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-ecolik12.db0/post-link.sh b/recipes/bioconductor-ecolik12.db0/post-link.sh new file mode 100644 index 0000000000000..c3c1e97d0798d --- /dev/null +++ b/recipes/bioconductor-ecolik12.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliK12.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliK12.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliK12.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolik12.db0/bioconductor-ecolik12.db0_3.7.1_src_all.tar.gz" +) +MD5="d2ee48a340d6222a8e78582748849d42" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecolik12.db0/pre-unlink.sh b/recipes/bioconductor-ecolik12.db0/pre-unlink.sh new file mode 100644 index 0000000000000..be5659df2086f --- /dev/null +++ b/recipes/bioconductor-ecolik12.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliK12.db0 diff --git a/recipes/bioconductor-ecolileucine/meta.yaml b/recipes/bioconductor-ecolileucine/meta.yaml new file mode 100644 index 0000000000000..13703c2fe18cc --- /dev/null +++ b/recipes/bioconductor-ecolileucine/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "ecoliLeucine" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8b615a131951847086512158b0d6c876 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ecolicdf >=2.18.0,<2.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Experimental data with Affymetrix E. coli chips, as reported in She-pin Hung, Pierre Baldi, and G. Wesley Hatfield, J. Biol. Chem., Vol. 277, Issue 43, 40309-40323, October 25, 2002' + diff --git a/recipes/bioconductor-ecolileucine/post-link.sh b/recipes/bioconductor-ecolileucine/post-link.sh new file mode 100644 index 0000000000000..977f8324f8e3c --- /dev/null +++ b/recipes/bioconductor-ecolileucine/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliLeucine_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ecoliLeucine_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliLeucine_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolileucine/bioconductor-ecolileucine_1.22.0_src_all.tar.gz" +) +MD5="8b615a131951847086512158b0d6c876" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecolileucine/pre-unlink.sh b/recipes/bioconductor-ecolileucine/pre-unlink.sh new file mode 100644 index 0000000000000..537bbb9603193 --- /dev/null +++ b/recipes/bioconductor-ecolileucine/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliLeucine diff --git a/recipes/bioconductor-ecoliprobe/meta.yaml b/recipes/bioconductor-ecoliprobe/meta.yaml new file mode 100644 index 0000000000000..1343b9072c32c --- /dev/null +++ b/recipes/bioconductor-ecoliprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ecoliprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 09586f9907bdbc43ba5ea4ce07c1f756 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was E\_coli\_probe\_tab.' + diff --git a/recipes/bioconductor-ecoliprobe/post-link.sh b/recipes/bioconductor-ecoliprobe/post-link.sh new file mode 100644 index 0000000000000..b4929ffe15fb4 --- /dev/null +++ b/recipes/bioconductor-ecoliprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecoliprobe/bioconductor-ecoliprobe_2.18.0_src_all.tar.gz" +) +MD5="09586f9907bdbc43ba5ea4ce07c1f756" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecoliprobe/pre-unlink.sh b/recipes/bioconductor-ecoliprobe/pre-unlink.sh new file mode 100644 index 0000000000000..a906f0cceb3ad --- /dev/null +++ b/recipes/bioconductor-ecoliprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliprobe diff --git a/recipes/bioconductor-ecolisakai.db0/meta.yaml b/recipes/bioconductor-ecolisakai.db0/meta.yaml new file mode 100644 index 0000000000000..058b9f4669b02 --- /dev/null +++ b/recipes/bioconductor-ecolisakai.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "ecoliSakai.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b0d399ca92ed5899e7c5770d86f38de2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for E coli Sakai Strain, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-ecolisakai.db0/post-link.sh b/recipes/bioconductor-ecolisakai.db0/post-link.sh new file mode 100644 index 0000000000000..31258e8b6818b --- /dev/null +++ b/recipes/bioconductor-ecolisakai.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ecoliSakai.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ecoliSakai.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/ecoliSakai.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ecolisakai.db0/bioconductor-ecolisakai.db0_3.7.1_src_all.tar.gz" +) +MD5="b0d399ca92ed5899e7c5770d86f38de2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ecolisakai.db0/pre-unlink.sh b/recipes/bioconductor-ecolisakai.db0/pre-unlink.sh new file mode 100644 index 0000000000000..c190b6feda8e0 --- /dev/null +++ b/recipes/bioconductor-ecolisakai.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ecoliSakai.db0 diff --git a/recipes/bioconductor-ecolitk/build.sh b/recipes/bioconductor-ecolitk/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ecolitk/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ecolitk/meta.yaml b/recipes/bioconductor-ecolitk/meta.yaml new file mode 100644 index 0000000000000..0d9ff2c8d5ae0 --- /dev/null +++ b/recipes/bioconductor-ecolitk/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.54.0" %} +{% set name = "ecolitk" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a0d9620024909dcbb12b20e3b5ebf92f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ecoliLeucine, ecolicdf, graph, multtest, affy +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Meta-data and tools to work with E. coli. The tools are mostly plotting functions to work with circular genomes. They can used with other genomes/plasmids.' + diff --git a/recipes/bioconductor-edaseq/build.sh b/recipes/bioconductor-edaseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-edaseq/build.sh +++ b/recipes/bioconductor-edaseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-edaseq/meta.yaml b/recipes/bioconductor-edaseq/meta.yaml index 1fa2529b83a28..520b63889c718 100644 --- a/recipes/bioconductor-edaseq/meta.yaml +++ b/recipes/bioconductor-edaseq/meta.yaml @@ -1,57 +1,64 @@ -{% set version = "2.14.1" %} +{% set version = "2.16.0" %} {% set name = "EDASeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8695f6701f4b9f1af7d5cb622d366151ad8678bcd298c3b0e1cb7565ae2e024 + md5: ed8283ab13f07c4d7a182c240471dd89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, yeastRNASeq, leeBamViews, edgeR, KernSmooth, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-aroma.light >=3.10.0,<3.12.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-aroma.light >=3.12.0,<3.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-aroma.light >=3.10.0,<3.12.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-aroma.light >=3.12.0,<3.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Numerical and graphical summaries of RNA-Seq read data. Within-lane normalization procedures to adjust for GC-content effect (or other gene-level effects) on read counts: loess robust local regression, global-scaling, and full-quantile normalization (Risso et al., 2011). Between-lane normalization procedures to adjust for distributional differences between lanes (e.g., sequencing depth): global-scaling and full-quantile normalization (Bullard et al., 2010).' extra: identifiers: - biotools:edaseq + parent_recipe: + name: bioconductor-edaseq + path: recipes/bioconductor-edaseq + version: 2.14.1 + diff --git a/recipes/bioconductor-edda/build.sh b/recipes/bioconductor-edda/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-edda/build.sh +++ b/recipes/bioconductor-edda/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-edda/meta.yaml b/recipes/bioconductor-edda/meta.yaml index 8e5d87f68cb87..489e35eedbad4 100644 --- a/recipes/bioconductor-edda/meta.yaml +++ b/recipes/bioconductor-edda/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "EDDA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bc1918bad514dd8e18c62d74dfe5cb719626d0378509529748e231aaeae687b8 + md5: f3c875c507c3f331aaf72cfca2d2760d build: number: 0 rpaths: @@ -18,17 +18,17 @@ build: - lib/ requirements: host: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr - r-snow run: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - 'r-rcpp >=0.10.4' - r-rocr @@ -41,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'EDDA can aid in the design of a range of common experiments such as RNA-seq, Nanostring assays, RIP-seq and Metagenomic sequencing, and enables researchers to comprehensively investigate the impact of experimental decisions on the ability to detect differential abundance. This work was published on 3 December 2014 at Genome Biology under the title "The importance of study design for detecting differentially abundant features in high-throughput experiments" (http://genomebiology.com/2014/15/12/527).' extra: identifiers: - biotools:edda - doi:10.1186/s13059-014-0527-7 + parent_recipe: + name: bioconductor-edda + path: recipes/bioconductor-edda + version: 1.18.0 + diff --git a/recipes/bioconductor-edge/build.sh b/recipes/bioconductor-edge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-edge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-edge/meta.yaml b/recipes/bioconductor-edge/meta.yaml new file mode 100644 index 0000000000000..45838191d091d --- /dev/null +++ b/recipes/bioconductor-edge/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "2.14.0" %} +{% set name = "edge" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6797ccce69d0cfc8d172ead461d3cec7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, ggplot2, reshape2 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-snm >=1.30.0,<1.31.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-jackstraw + - r-mass + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-snm >=1.30.0,<1.31.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-jackstraw + - r-mass + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The edge package implements methods for carrying out differential expression analyses of genome-wide gene expression studies. Significance testing using the optimal discovery procedure and generalized likelihood ratio tests (equivalent to F-tests and t-tests) are implemented for general study designs. Special functions are available to facilitate the analysis of common study designs, including time course experiments. Other packages such as snm, sva, and qvalue are integrated in edge to provide a wide range of tools for gene expression analysis.' + diff --git a/recipes/bioconductor-edger/build.sh b/recipes/bioconductor-edger/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-edger/build.sh +++ b/recipes/bioconductor-edger/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-edger/meta.yaml b/recipes/bioconductor-edger/meta.yaml index 36f927a7ce8cb..70138c40ebcee 100644 --- a/recipes/bioconductor-edger/meta.yaml +++ b/recipes/bioconductor-edger/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "3.22.5" %} +{% set version = "3.24.1" %} {% set name = "edgeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 47d2234f29a4717e4f7079f23ef300d910e81adf4721d58d62aaf18ae06c6c5e + md5: 2612716ed3a2800e539c80ae3fbef690 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: AnnotationDbi, jsonlite, org.Hs.eg.db, readr, rhdf5, splines +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-limma >=3.36.0,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-locfit - r-rcpp run: - - 'bioconductor-limma >=3.36.0,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-locfit - r-rcpp @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Differential expression analysis of RNA-seq expression profiles with biological replication. Implements a range of statistical methodology based on the negative binomial distributions, including empirical Bayes estimation, exact tests, generalized linear models and quasi-likelihood tests. As well as RNA-seq, it be applied to differential signal analysis of other types of genomic data that produce counts, including ChIP-seq, Bisulfite-seq, SAGE and CAGE.' extra: identifiers: - biotools:edger + parent_recipe: + name: bioconductor-edger + path: recipes/bioconductor-edger + version: 3.22.5 + diff --git a/recipes/bioconductor-eegc/build.sh b/recipes/bioconductor-eegc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-eegc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eegc/meta.yaml b/recipes/bioconductor-eegc/meta.yaml new file mode 100644 index 0000000000000..6b32ea092ad88 --- /dev/null +++ b/recipes/bioconductor-eegc/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.8.0" %} +{% set name = "eegc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 80ae17a861a02b93bac38afb632948b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gplots + - r-igraph + - r-pheatmap + - r-r.utils + - r-sna + - r-wordcloud + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gplots + - r-igraph + - r-pheatmap + - r-r.utils + - r-sna + - r-wordcloud +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package has been developed to evaluate cellular engineering processes for direct differentiation of stem cells or conversion (transdifferentiation) of somatic cells to primary cells based on high throughput gene expression data screened either by DNA microarray or RNA sequencing. The package takes gene expression profiles as inputs from three types of samples: (i) somatic or stem cells to be (trans)differentiated (input of the engineering process), (ii) induced cells to be evaluated (output of the engineering process) and (iii) target primary cells (reference for the output). The package performs differential gene expression analysis for each pair-wise sample comparison to identify and evaluate the transcriptional differences among the 3 types of samples (input, output, reference). The ideal goal is to have induced and primary reference cell showing overlapping profiles, both very different from the original cells.' + diff --git a/recipes/bioconductor-egad/build.sh b/recipes/bioconductor-egad/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-egad/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-egad/meta.yaml b/recipes/bioconductor-egad/meta.yaml new file mode 100644 index 0000000000000..2da78f43b6bda --- /dev/null +++ b/recipes/bioconductor-egad/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.10.0" %} +{% set name = "EGAD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 798b2f43513b64bec9a70c5a6b387efe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-arrayqualitymetrics >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-gplots + - r-igraph + - r-mass + - r-matrix + - r-plyr + - r-rcolorbrewer + - r-rcurl + - r-zoo + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-arrayqualitymetrics >=3.38.0,<3.39.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-gplots + - r-igraph + - r-mass + - r-matrix + - r-plyr + - r-rcolorbrewer + - r-rcurl + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package implements a series of highly efficient tools to calculate functional properties of networks based on guilt by association methods.' + diff --git a/recipes/bioconductor-egsea/build.sh b/recipes/bioconductor-egsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-egsea/build.sh +++ b/recipes/bioconductor-egsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-egsea/meta.yaml b/recipes/bioconductor-egsea/meta.yaml index 56e32af05b484..9136863f191f3 100644 --- a/recipes/bioconductor-egsea/meta.yaml +++ b/recipes/bioconductor-egsea/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "EGSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 72b0b4dcb8d1a799cbec3f65df9d7a75fd91084c06fe75beeb81fa4946769dab + md5: 8f51d5d82b08d86f6c433712921d2596 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-egseadata >=1.8.0,<1.10.0' - - 'bioconductor-gage >=2.30.0,<2.32.0' - - 'bioconductor-glimma >=1.8.2,<1.10.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-padog >=1.22.0,<1.24.0' - - 'bioconductor-pathview >=1.20.0,<1.22.0' - - 'bioconductor-safe >=3.20.0,<3.22.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-egseadata >=1.10.0,<1.11.0' + - 'bioconductor-gage >=2.32.0,<2.33.0' + - 'bioconductor-glimma >=1.10.0,<1.11.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-padog >=1.24.0,<1.25.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-safe >=3.22.0,<3.23.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' @@ -46,22 +48,22 @@ requirements: - r-rcolorbrewer - 'r-stringi >=0.5.0' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-egseadata >=1.8.0,<1.10.0' - - 'bioconductor-gage >=2.30.0,<2.32.0' - - 'bioconductor-glimma >=1.8.2,<1.10.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.rn.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-padog >=1.22.0,<1.24.0' - - 'bioconductor-pathview >=1.20.0,<1.22.0' - - 'bioconductor-safe >=3.20.0,<3.22.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-egseadata >=1.10.0,<1.11.0' + - 'bioconductor-gage >=2.32.0,<2.33.0' + - 'bioconductor-glimma >=1.10.0,<1.11.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-padog >=1.24.0,<1.25.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-safe >=3.22.0,<3.23.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-dt - 'r-ggplot2 >=1.0.0' @@ -77,9 +79,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package implements the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing.' extra: identifiers: - biotools:egsea + parent_recipe: + name: bioconductor-egsea + path: recipes/bioconductor-egsea + version: 1.8.0 + diff --git a/recipes/bioconductor-egseadata/meta.yaml b/recipes/bioconductor-egseadata/meta.yaml index e1b2091037528..a8b5c136ec935 100644 --- a/recipes/bioconductor-egseadata/meta.yaml +++ b/recipes/bioconductor-egseadata/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "EGSEAdata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 128219a76de39e2e0f00ec6c485d1c8608b3107221a1a810a77c5d1e8f1b927a + md5: 666b85ee723e0125632a40a30b3f602e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: EGSEA requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package includes gene set collections that are used for the Ensemble of Gene Set Enrichment Analyses (EGSEA) method for gene set testing. It includes Human and Mouse versions of the MSidDB (Subramanian, et al. (2005) PNAS, 102(43):15545-15550) and GeneSetDB (Araki, et al. (2012) FEBS Open Bio, 2:76-82) collections.' - +extra: + parent_recipe: + name: bioconductor-egseadata + path: recipes/bioconductor-egseadata + version: 1.8.0 diff --git a/recipes/bioconductor-egseadata/post-link.sh b/recipes/bioconductor-egseadata/post-link.sh index 2f6b1c5a7517f..cefd8f7c81cb9 100644 --- a/recipes/bioconductor-egseadata/post-link.sh +++ b/recipes/bioconductor-egseadata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="EGSEAdata_1.8.0.tar.gz" +FN="EGSEAdata_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/EGSEAdata_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/EGSEAdata_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/EGSEAdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/EGSEAdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-egseadata/bioconductor-egseadata_1.10.0_src_all.tar.gz" ) -MD5="bc854d47778e6ee4fa029d65eda9134b" +MD5="666b85ee723e0125632a40a30b3f602e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-eir/build.sh b/recipes/bioconductor-eir/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-eir/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eir/meta.yaml b/recipes/bioconductor-eir/meta.yaml new file mode 100644 index 0000000000000..1a32a5624d29a --- /dev/null +++ b/recipes/bioconductor-eir/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.22.0" %} +{% set name = "eiR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 02df663489eb5a3924b07e84a86f38e4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitcitations, knitr, knitrBootstrap +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-gesper >=1.14.0,<1.15.0' + - r-base + - r-dbi + - r-digest + - 'r-rcppannoy >=0.0.9' + - r-rcurl + - r-runit + - r-snow + - r-snowfall + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-gesper >=1.14.0,<1.15.0' + - r-base + - r-dbi + - r-digest + - 'r-rcppannoy >=0.0.9' + - r-rcurl + - r-runit + - r-snow + - r-snowfall + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The eiR package provides utilities for accelerated structure similarity searching of very large small molecule data sets using an embedding and indexing approach.' + diff --git a/recipes/bioconductor-eisa/build.sh b/recipes/bioconductor-eisa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-eisa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eisa/meta.yaml b/recipes/bioconductor-eisa/meta.yaml new file mode 100644 index 0000000000000..fa6486423c200 --- /dev/null +++ b/recipes/bioconductor-eisa/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.34.0" %} +{% set name = "eisa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 114415b5b584378e8c2f93e081833045 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: igraph (>= 0.6), Matrix, GOstats, GO.db, KEGG.db, biclust, MASS, xtable, ALL, hgu95av2.db, targetscan.Hs.eg.db, org.Hs.eg.db +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - r-base + - r-dbi + - r-isa2 + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - r-base + - r-dbi + - r-isa2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The Iterative Signature Algorithm (ISA) is a biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. The ISA is capable of finding overlapping modules and it is resilient to noise. This package provides a convenient interface to the ISA, using standard BioConductor data structures; and also contains various visualization tools that can be used with other biclustering algorithms.' + diff --git a/recipes/bioconductor-elbow/build.sh b/recipes/bioconductor-elbow/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-elbow/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-elbow/meta.yaml b/recipes/bioconductor-elbow/meta.yaml new file mode 100644 index 0000000000000..7d2cc7954876e --- /dev/null +++ b/recipes/bioconductor-elbow/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "ELBOW" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9bc217d096532f8d8b2e97c6b7fab889 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DESeq, GEOquery, limma, simpleaffy, affyPLM, RColorBrewer, hgu133plus2cdf, hgu133plus2probe +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Elbow an improved fold change test that uses cluster analysis and pattern recognition to set cut off limits that are derived directly from intrareplicate variance without assuming a normal distribution for as few as 2 biological replicates. Elbow also provides the same consistency as fold testing in cross platform analysis. Elbow has lower false positive and false negative rates than standard fold testing when both are evaluated using T testing and Statistical Analysis of Microarray using 12 replicates (six replicates each for initial and final conditions). Elbow provides a null value based on initial condition replicates and gives error bounds for results to allow better evaluation of significance.' + diff --git a/recipes/bioconductor-elmer.data/meta.yaml b/recipes/bioconductor-elmer.data/meta.yaml index e52bdd780efb2..af2d6e57b3e76 100644 --- a/recipes/bioconductor-elmer.data/meta.yaml +++ b/recipes/bioconductor-elmer.data/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "2.4.2" %} +{% set version = "2.6.0" %} {% set name = "ELMER.data" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: af4b75a2c46099b495720927b37349df16165df011538215b3acdac49193df7e + md5: 6c2fe2971cd966175cb61c146921107f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, dplyr, devtools, DT requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 - summary: ' Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily' - + summary: 'Supporting data for the ELMER package. It includes: - elmer.data.example.promoter: mae.promoter - elmer.data.example: data - EPIC.hg38.manifest - EPIC.hg19.manifest - hm450.hg38.manifest - hm450.hg19.manifest - hocomoco.table - human.TF - LUSC_meth_refined: Meth - LUSC_RNA_refined: GeneExp - Probes.motif.hg19.450K - Probes.motif.hg19.EPIC - Probes.motif.hg38.450K - Probes.motif.hg38.EPIC - TF.family - TF.subfamily' +extra: + parent_recipe: + name: bioconductor-elmer.data + path: recipes/bioconductor-elmer.data + version: 2.4.2 diff --git a/recipes/bioconductor-elmer.data/post-link.sh b/recipes/bioconductor-elmer.data/post-link.sh index 81be850fb5fdb..2c387eb156f28 100644 --- a/recipes/bioconductor-elmer.data/post-link.sh +++ b/recipes/bioconductor-elmer.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ELMER.data_2.4.2.tar.gz" +FN="ELMER.data_2.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ELMER.data_2.4.2.tar.gz" - "https://bioarchive.galaxyproject.org/ELMER.data_2.4.2.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.4.2_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ELMER.data_2.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/ELMER.data_2.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-elmer.data/bioconductor-elmer.data_2.6.0_src_all.tar.gz" ) -MD5="c47971f2f5b286716535fde2cfc216f6" +MD5="6c2fe2971cd966175cb61c146921107f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-elmer/build.sh b/recipes/bioconductor-elmer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-elmer/build.sh +++ b/recipes/bioconductor-elmer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-elmer/conda_build_config.yaml b/recipes/bioconductor-elmer/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-elmer/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-elmer/meta.yaml b/recipes/bioconductor-elmer/meta.yaml index c983ca8b8e4b2..73219a6b653b8 100644 --- a/recipes/bioconductor-elmer/meta.yaml +++ b/recipes/bioconductor-elmer/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "2.4.4" %} +{% set version = "2.6.1" %} {% set name = "ELMER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 81c6f4ab69313670441f329ff2c6e9d13b8d93f7acc8e0b567287cff2042ec50 + md5: ee51a1a511d97cfa74ffd82100c16f10 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat, data.table, DT, GenomicInteractions, webshot, rtracklayer, R.utils, covr requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-elmer.data >=2.4.2,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-elmer.data >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - r-base - r-circlize - r-doparallel @@ -48,20 +50,22 @@ requirements: - r-rmarkdown - r-rvest - r-stringr + - r-tibble + - r-tidyr - r-xml2 run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-elmer.data >=2.4.2,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-multiassayexperiment >=1.6.0,<1.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-elmer.data >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - r-base - r-circlize - r-doparallel @@ -80,11 +84,19 @@ requirements: - r-rmarkdown - r-rvest - r-stringr + - r-tibble + - r-tidyr - r-xml2 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ELMER is designed to use DNA methylation and gene expression from a large number of samples to infere regulatory element landscape and transcription factor network in primary tissue.' +extra: + parent_recipe: + name: bioconductor-elmer + path: recipes/bioconductor-elmer + version: 2.4.4 + diff --git a/recipes/bioconductor-emdomics/build.sh b/recipes/bioconductor-emdomics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-emdomics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-emdomics/meta.yaml b/recipes/bioconductor-emdomics/meta.yaml new file mode 100644 index 0000000000000..618051c6d9426 --- /dev/null +++ b/recipes/bioconductor-emdomics/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "2.12.0" %} +{% set name = "EMDomics" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f9d117d39c59207bccc6f6ecad2f5e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-cdft + - r-emdist + - r-ggplot2 + - r-matrixstats + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-cdft + - r-emdist + - r-ggplot2 + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The EMDomics algorithm is used to perform a supervised multi-class analysis to measure the magnitude and statistical significance of observed continuous genomics data between groups. Usually the data will be gene expression values from array-based or sequence-based experiments, but data from other types of experiments can also be analyzed (e.g. copy number variation). Traditional methods like Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA) use significance tests based on summary statistics (mean and standard deviation) of the distributions. This approach lacks power to identify expression differences between groups that show high levels of intra-group heterogeneity. The Earth Mover''s Distance (EMD) algorithm instead computes the "work" needed to transform one distribution into another, thus providing a metric of the overall difference in shape between two distributions. Permutation of sample labels is used to generate q-values for the observed EMD scores. This package also incorporates the Komolgorov-Smirnov (K-S) test and the Cramer von Mises test (CVM), which are both common distribution comparison tests.' + diff --git a/recipes/bioconductor-empiricalbrownsmethod/build.sh b/recipes/bioconductor-empiricalbrownsmethod/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/build.sh +++ b/recipes/bioconductor-empiricalbrownsmethod/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml index 14251732b18b7..27bac5005b59b 100644 --- a/recipes/bioconductor-empiricalbrownsmethod/meta.yaml +++ b/recipes/bioconductor-empiricalbrownsmethod/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "EmpiricalBrownsMethod" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8f77f71f7ff1942f6d1f76fc6cb46ad10053f2d0843a199f085072f748b48931 + md5: 2d91e211bf843eefad77a8526c65a370 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Combining P-values from multiple statistical tests is common in bioinformatics. However, this procedure is non-trivial for dependent P-values. This package implements an empirical adaptation of Brown’s Method (an extension of Fisher’s Method) for combining dependent P-values which is appropriate for highly correlated data sets found in high-throughput biological experiments.' extra: identifiers: - biotools:empiricalbrownsmethod - doi:10.1093/bioinformatics/btw438 + parent_recipe: + name: bioconductor-empiricalbrownsmethod + path: recipes/bioconductor-empiricalbrownsmethod + version: 1.8.0 + diff --git a/recipes/bioconductor-encodexplorer/build.sh b/recipes/bioconductor-encodexplorer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-encodexplorer/build.sh +++ b/recipes/bioconductor-encodexplorer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-encodexplorer/meta.yaml b/recipes/bioconductor-encodexplorer/meta.yaml index e4d9725a79e2f..530d38104976d 100644 --- a/recipes/bioconductor-encodexplorer/meta.yaml +++ b/recipes/bioconductor-encodexplorer/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "ENCODExplorer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f0da70176e0eede01132fbe727e60d0640b4c40c59618a0ffcb9df0377521d24 + md5: 6bd1aa3aa9897fbd1d85c19d47c9aaaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit,BiocGenerics,knitr, curl, httr requirements: host: - r-base @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package allows user to quickly access ENCODE project files metadata and give access to helper functions to query the ENCODE rest api, download ENCODE datasets and save the database in SQLite format.' extra: identifiers: - biotools:encodexplorer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-encodexplorer + path: recipes/bioconductor-encodexplorer + version: 2.6.0 + diff --git a/recipes/bioconductor-enhancedvolcano/build.sh b/recipes/bioconductor-enhancedvolcano/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enhancedvolcano/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enhancedvolcano/meta.yaml b/recipes/bioconductor-enhancedvolcano/meta.yaml new file mode 100644 index 0000000000000..bf10addbf5ad7 --- /dev/null +++ b/recipes/bioconductor-enhancedvolcano/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "EnhancedVolcano" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: be835575dbb171d59157118fdf6f9471 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, DESeq2, pasilla, airway, gridExtra, magrittr +requirements: + host: + - r-base + - r-ggplot2 + - r-ggrepel + run: + - r-base + - r-ggplot2 + - r-ggrepel +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Volcano plots represent a useful way to visualise the results of differential expression analyses. Here, we present a highly-configurable function that produces publication-ready volcano plots. EnhancedVolcano will attempt to fit as many transcript names in the plot window as possible, thus avoiding ''clogging'' up the plot with labels that could not otherwise have been read.' + diff --git a/recipes/bioconductor-enmix/build.sh b/recipes/bioconductor-enmix/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enmix/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enmix/meta.yaml b/recipes/bioconductor-enmix/meta.yaml new file mode 100644 index 0000000000000..053bcc1a58786 --- /dev/null +++ b/recipes/bioconductor-enmix/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.18.0" %} +{% set name = "ENmix" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0553f4e4210daa532f8686ec4ea8cc46 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: minfiData (>= 0.4.1), RPMM, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-doparallel + - r-foreach + - r-mass + run: + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-doparallel + - r-foreach + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The ENmix package provides a set of quality control and data pre-processing tools for Illumina HumanMethylation450 and MethylationEPIC Beadchips. It includes ENmix background correction, RELIC dye bias correction, RCP probe-type bias adjustment, along with a number of additional tools. These functions can be used to remove unwanted experimental noise and thus to improve accuracy and reproducibility of methylation measures. ENmix functions are flexible and transparent. Users have option to choose a single pipeline command to finish all data pre-processing steps (including background correction, dye-bias adjustment, inter-array normalization and probe-type bias correction) or to use individual functions sequentially to perform data pre-processing in a more customized manner. In addition the ENmix package has selectable complementary functions for efficient data visualization (such as data distribution plots); quality control (identifing and filtering low quality data points, samples, probes, and outliers, along with imputation of missing values); identification of probes with multimodal distributions due to SNPs or other factors; exploration of data variance structure using principal component regression analysis plot; preparation of experimental factors related surrogate control variables to be adjusted in downstream statistical analysis; and an efficient algorithm oxBS-MLE to estimate 5-methylcytosine and 5-hydroxymethylcytosine level.' + diff --git a/recipes/bioconductor-enrichedheatmap/build.sh b/recipes/bioconductor-enrichedheatmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-enrichedheatmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichedheatmap/meta.yaml b/recipes/bioconductor-enrichedheatmap/meta.yaml new file mode 100644 index 0000000000000..192c24854b533 --- /dev/null +++ b/recipes/bioconductor-enrichedheatmap/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.12.0" %} +{% set name = "EnrichedHeatmap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7e80d59a04785ab940be2ecb1c3b942e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat (>= 0.3), knitr, markdown, genefilter, RColorBrewer +requirements: + host: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-circlize >=0.4.1' + - r-getoptlong + - r-locfit + - r-matrixstats + - r-rcpp + run: + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-circlize >=0.4.1' + - r-getoptlong + - r-locfit + - r-matrixstats + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Enriched heatmap is a special type of heatmap which visualizes the enrichment of genomic signals on specific target regions. Here we implement enriched heatmap by ComplexHeatmap package. Since this type of heatmap is just a normal heatmap but with some special settings, with the functionality of ComplexHeatmap, it would be much easier to customize the heatmap as well as concatenating to a list of heatmaps to show correspondance between different data sources.' + diff --git a/recipes/bioconductor-enrichmentbrowser/build.sh b/recipes/bioconductor-enrichmentbrowser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-enrichmentbrowser/build.sh +++ b/recipes/bioconductor-enrichmentbrowser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml b/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-enrichmentbrowser/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-enrichmentbrowser/meta.yaml b/recipes/bioconductor-enrichmentbrowser/meta.yaml index 6e46048b42106..b91297eedc041 100644 --- a/recipes/bioconductor-enrichmentbrowser/meta.yaml +++ b/recipes/bioconductor-enrichmentbrowser/meta.yaml @@ -1,75 +1,79 @@ -{% set version = "2.10.11" %} +{% set version = "2.12.0" %} {% set name = "EnrichmentBrowser" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3bd9d31cd2a7514ce13db33011a27f703257617bd0f4e0a04734295358d9acee + md5: d1ef550adea70fa1584228da5dc23de7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, BiocStyle, airway, hgu95av2.db, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' - - 'bioconductor-biocgraph >=1.42.0,<1.44.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-graphite >=1.26.1,<1.28.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pathview >=1.20.0,<1.22.0' - - 'bioconductor-reportingtools >=2.20.0,<2.22.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-safe >=3.20.0,<3.22.0' - - 'bioconductor-spia >=2.32.0,<2.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocgraph >=1.44.0,<1.45.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-reportingtools >=2.22.0,<2.23.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-safe >=3.22.0,<3.23.0' + - 'bioconductor-spia >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base + - r-biocmanager - r-hwriter - r-mass - r-rappdirs run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' - - 'bioconductor-biocgraph >=1.42.0,<1.44.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-graphite >=1.26.1,<1.28.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pathview >=1.20.0,<1.22.0' - - 'bioconductor-reportingtools >=2.20.0,<2.22.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-safe >=3.20.0,<3.22.0' - - 'bioconductor-spia >=2.32.0,<2.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocgraph >=1.44.0,<1.45.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-reportingtools >=2.22.0,<2.23.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-safe >=3.22.0,<3.23.0' + - 'bioconductor-spia >=2.34.0,<2.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base + - r-biocmanager - r-hwriter - r-mass - r-rappdirs @@ -77,8 +81,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The EnrichmentBrowser package implements essential functionality for the enrichment analysis of gene expression data. The analysis combines the advantages of set-based and network-based enrichment analysis in order to derive high-confidence gene sets and biological pathways that are differentially regulated in the expression data under investigation. Besides, the package facilitates the visualization and exploration of such sets and pathways.' - +extra: + parent_recipe: + name: bioconductor-enrichmentbrowser + path: recipes/bioconductor-enrichmentbrowser + version: 2.10.11 diff --git a/recipes/bioconductor-enrichplot/build.sh b/recipes/bioconductor-enrichplot/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-enrichplot/build.sh +++ b/recipes/bioconductor-enrichplot/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-enrichplot/meta.yaml b/recipes/bioconductor-enrichplot/meta.yaml index 5980b210fbb3a..53b223637a20c 100644 --- a/recipes/bioconductor-enrichplot/meta.yaml +++ b/recipes/bioconductor-enrichplot/meta.yaml @@ -1,53 +1,68 @@ -{% set version = "1.0.2" %} +{% set version = "1.2.0" %} {% set name = "enrichplot" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: eff2bd856c5e14cca9b7af6f8fc853dd22dac2ee057acbed0f248da604b4dbbf + md5: 27648033d0cf6a3a71f8ecbef075b0b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: clusterProfiler, knitr, org.Hs.eg.db, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - r-base - r-cowplot + - r-europepmc - r-ggplot2 + - r-ggplotify - r-ggraph - r-ggridges + - r-gridextra - r-igraph + - r-purrr + - r-rcolorbrewer - r-reshape2 - r-upsetr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' - r-base - r-cowplot + - r-europepmc - r-ggplot2 + - r-ggplotify - r-ggraph - r-ggridges + - r-gridextra - r-igraph + - r-purrr + - r-rcolorbrewer - r-reshape2 - r-upsetr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ''enrichplot'' package implements several visualization methods for interpreting functional enrichment results obtained from ORA or GSEA analysis. All the visualization methods are developed based on ''ggplot2'' graphics.' - - +extra: + parent_recipe: + name: bioconductor-enrichplot + path: recipes/bioconductor-enrichplot + version: 1.0.2 diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml index 7655d071d9588..74a79c4133df4 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml +++ b/recipes/bioconductor-ensdb.hsapiens.v75/meta.yaml @@ -1,35 +1,40 @@ {% set version = "2.99.0" %} {% set name = "EnsDb.Hsapiens.v75" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2c59f95959f344b2a3eaa65a00086b01a420823e30b0810fc81e49b08dcba64b + md5: 6c896475252903972bfc6c0eb0d8f334 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - r-base run: - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from Ensembl.' - +extra: + parent_recipe: + name: bioconductor-ensdb.hsapiens.v75 + path: recipes/bioconductor-ensdb.hsapiens.v75 + version: 2.99.0 diff --git a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh index 948e9a99d7114..7f5f8d69d7739 100644 --- a/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh +++ b/recipes/bioconductor-ensdb.hsapiens.v75/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="EnsDb.Hsapiens.v75_2.99.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v75_2.99.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v75/bioconductor-ensdb.hsapiens.v75_2.99.0_src_all.tar.gz" diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml new file mode 100644 index 0000000000000..9e713cc2bced6 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v79/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Hsapiens.v79" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 16b5629805c07649b2aa501d34fcc588 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh new file mode 100644 index 0000000000000..f8ef604b80fdd --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v79/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Hsapiens.v79_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v79_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v79_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v79/bioconductor-ensdb.hsapiens.v79_2.99.0_src_all.tar.gz" +) +MD5="16b5629805c07649b2aa501d34fcc588" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.hsapiens.v79/pre-unlink.sh b/recipes/bioconductor-ensdb.hsapiens.v79/pre-unlink.sh new file mode 100644 index 0000000000000..613f131fb6c0f --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v79/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Hsapiens.v79 diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml new file mode 100644 index 0000000000000..db596488669b6 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v86/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Hsapiens.v86" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0c9e52512ff6dbbbdb754c4d41149939 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh b/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh new file mode 100644 index 0000000000000..4c8b47133682e --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v86/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Hsapiens.v86_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Hsapiens.v86_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Hsapiens.v86_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.hsapiens.v86/bioconductor-ensdb.hsapiens.v86_2.99.0_src_all.tar.gz" +) +MD5="0c9e52512ff6dbbbdb754c4d41149939" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.hsapiens.v86/pre-unlink.sh b/recipes/bioconductor-ensdb.hsapiens.v86/pre-unlink.sh new file mode 100644 index 0000000000000..6c04f0919ba29 --- /dev/null +++ b/recipes/bioconductor-ensdb.hsapiens.v86/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Hsapiens.v86 diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml new file mode 100644 index 0000000000000..dd3ef93ec2011 --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v75/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Mmusculus.v75" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 081bf6f90ff77031b634b4fe32e00be8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh b/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh new file mode 100644 index 0000000000000..544e068e619a9 --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v75/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Mmusculus.v75_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Mmusculus.v75_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v75_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v75/bioconductor-ensdb.mmusculus.v75_2.99.0_src_all.tar.gz" +) +MD5="081bf6f90ff77031b634b4fe32e00be8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.mmusculus.v75/pre-unlink.sh b/recipes/bioconductor-ensdb.mmusculus.v75/pre-unlink.sh new file mode 100644 index 0000000000000..a718a8224c57c --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v75/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Mmusculus.v75 diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml new file mode 100644 index 0000000000000..e1880b0484d4e --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v79/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Mmusculus.v79" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 28bbab743b0d2d550dbfa0bcd3274fad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh b/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh new file mode 100644 index 0000000000000..db6d6bc699b6f --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v79/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Mmusculus.v79_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Mmusculus.v79_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Mmusculus.v79_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.mmusculus.v79/bioconductor-ensdb.mmusculus.v79_2.99.0_src_all.tar.gz" +) +MD5="28bbab743b0d2d550dbfa0bcd3274fad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.mmusculus.v79/pre-unlink.sh b/recipes/bioconductor-ensdb.mmusculus.v79/pre-unlink.sh new file mode 100644 index 0000000000000..44919273fc389 --- /dev/null +++ b/recipes/bioconductor-ensdb.mmusculus.v79/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Mmusculus.v79 diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml new file mode 100644 index 0000000000000..0a3f7c503ca90 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Rnorvegicus.v75" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40ff53b41aa6fad0d5bd15f9c6f3bad8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh b/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh new file mode 100644 index 0000000000000..72bcd438b5f69 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v75_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v75/bioconductor-ensdb.rnorvegicus.v75_2.99.0_src_all.tar.gz" +) +MD5="40ff53b41aa6fad0d5bd15f9c6f3bad8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v75/pre-unlink.sh b/recipes/bioconductor-ensdb.rnorvegicus.v75/pre-unlink.sh new file mode 100644 index 0000000000000..477bab151aa46 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v75/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Rnorvegicus.v75 diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml new file mode 100644 index 0000000000000..6360aafc9a7d6 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.99.0" %} +{% set name = "EnsDb.Rnorvegicus.v79" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7d305bd0d1a073bd8c60063ae210a7a9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from Ensembl.' + diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh b/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh new file mode 100644 index 0000000000000..bee10abd82f46 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" + "https://bioarchive.galaxyproject.org/EnsDb.Rnorvegicus.v79_2.99.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ensdb.rnorvegicus.v79/bioconductor-ensdb.rnorvegicus.v79_2.99.0_src_all.tar.gz" +) +MD5="7d305bd0d1a073bd8c60063ae210a7a9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ensdb.rnorvegicus.v79/pre-unlink.sh b/recipes/bioconductor-ensdb.rnorvegicus.v79/pre-unlink.sh new file mode 100644 index 0000000000000..568af85be0454 --- /dev/null +++ b/recipes/bioconductor-ensdb.rnorvegicus.v79/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EnsDb.Rnorvegicus.v79 diff --git a/recipes/bioconductor-ensembldb/build.sh b/recipes/bioconductor-ensembldb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ensembldb/build.sh +++ b/recipes/bioconductor-ensembldb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ensembldb/meta.yaml b/recipes/bioconductor-ensembldb/meta.yaml index d08f8fccd9664..61f73310a4f76 100644 --- a/recipes/bioconductor-ensembldb/meta.yaml +++ b/recipes/bioconductor-ensembldb/meta.yaml @@ -1,54 +1,56 @@ -{% set version = "2.4.1" %} +{% set version = "2.6.3" %} {% set name = "ensembldb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 86a3df73a98d820149084c5f0114d433e5533a6cc3914f7e2d60331f3b234bd0 + md5: 1541d39916d19f6a8c573d5b97955453 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, EnsDb.Hsapiens.v86 (>= 0.99.8), testthat, BSgenome.Hsapiens.NCBI.GRCh38, ggbio (>= 1.24.0), Gviz (>= 1.20.0), magrittr, AnnotationHub requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-curl - r-dbi - 'r-rsqlite >=1.1' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-curl - r-dbi @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.' extra: identifiers: - biotools:ensembldb - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ensembldb + path: recipes/bioconductor-ensembldb + version: 2.4.1 + diff --git a/recipes/bioconductor-ensemblvep/build.sh b/recipes/bioconductor-ensemblvep/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ensemblvep/build.sh +++ b/recipes/bioconductor-ensemblvep/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ensemblvep/meta.yaml b/recipes/bioconductor-ensemblvep/meta.yaml index 81483edf1f1dc..b582b4003e4ca 100644 --- a/recipes/bioconductor-ensemblvep/meta.yaml +++ b/recipes/bioconductor-ensemblvep/meta.yaml @@ -1,48 +1,56 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "ensemblVEP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f2f3fcd2a74c01c898a2e2e543a808c3f9c9051bd6c6343d6764cc54bdb94306 + md5: fdbeb189d18514fa1631a98270057bcf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit +# SystemRequirements: Ensembl VEP (API version 94) and the Perl modules DBI and DBD::mysql must be installed. See the package README and Ensembl installation instructions: http://www.ensembl.org/info/docs/tools/vep/script/vep_download.html#installer requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Query the Ensembl Variant Effect Predictor via the perl API.' extra: identifiers: - biotools:ensemblvep - doi:10.1186/s13059-016-0974-4 + parent_recipe: + name: bioconductor-ensemblvep + path: recipes/bioconductor-ensemblvep + version: 1.22.1 + diff --git a/recipes/bioconductor-envisionquery/build.sh b/recipes/bioconductor-envisionquery/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-envisionquery/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-envisionquery/meta.yaml b/recipes/bioconductor-envisionquery/meta.yaml new file mode 100644 index 0000000000000..cfbc6fe09badc --- /dev/null +++ b/recipes/bioconductor-envisionquery/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.30.0" %} +{% set name = "ENVISIONQuery" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c5c1fc6faa77de4dce984b8311aad152 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-rjava + - r-xml + run: + - r-base + - r-rjava + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Tools to retrieve data from ENVISION, the Database for Annotation, Visualization and Integrated Discovery portal' + diff --git a/recipes/bioconductor-epidish/build.sh b/recipes/bioconductor-epidish/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epidish/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epidish/meta.yaml b/recipes/bioconductor-epidish/meta.yaml new file mode 100644 index 0000000000000..70fe404b7e334 --- /dev/null +++ b/recipes/bioconductor-epidish/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.4.1" %} +{% set name = "EpiDISH" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4acbfaf1f6e45ca12fef51b9b3e8f1eb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: roxygen2, GEOquery, BiocStyle, knitr, rmarkdown, Biobase, testthat +requirements: + host: + - r-base + - r-e1071 + - r-mass + - r-quadprog + run: + - r-base + - r-e1071 + - r-mass + - r-quadprog +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'EpiDISH is a R package to infer the proportions of a priori known cell subtypes present in a sample representing a mixture of such cell-types. Inference proceeds via one of 3 methods (Robust Partial Correlations-RPC, Cibersort (CBS), Constrained Projection (CP)), as determined by user.' + diff --git a/recipes/bioconductor-epigenomix/build.sh b/recipes/bioconductor-epigenomix/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epigenomix/build.sh +++ b/recipes/bioconductor-epigenomix/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epigenomix/meta.yaml b/recipes/bioconductor-epigenomix/meta.yaml index 5b5af43287577..02e8941369116 100644 --- a/recipes/bioconductor-epigenomix/meta.yaml +++ b/recipes/bioconductor-epigenomix/meta.yaml @@ -1,53 +1,59 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "epigenomix" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fa526d60cae35c4ff89fa4e1124e746c196d691176af8a5ccfba04554b883203 + md5: 290798e17819a26cfa3171ecefab0307 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-mcmcpack run: - - 'bioconductor-beadarray >=2.30.0,<2.32.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beadarray >=2.32.0,<2.33.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-mcmcpack test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'A package for the integrative analysis of RNA-seq or microarray based gene transcription and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types.' extra: identifiers: - biotools:epigenomix + parent_recipe: + name: bioconductor-epigenomix + path: recipes/bioconductor-epigenomix + version: 1.20.0 + diff --git a/recipes/bioconductor-epinem/build.sh b/recipes/bioconductor-epinem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epinem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epinem/meta.yaml b/recipes/bioconductor-epinem/meta.yaml new file mode 100644 index 0000000000000..2d19f1d97edfd --- /dev/null +++ b/recipes/bioconductor-epinem/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "epiNEM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6e8ad9c7f2ce1f6fa87bc01d4b0ab653 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics, STRINGdb, devtools, rmarkdown, GOSemSim, AnnotationHub, org.Sc.sgd.db +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' + - r-base + - r-boolnet + - r-e1071 + - r-gtools + - r-igraph + - r-lattice + - r-latticeextra + - r-pcalg + - r-rcolorbrewer + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' + - r-base + - r-boolnet + - r-e1071 + - r-gtools + - r-igraph + - r-lattice + - r-latticeextra + - r-pcalg + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'epiNEM is an extension of the original Nested Effects Models (NEM). EpiNEM is able to take into account double knockouts and infer more complex network signalling pathways.' + diff --git a/recipes/bioconductor-epivizr/build.sh b/recipes/bioconductor-epivizr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epivizr/build.sh +++ b/recipes/bioconductor-epivizr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizr/conda_build_config.yaml b/recipes/bioconductor-epivizr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-epivizr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-epivizr/meta.yaml b/recipes/bioconductor-epivizr/meta.yaml index f8a241a1652a5..90ffb710d8b5a 100644 --- a/recipes/bioconductor-epivizr/meta.yaml +++ b/recipes/bioconductor-epivizr/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "epivizr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a243a05d22a20567ba00e31498bdfc27e046e1e0d066f4ace32f84b5655b8a20 + md5: 598be3e3e7c653398de1a63851e204e1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, roxygen2, knitr, Biobase, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle requirements: host: - - 'bioconductor-epivizrdata >=1.8.0,<1.10.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-epivizrdata >=1.8.0,<1.10.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides connections to the epiviz web app (http://epiviz.cbcb.umd.edu) for interactive visualization of genomic data. Objects in R/bioc interactive sessions can be displayed in genome browser tracks or plots to be explored by navigation through genomic regions. Fundamental Bioconductor data structures are supported (e.g., GenomicRanges and RangedSummarizedExperiment objects), while providing an easy mechanism to support other data structures (through package epivizrData). Visualizations (using d3.js) can be easily added to the web app as well.' extra: identifiers: - biotools:epivizr - doi:10.1038/nmeth.3038 + parent_recipe: + name: bioconductor-epivizr + path: recipes/bioconductor-epivizr + version: 2.10.0 + diff --git a/recipes/bioconductor-epivizrchart/build.sh b/recipes/bioconductor-epivizrchart/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-epivizrchart/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrchart/meta.yaml b/recipes/bioconductor-epivizrchart/meta.yaml new file mode 100644 index 0000000000000..dd4a90919d80b --- /dev/null +++ b/recipes/bioconductor-epivizrchart/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "epivizrChart" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a0c65f110f53a24eb774b181b4cd21b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, roxygen2, knitr, Biobase, GenomicRanges, S4Vectors, IRanges, SummarizedExperiment, antiProfilesData, hgu133plus2.db, Mus.musculus, BiocStyle, Homo.sapiens, shiny, minfi, Rsamtools, rtracklayer, RColorBrewer, magrittr, AnnotationHub +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - r-base + - r-htmltools + - r-rjson + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - r-base + - r-htmltools + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides an API for interactive visualization of genomic data using epiviz web components. Objects in R/BioConductor can be used to generate interactive R markdown/notebook documents or can be visualized in the R Studio''s default viewer.' + diff --git a/recipes/bioconductor-epivizrdata/build.sh b/recipes/bioconductor-epivizrdata/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epivizrdata/build.sh +++ b/recipes/bioconductor-epivizrdata/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrdata/conda_build_config.yaml b/recipes/bioconductor-epivizrdata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-epivizrdata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-epivizrdata/meta.yaml b/recipes/bioconductor-epivizrdata/meta.yaml index 0cdd89356bbc3..411f5f72dded0 100644 --- a/recipes/bioconductor-epivizrdata/meta.yaml +++ b/recipes/bioconductor-epivizrdata/meta.yaml @@ -1,54 +1,61 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "epivizrData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 82701cbf197744d711c5f62274c56ce1b2d23d966bbd6443c20a890bf3f16d7d + md5: a9fd3870de8f49edaf48ebfbc400d35b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, roxygen2, bumphunter, hgu133plus2.db, Mus.musculus, TxDb.Mmusculus.UCSC.mm10.knownGene, rjson, knitr, rmarkdown, BiocStyle, EnsDb.Mmusculus.v79, AnnotationHub, rtracklayer, utils, RMySQL, DBI requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Serve data from Bioconductor Objects through a WebSocket connection.' extra: identifiers: - biotools:epivizrdata - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-epivizrdata + path: recipes/bioconductor-epivizrdata + version: 1.8.0 + diff --git a/recipes/bioconductor-epivizrserver/build.sh b/recipes/bioconductor-epivizrserver/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epivizrserver/build.sh +++ b/recipes/bioconductor-epivizrserver/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrserver/meta.yaml b/recipes/bioconductor-epivizrserver/meta.yaml index 2581dbc5d1cce..e5d98608d2a7e 100644 --- a/recipes/bioconductor-epivizrserver/meta.yaml +++ b/recipes/bioconductor-epivizrserver/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "epivizrServer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 249216e081abc9788c738f59e75abefdcab4db7ebef41a7a8563e11304b02df8 + md5: 537fc02d780e78830cd3d470cdee219a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle requirements: host: - r-base @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides objects to manage WebSocket connections to epiviz apps. Other epivizr package use this infrastructure.' extra: identifiers: - biotools:epivizrserver - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-epivizrserver + path: recipes/bioconductor-epivizrserver + version: 1.8.1 + diff --git a/recipes/bioconductor-epivizrstandalone/build.sh b/recipes/bioconductor-epivizrstandalone/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-epivizrstandalone/build.sh +++ b/recipes/bioconductor-epivizrstandalone/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml b/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-epivizrstandalone/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-epivizrstandalone/meta.yaml b/recipes/bioconductor-epivizrstandalone/meta.yaml index 8b3231fa8e107..e62344dbcfbb8 100644 --- a/recipes/bioconductor-epivizrstandalone/meta.yaml +++ b/recipes/bioconductor-epivizrstandalone/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "epivizrStandalone" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ebd600132569c5c391c33f593379fc3cc5aff9c3a46cb256adda1d4a0a5eb47e + md5: 1c5b85237ceb90203bab2c0e7e9f5f7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, OrganismDbi (>= 1.13.9), Mus.musculus, Biobase, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-epivizr >=2.10.0,<2.12.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-epivizr >=2.12.0,<2.13.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-git2r run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-epivizr >=2.10.0,<2.12.0' - - 'bioconductor-epivizrserver >=1.8.1,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-epivizr >=2.12.0,<2.13.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-git2r test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package imports the epiviz visualization JavaScript app for genomic data interactive visualization. The ''epivizrServer'' package is used to provide a web server running completely within R. This standalone version allows to browse arbitrary genomes through genome annotations provided by Bioconductor packages.' extra: identifiers: - biotools:epivizrstandalone - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-epivizrstandalone + path: recipes/bioconductor-epivizrstandalone + version: 1.8.0 + diff --git a/recipes/bioconductor-erccdashboard/build.sh b/recipes/bioconductor-erccdashboard/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-erccdashboard/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-erccdashboard/meta.yaml b/recipes/bioconductor-erccdashboard/meta.yaml new file mode 100644 index 0000000000000..14f61c1c1980f --- /dev/null +++ b/recipes/bioconductor-erccdashboard/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.16.0" %} +{% set name = "erccdashboard" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 61275082c4842a2c56259a4edbbec665 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - 'r-ggplot2 >=2.1.0' + - r-gplots + - 'r-gridextra >=2.0.0' + - r-gtools + - r-locfit + - r-mass + - r-plyr + - r-reshape2 + - r-rocr + - r-scales + - r-stringr + run: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - 'r-ggplot2 >=2.1.0' + - r-gplots + - 'r-gridextra >=2.0.0' + - r-gtools + - r-locfit + - r-mass + - r-plyr + - r-reshape2 + - r-rocr + - r-scales + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Technical performance metrics for differential gene expression experiments using External RNA Controls Consortium (ERCC) spike-in ratio mixtures.' + diff --git a/recipes/bioconductor-erma/build.sh b/recipes/bioconductor-erma/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-erma/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-erma/meta.yaml b/recipes/bioconductor-erma/meta.yaml new file mode 100644 index 0000000000000..82b0a03912a3d --- /dev/null +++ b/recipes/bioconductor-erma/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "0.14.0" %} +{% set name = "erma" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4cba185c4cd0cc49bf6d10bc4864f2f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rmarkdown, BiocStyle, knitr, GO.db, png, DT, doParallel +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-shiny + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Software and data to support epigenomic road map adventures.' + diff --git a/recipes/bioconductor-erssa/build.sh b/recipes/bioconductor-erssa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-erssa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-erssa/meta.yaml b/recipes/bioconductor-erssa/meta.yaml new file mode 100644 index 0000000000000..075ef21347ceb --- /dev/null +++ b/recipes/bioconductor-erssa/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "ERSSA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9e7e15475b35dd6b76178e7d122d339b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - r-base + - 'r-ggplot2 >=3.0.0' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1-2' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - r-base + - 'r-ggplot2 >=3.0.0' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1-2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'The ERSSA package takes user supplied RNA-seq differential expression dataset and calculates the number of differentially expressed genes at varying biological replicate levels. This allows the user to determine, without relying on any a priori assumptions, whether sufficient differential detection has been acheived with their RNA-seq dataset.' + diff --git a/recipes/bioconductor-esatac/build.sh b/recipes/bioconductor-esatac/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-esatac/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-esatac/meta.yaml b/recipes/bioconductor-esatac/meta.yaml new file mode 100644 index 0000000000000..1c40b016987c7 --- /dev/null +++ b/recipes/bioconductor-esatac/meta.yaml @@ -0,0 +1,99 @@ +{% set version = "1.4.0" %} +{% set name = "esATAC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b1bf9585538209631a24a0d6d4c7647 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, DiagrammeRsvg, testthat, webshot +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chipseeker >=1.18.0,<1.19.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-jaspar2016 >=1.10.0,<1.11.0' + - 'bioconductor-motifmatchr >=1.4.0,<1.5.0' + - 'bioconductor-rbowtie2 >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - r-biocmanager + - r-corrplot + - r-diagrammer + - r-digest + - r-ggplot2 + - r-igraph + - r-knitr + - r-magrittr + - r-r.utils + - 'r-rcpp >=0.12.11' + - r-rjava + - r-rmarkdown + - r-venndiagram + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chipseeker >=1.18.0,<1.19.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-jaspar2016 >=1.10.0,<1.11.0' + - 'bioconductor-motifmatchr >=1.4.0,<1.5.0' + - 'bioconductor-rbowtie2 >=1.4.0,<1.5.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - r-biocmanager + - r-corrplot + - r-diagrammer + - r-digest + - r-ggplot2 + - r-igraph + - r-knitr + - r-magrittr + - r-r.utils + - 'r-rcpp >=0.12.11' + - r-rjava + - r-rmarkdown + - r-venndiagram + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'This package provides a framework and complete preset pipeline for quantification and analysis of ATAC-seq Reads. It covers raw sequencing reads preprocessing (FASTQ files), reads alignment (Rbowtie2), aligned reads file operations (SAM, BAM, and BED files), peak calling (F-seq), genome annotations (Motif, GO, SNP analysis) and quality control report. The package is managed by dataflow graph. It is easy for user to pass variables seamlessly between processes and understand the workflow. Users can process FASTQ files through end-to-end preset pipeline which produces a pretty HTML report for quality control and preliminary statistical results, or customize workflow starting from any intermediate stages with esATAC functions easily and flexibly.' + diff --git a/recipes/bioconductor-esetvis/build.sh b/recipes/bioconductor-esetvis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-esetvis/build.sh +++ b/recipes/bioconductor-esetvis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-esetvis/conda_build_config.yaml b/recipes/bioconductor-esetvis/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-esetvis/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-esetvis/meta.yaml b/recipes/bioconductor-esetvis/meta.yaml index 69d1027f6964a..08c072b4626ff 100644 --- a/recipes/bioconductor-esetvis/meta.yaml +++ b/recipes/bioconductor-esetvis/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "esetVis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: defb62207facbad84b2d420d50833c9cee8ba17dfd943c024dcc9422b3c9733c + md5: 00dabd51d6f8ed126f3c6a53ef514e96 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ggplot2, ggvis, rbokeh, ggrepel, knitr, rmarkdown, ALL, hgu95av2.db, AnnotationDbi, pander, SummarizedExperiment requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-mlp >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mlp >=1.30.0,<1.31.0' - r-base - r-hexbin - r-mass - r-mpm - r-rtsne run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-mlp >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mlp >=1.30.0,<1.31.0' - r-base - r-hexbin - r-mass @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Utility functions for visualization of expressionSet (or SummarizedExperiment) Bioconductor object, including spectral map, tsne and linear discriminant analysis. Static plot via the ggplot2 package or interactive via the ggvis or rbokeh packages are available.' extra: identifiers: - biotools:esetvis - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-esetvis + path: recipes/bioconductor-esetvis + version: 1.6.3 + diff --git a/recipes/bioconductor-estrogen/meta.yaml b/recipes/bioconductor-estrogen/meta.yaml new file mode 100644 index 0000000000000..83128e6d8dd9a --- /dev/null +++ b/recipes/bioconductor-estrogen/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.28.0" %} +{% set name = "estrogen" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5a2bbc25340ef7cc6c9cf4a579e4c190 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: affy, hgu95av2, hgu95av2cdf, vsn, knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Data from 8 Affymetrix genechips, looking at a 2x2 factorial design (with 2 repeats per level).' + diff --git a/recipes/bioconductor-estrogen/post-link.sh b/recipes/bioconductor-estrogen/post-link.sh new file mode 100644 index 0000000000000..37691a91d6210 --- /dev/null +++ b/recipes/bioconductor-estrogen/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="estrogen_1.28.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/estrogen_1.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/estrogen_1.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-estrogen/bioconductor-estrogen_1.28.0_src_all.tar.gz" +) +MD5="5a2bbc25340ef7cc6c9cf4a579e4c190" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-estrogen/pre-unlink.sh b/recipes/bioconductor-estrogen/pre-unlink.sh new file mode 100644 index 0000000000000..b0b81b8b03226 --- /dev/null +++ b/recipes/bioconductor-estrogen/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ estrogen diff --git a/recipes/bioconductor-etec16s/meta.yaml b/recipes/bioconductor-etec16s/meta.yaml new file mode 100644 index 0000000000000..1e2711484c4d9 --- /dev/null +++ b/recipes/bioconductor-etec16s/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.10.0" %} +{% set name = "etec16s" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ab6de328373655b42c1915fa52fcb47e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: '16S rRNA gene sequencing data to study changes in the faecal microbiota of 12 volunteers during a human challenge study with ETEC (H10407) and subsequent treatment with ciprofloxacin.' + diff --git a/recipes/bioconductor-etec16s/post-link.sh b/recipes/bioconductor-etec16s/post-link.sh new file mode 100644 index 0000000000000..0db9292d24c60 --- /dev/null +++ b/recipes/bioconductor-etec16s/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="etec16s_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/etec16s_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/etec16s_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-etec16s/bioconductor-etec16s_1.10.0_src_all.tar.gz" +) +MD5="ab6de328373655b42c1915fa52fcb47e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-etec16s/pre-unlink.sh b/recipes/bioconductor-etec16s/pre-unlink.sh new file mode 100644 index 0000000000000..5774c42f0d088 --- /dev/null +++ b/recipes/bioconductor-etec16s/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ etec16s diff --git a/recipes/bioconductor-eudysbiome/build.sh b/recipes/bioconductor-eudysbiome/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-eudysbiome/build.sh +++ b/recipes/bioconductor-eudysbiome/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eudysbiome/meta.yaml b/recipes/bioconductor-eudysbiome/meta.yaml index 8eb9719d27212..7c6c07e2772d0 100644 --- a/recipes/bioconductor-eudysbiome/meta.yaml +++ b/recipes/bioconductor-eudysbiome/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "eudysbiome" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1f6f59838e0b54b8d40b30cc6408cc1aac192bd72fd75e84d10fbf082fcc1370 + md5: b8a7504e2d5c6793c7d82819f060cd3c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-plyr - r-r.utils run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-plyr - r-r.utils @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'eudysbiome a package that permits to annotate the differential genera as harmful/harmless based on their ability to contribute to host diseases (as indicated in literature) or unknown based on their ambiguous genus classification. Further, the package statistically measures the eubiotic (harmless genera increase or harmful genera decrease) or dysbiotic(harmless genera decrease or harmful genera increase) impact of a given treatment or environmental change on the (gut-intestinal, GI) microbiome in comparison to the microbiome of the reference condition.' extra: identifiers: - biotools:eudysbiome - doi:10.1186/s12918-016-0344-6 + parent_recipe: + name: bioconductor-eudysbiome + path: recipes/bioconductor-eudysbiome + version: 1.10.0 + diff --git a/recipes/bioconductor-eupathdb/meta.yaml b/recipes/bioconductor-eupathdb/meta.yaml new file mode 100644 index 0000000000000..e3d11bee53dc6 --- /dev/null +++ b/recipes/bioconductor-eupathdb/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.1" %} +{% set name = "EuPathDB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1451c3ab6c224d9a4cfbdf27dc5c2680 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: dplyr, knitr, BiocStyle, rmarkdown, jsonlite +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - r-biocmanager + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - r-biocmanager + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Brings together annotation resources from the various EuPathDB databases (PlasmoDB, ToxoDB, TriTrypDB, etc.) and makes them available in R using the AnnotationHub framework.' + diff --git a/recipes/bioconductor-eupathdb/post-link.sh b/recipes/bioconductor-eupathdb/post-link.sh new file mode 100644 index 0000000000000..a6829e4930814 --- /dev/null +++ b/recipes/bioconductor-eupathdb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="EuPathDB_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/EuPathDB_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/EuPathDB_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-eupathdb/bioconductor-eupathdb_1.0.1_src_all.tar.gz" +) +MD5="1451c3ab6c224d9a4cfbdf27dc5c2680" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-eupathdb/pre-unlink.sh b/recipes/bioconductor-eupathdb/pre-unlink.sh new file mode 100644 index 0000000000000..6b8ab372c18f7 --- /dev/null +++ b/recipes/bioconductor-eupathdb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ EuPathDB diff --git a/recipes/bioconductor-eventpointer/build.sh b/recipes/bioconductor-eventpointer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-eventpointer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eventpointer/meta.yaml b/recipes/bioconductor-eventpointer/meta.yaml new file mode 100644 index 0000000000000..b1053f1727ee0 --- /dev/null +++ b/recipes/bioconductor-eventpointer/meta.yaml @@ -0,0 +1,79 @@ +{% set version = "2.0.1" %} +{% set name = "EventPointer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ecd974e8c801868993f80115b6dc07fe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sgseq >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cobs + - r-doparallel + - r-foreach + - r-igraph + - r-mass + - r-matrix + - r-matrixstats + - r-nnls + - r-prodlim + - r-stringr + run: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sgseq >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cobs + - r-doparallel + - r-foreach + - r-igraph + - r-mass + - r-matrix + - r-matrixstats + - r-nnls + - r-prodlim + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'EventPointer is an R package to identify alternative splicing events that involve either simple (case-control experiment) or complex experimental designs such as time course experiments and studies including paired-samples. The algorithm can be used to analyze data from either junction arrays (Affymetrix Arrays) or sequencing data (RNA-Seq). The software returns a data.frame with the detected alternative splicing events: gene name, type of event (cassette, alternative 3'',...,etc), genomic position, statistical significance and increment of the percent spliced in (Delta PSI) for all the events. The algorithm can generate a series of files to visualize the detected alternative splicing events in IGV. This eases the interpretation of results and the design of primers for standard PCR validation.' + diff --git a/recipes/bioconductor-excluster/build.sh b/recipes/bioconductor-excluster/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-excluster/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-excluster/meta.yaml b/recipes/bioconductor-excluster/meta.yaml new file mode 100644 index 0000000000000..5aa414f3f4e9c --- /dev/null +++ b/recipes/bioconductor-excluster/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "ExCluster" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f46f2947dbef303b274520f5ae7e3531 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-matrixstats + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'ExCluster flattens Ensembl and GENCODE GTF files into GFF files, which are used to count reads per non-overlapping exon bin from BAM files. This read counting is done using the function featureCounts from the package Rsubread. Library sizes are normalized across all biological replicates, and ExCluster then compares two different conditions to detect signifcantly differentially spliced genes. This process requires at least two independent biological repliates per condition, and ExCluster accepts only exactly two conditions at a time. ExCluster ultimately produces false discovery rates (FDRs) per gene, which are used to detect significance. Exon log2 fold change (log2FC) means and variances may be plotted for each significantly differentially spliced gene, which helps scientists develop hypothesis and target differential splicing events for RT-qPCR validation in the wet lab.' + diff --git a/recipes/bioconductor-eximir/build.sh b/recipes/bioconductor-eximir/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-eximir/build.sh +++ b/recipes/bioconductor-eximir/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-eximir/conda_build_config.yaml b/recipes/bioconductor-eximir/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-eximir/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-eximir/meta.yaml b/recipes/bioconductor-eximir/meta.yaml index 3ddee083dae78..4bed43979eb61 100644 --- a/recipes/bioconductor-eximir/meta.yaml +++ b/recipes/bioconductor-eximir/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "ExiMiR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8db4a380e83229f0c0604eca519026a9744e64b89aa01080a9349f1cec553c68 + md5: 541711a5a0c2f740bc70a23b50d3b432 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: mirna10cdf requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains functions for reading raw data in ImaGene TXT format obtained from Exiqon miRCURY LNA arrays, annotating them with appropriate GAL files, and normalizing them using a spike-in probe-based method. Other platforms and data formats are also supported.' extra: identifiers: - biotools:eximir - doi:10.1186/1756-0500-7-302 + parent_recipe: + name: bioconductor-eximir + path: recipes/bioconductor-eximir + version: 2.22.0 + diff --git a/recipes/bioconductor-exomecopy/build.sh b/recipes/bioconductor-exomecopy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-exomecopy/build.sh +++ b/recipes/bioconductor-exomecopy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-exomecopy/meta.yaml b/recipes/bioconductor-exomecopy/meta.yaml index 4242b30f949a1..9c9f550553528 100644 --- a/recipes/bioconductor-exomecopy/meta.yaml +++ b/recipes/bioconductor-exomecopy/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "exomeCopy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1cff39c955f7c20aaa429cea83cfb8fd831ed4d36500157521e831f20c6a7aab + md5: 4512e1db1fe55da16916eccd3a45fd14 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Biostrings requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base build: - {{ compiler('c') }} @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.' extra: identifiers: - biotools:exomecopy - doi:10.2202/1544-6115.1732 + parent_recipe: + name: bioconductor-exomecopy + path: recipes/bioconductor-exomecopy + version: 1.26.0 + diff --git a/recipes/bioconductor-exomepeak/build.sh b/recipes/bioconductor-exomepeak/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-exomepeak/build.sh +++ b/recipes/bioconductor-exomepeak/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-exomepeak/meta.yaml b/recipes/bioconductor-exomepeak/meta.yaml index 0a0eccb015c51..38c66e1982b53 100644 --- a/recipes/bioconductor-exomepeak/meta.yaml +++ b/recipes/bioconductor-exomepeak/meta.yaml @@ -1,41 +1,47 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "exomePeak" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 53444fe6488672d2fa8d19530ba737e9ccd13e32b6b0c38625180aec4ff7b3ba + md5: 966b325c0553337d4f866c6ad8978bd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package (Meng, Jia, et al. "Exome-based analysis for RNA epigenome sequencing data." Bioinformatics 29.12 (2013): 1565-1567.) with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. The package is still under active development, and we welcome all biology and computation scientist for all kinds of collaborations and communications. Please feel free to contact Dr. Jia Meng if you have any questions.' extra: identifiers: - biotools:exomepeak + parent_recipe: + name: bioconductor-exomepeak + path: recipes/bioconductor-exomepeak + version: 2.14.0 + diff --git a/recipes/bioconductor-experimenthub/build.sh b/recipes/bioconductor-experimenthub/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-experimenthub/build.sh +++ b/recipes/bioconductor-experimenthub/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-experimenthub/conda_build_config.yaml b/recipes/bioconductor-experimenthub/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-experimenthub/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-experimenthub/meta.yaml b/recipes/bioconductor-experimenthub/meta.yaml index 9b6030e6595f8..b111bc873058c 100644 --- a/recipes/bioconductor-experimenthub/meta.yaml +++ b/recipes/bioconductor-experimenthub/meta.yaml @@ -1,40 +1,48 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "ExperimentHub" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: db4e6cc33e53dd3de0b6bd413f1679fed043dfe5d487229484d3c5172d9e58eb + md5: c4a23733d1283fbc667b67cb0a630110 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-curl run: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-curl test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a client for the Bioconductor ExperimentHub web resource. ExperimentHub provides a central location where curated data from experiments, publications or training courses can be accessed. Each resource has associated metadata, tags and date of modification. The client creates and manages a local cache of files retrieved enabling quick and reproducible access.' +extra: + parent_recipe: + name: bioconductor-experimenthub + path: recipes/bioconductor-experimenthub + version: 1.6.1 + diff --git a/recipes/bioconductor-experimenthubdata/build.sh b/recipes/bioconductor-experimenthubdata/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-experimenthubdata/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-experimenthubdata/meta.yaml b/recipes/bioconductor-experimenthubdata/meta.yaml new file mode 100644 index 0000000000000..0ec8068db0d4c --- /dev/null +++ b/recipes/bioconductor-experimenthubdata/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.8.0" %} +{% set name = "ExperimentHubData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d12ea3b540ea4e10072c39cf6637d576 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomeInfoDb, RUnit, knitr, BiocStyle +requirements: + host: + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-bioccheck >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-curl + - r-dbi + - r-httr + run: + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-bioccheck >=1.18.0,<1.19.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-curl + - r-dbi + - r-httr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Functions to add metadata to ExperimentHub db and resource files to AWS S3 buckets.' + diff --git a/recipes/bioconductor-explorase/build.sh b/recipes/bioconductor-explorase/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-explorase/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-explorase/meta.yaml b/recipes/bioconductor-explorase/meta.yaml new file mode 100644 index 0000000000000..6c07e54f25c72 --- /dev/null +++ b/recipes/bioconductor-explorase/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.46.0" %} +{% set name = "explorase" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2064b8b45518a6a033abc5e46c312bf7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: cairoDevice +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-rggobi + - r-rgtk2 + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-rggobi + - r-rgtk2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'explore and analyze *omics data with R and GGobi' + diff --git a/recipes/bioconductor-expressionatlas/build.sh b/recipes/bioconductor-expressionatlas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-expressionatlas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-expressionatlas/meta.yaml b/recipes/bioconductor-expressionatlas/meta.yaml new file mode 100644 index 0000000000000..cf2e1e6aaf9cb --- /dev/null +++ b/recipes/bioconductor-expressionatlas/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.10.0" %} +{% set name = "ExpressionAtlas" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fa4131206692f3b828491081f9468738 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-httr + - r-xml + - r-xml2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-httr + - r-xml + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package is for searching for datasets in EMBL-EBI Expression Atlas, and downloading them into R for further analysis. Each Expression Atlas dataset is represented as a SimpleList object with one element per platform. Sequencing data is contained in a SummarizedExperiment object, while microarray data is contained in an ExpressionSet or MAList object.' + diff --git a/recipes/bioconductor-expressionview/build.sh b/recipes/bioconductor-expressionview/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-expressionview/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-expressionview/meta.yaml b/recipes/bioconductor-expressionview/meta.yaml new file mode 100644 index 0000000000000..493e9f063cba2 --- /dev/null +++ b/recipes/bioconductor-expressionview/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.34.0" %} +{% set name = "ExpressionView" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 24263ace50dde80c1d85d8382ca5a612 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ALL, hgu95av2.db, biclust, affy +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-eisa >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - r-base + - r-bitops + - r-catools + - r-isa2 + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-eisa >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - r-base + - r-bitops + - r-catools + - r-isa2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'ExpressionView visualizes possibly overlapping biclusters in a gene expression matrix. It can use the result of the ISA method (eisa package) or the algorithms in the biclust package or others. The viewer itself was developed using Adobe Flex and runs in a flash-enabled web browser.' + diff --git a/recipes/bioconductor-faahko/meta.yaml b/recipes/bioconductor-faahko/meta.yaml index 786051a31cc65..a493273971de9 100644 --- a/recipes/bioconductor-faahko/meta.yaml +++ b/recipes/bioconductor-faahko/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "faahKO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f156932d08ab79f0607ce6b3584b868bd161615ea6f427af12e718ff41846923 + md5: c59e4588f572f3b56555cfd8d905107e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'Positive ionization mode data in NetCDF file format. Centroided subset from 200-600 m/z and 2500-4500 seconds. Data originally reported in "Assignment of Endogenous Substrates to Enzymes by Global Metabolite Profiling" Biochemistry; 2004; 43(45). Also includes detected peaks in an xcmsSet.' - +extra: + parent_recipe: + name: bioconductor-faahko + path: recipes/bioconductor-faahko + version: 1.20.0 diff --git a/recipes/bioconductor-faahko/post-link.sh b/recipes/bioconductor-faahko/post-link.sh index c5af208cb421f..afe71cbc3dd03 100644 --- a/recipes/bioconductor-faahko/post-link.sh +++ b/recipes/bioconductor-faahko/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="faahKO_1.20.0.tar.gz" +FN="faahKO_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/faahKO_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/faahKO_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/faahKO_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/faahKO_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-faahko/bioconductor-faahko_1.22.0_src_all.tar.gz" ) -MD5="5cfa6b1656efb3167d8fbccbc99b97d4" +MD5="c59e4588f572f3b56555cfd8d905107e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-fabia/build.sh b/recipes/bioconductor-fabia/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fabia/build.sh +++ b/recipes/bioconductor-fabia/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fabia/meta.yaml b/recipes/bioconductor-fabia/meta.yaml index ccd1535733846..6a69d6c799d7f 100644 --- a/recipes/bioconductor-fabia/meta.yaml +++ b/recipes/bioconductor-fabia/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "fabia" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 40e0d6731dd6764a85176646d1b38e4ec34ea565e691b56ea7185df21a5ac04f + md5: f98407e943a5d51e71b5d14cda70fa18 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -31,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'Biclustering by "Factor Analysis for Bicluster Acquisition" (FABIA). FABIA is a model-based technique for biclustering, that is clustering rows and columns simultaneously. Biclusters are found by factor analysis where both the factors and the loading matrix are sparse. FABIA is a multiplicative model that extracts linear dependencies between samples and feature patterns. It captures realistic non-Gaussian data distributions with heavy tails as observed in gene expression measurements. FABIA utilizes well understood model selection techniques like the EM algorithm and variational approaches and is embedded into a Bayesian framework. FABIA ranks biclusters according to their information content and separates spurious biclusters from true biclusters. The code is written in C.' extra: identifiers: - biotools:fabia + parent_recipe: + name: bioconductor-fabia + path: recipes/bioconductor-fabia + version: 2.26.0 + diff --git a/recipes/bioconductor-fabiadata/meta.yaml b/recipes/bioconductor-fabiadata/meta.yaml new file mode 100644 index 0000000000000..7df8948349865 --- /dev/null +++ b/recipes/bioconductor-fabiadata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.20.0" %} +{% set name = "fabiaData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1e781ec38c4767dd2ab23517fae76c59 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: fabia +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 2.1)' + summary: 'Supplying gene expression data sets for the demos of the biclustering method "Factor Analysis for Bicluster Acquisition" (FABIA). The following three data sets are provided: A) breast cancer (van''t Veer, Nature, 2002), B) multiple tissues (Su, PNAS, 2002), and C) diffuse large-B-cell lymphoma (Rosenwald, N Engl J Med, 2002).' + diff --git a/recipes/bioconductor-fabiadata/post-link.sh b/recipes/bioconductor-fabiadata/post-link.sh new file mode 100644 index 0000000000000..aa26e26965a32 --- /dev/null +++ b/recipes/bioconductor-fabiadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="fabiaData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fabiaData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/fabiaData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fabiadata/bioconductor-fabiadata_1.20.0_src_all.tar.gz" +) +MD5="1e781ec38c4767dd2ab23517fae76c59" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fabiadata/pre-unlink.sh b/recipes/bioconductor-fabiadata/pre-unlink.sh new file mode 100644 index 0000000000000..94753377bb2d3 --- /dev/null +++ b/recipes/bioconductor-fabiadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ fabiaData diff --git a/recipes/bioconductor-facopy.annot/meta.yaml b/recipes/bioconductor-facopy.annot/meta.yaml new file mode 100644 index 0000000000000..868edcb4b84e8 --- /dev/null +++ b/recipes/bioconductor-facopy.annot/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "facopy.annot" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: db7545bcf43738e8ba6894a2ec423c19 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides facopy with genome annotation on chromosome arms, genomic features and copy number alterations.' + diff --git a/recipes/bioconductor-facopy.annot/post-link.sh b/recipes/bioconductor-facopy.annot/post-link.sh new file mode 100644 index 0000000000000..be1f3e5d13e2a --- /dev/null +++ b/recipes/bioconductor-facopy.annot/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="facopy.annot_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/facopy.annot_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/facopy.annot_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-facopy.annot/bioconductor-facopy.annot_1.2.0_src_all.tar.gz" +) +MD5="db7545bcf43738e8ba6894a2ec423c19" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-facopy.annot/pre-unlink.sh b/recipes/bioconductor-facopy.annot/pre-unlink.sh new file mode 100644 index 0000000000000..f83ee590b51d7 --- /dev/null +++ b/recipes/bioconductor-facopy.annot/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ facopy.annot diff --git a/recipes/bioconductor-facsdorit/meta.yaml b/recipes/bioconductor-facsdorit/meta.yaml new file mode 100644 index 0000000000000..af2e9e2f2cb25 --- /dev/null +++ b/recipes/bioconductor-facsdorit/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "facsDorit" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9072988b0ba231cb46fb323fd326c7fe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-prada >=1.58.0,<1.59.0' + - r-base + run: + - 'bioconductor-prada >=1.58.0,<1.59.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'FACS example data for cell-based assays. This data is used in the examples and vignettes of the package prada.' + diff --git a/recipes/bioconductor-facsdorit/post-link.sh b/recipes/bioconductor-facsdorit/post-link.sh new file mode 100644 index 0000000000000..0c6ff92abf036 --- /dev/null +++ b/recipes/bioconductor-facsdorit/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="facsDorit_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/facsDorit_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/facsDorit_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-facsdorit/bioconductor-facsdorit_1.24.0_src_all.tar.gz" +) +MD5="9072988b0ba231cb46fb323fd326c7fe" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-facsdorit/pre-unlink.sh b/recipes/bioconductor-facsdorit/pre-unlink.sh new file mode 100644 index 0000000000000..e852ddb94730a --- /dev/null +++ b/recipes/bioconductor-facsdorit/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ facsDorit diff --git a/recipes/bioconductor-factdesign/build.sh b/recipes/bioconductor-factdesign/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-factdesign/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-factdesign/meta.yaml b/recipes/bioconductor-factdesign/meta.yaml new file mode 100644 index 0000000000000..7346671625fa6 --- /dev/null +++ b/recipes/bioconductor-factdesign/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.58.0" %} +{% set name = "factDesign" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 19e692c687b778b8a0a5cb377ba8b4ac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: affy, genefilter, multtest +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This package provides a set of tools for analyzing data from a factorial designed microarray experiment, or any microarray experiment for which a linear model is appropriate. The functions can be used to evaluate tests of contrast of biological interest and perform single outlier detection.' + diff --git a/recipes/bioconductor-famagg/build.sh b/recipes/bioconductor-famagg/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-famagg/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-famagg/meta.yaml b/recipes/bioconductor-famagg/meta.yaml new file mode 100644 index 0000000000000..a215ecece3115 --- /dev/null +++ b/recipes/bioconductor-famagg/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.10.0" %} +{% set name = "FamAgg" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 54719121212a63c8349c9d6a0f210ecb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RUnit, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - 'r-gap >=1.1-17' + - r-igraph + - r-kinship2 + - r-matrix + - r-survey + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - 'r-gap >=1.1-17' + - r-igraph + - r-kinship2 + - r-matrix + - r-survey +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Framework providing basic pedigree analysis and plotting utilities as well as a variety of methods to evaluate familial aggregation of traits in large pedigrees.' + diff --git a/recipes/bioconductor-fantom3and4cage/meta.yaml b/recipes/bioconductor-fantom3and4cage/meta.yaml new file mode 100644 index 0000000000000..e413b71c143bc --- /dev/null +++ b/recipes/bioconductor-fantom3and4cage/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "FANTOM3and4CAGE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c55a0fa84038a6e16773118479ae213c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'CAGE (Cap Analysis Gene Expression) data from FANTOM3 and FANTOM4 projects produced by RIKEN Omics Science Center.' + diff --git a/recipes/bioconductor-fantom3and4cage/post-link.sh b/recipes/bioconductor-fantom3and4cage/post-link.sh new file mode 100644 index 0000000000000..28f77a65fd969 --- /dev/null +++ b/recipes/bioconductor-fantom3and4cage/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FANTOM3and4CAGE_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FANTOM3and4CAGE_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/FANTOM3and4CAGE_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fantom3and4cage/bioconductor-fantom3and4cage_1.18.0_src_all.tar.gz" +) +MD5="c55a0fa84038a6e16773118479ae213c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fantom3and4cage/pre-unlink.sh b/recipes/bioconductor-fantom3and4cage/pre-unlink.sh new file mode 100644 index 0000000000000..a0ddda7267831 --- /dev/null +++ b/recipes/bioconductor-fantom3and4cage/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FANTOM3and4CAGE diff --git a/recipes/bioconductor-farms/build.sh b/recipes/bioconductor-farms/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-farms/build.sh +++ b/recipes/bioconductor-farms/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-farms/conda_build_config.yaml b/recipes/bioconductor-farms/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-farms/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-farms/meta.yaml b/recipes/bioconductor-farms/meta.yaml index da392428ee9da..5370afc153fa5 100644 --- a/recipes/bioconductor-farms/meta.yaml +++ b/recipes/bioconductor-farms/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "farms" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9b6425ac3540e59ad7b06bf8c160fc2be63ac7f3c5e715ace54be25a635bed13 + md5: a16c7d5833eabebebe06a37ab2c92ead build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata, Biobase, utils requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'The package provides the summarization algorithm called Factor Analysis for Robust Microarray Summarization (FARMS) and a novel unsupervised feature selection criterion called "I/NI-calls"' extra: identifiers: - biotools:farms + parent_recipe: + name: bioconductor-farms + path: recipes/bioconductor-farms + version: 1.32.0 + diff --git a/recipes/bioconductor-fastliquidassociation/build.sh b/recipes/bioconductor-fastliquidassociation/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fastliquidassociation/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fastliquidassociation/meta.yaml b/recipes/bioconductor-fastliquidassociation/meta.yaml new file mode 100644 index 0000000000000..b8bde60637eda --- /dev/null +++ b/recipes/bioconductor-fastliquidassociation/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.18.0" %} +{% set name = "fastLiquidAssociation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f264e290f452047d63defed48f91ada0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GOstats, yeastCC, org.Sc.sgd.db +requirements: + host: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-liquidassociation >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-doparallel + - r-hmisc + - r-wgcna + run: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-liquidassociation >=1.36.0,<1.37.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-doparallel + - r-hmisc + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package extends the function of the LiquidAssociation package for genome-wide application. It integrates a screening method into the LA analysis to reduce the number of triplets to be examined for a high LA value and provides code for use in subsequent significance analyses.' + diff --git a/recipes/bioconductor-fastqcleaner/build.sh b/recipes/bioconductor-fastqcleaner/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fastqcleaner/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fastqcleaner/meta.yaml b/recipes/bioconductor-fastqcleaner/meta.yaml new file mode 100644 index 0000000000000..7efd8d5061c9e --- /dev/null +++ b/recipes/bioconductor-fastqcleaner/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.0.0" %} +{% set name = "FastqCleaner" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 24a7168bea8c5d1abfd726fd43e53484 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-dt + - r-htmltools + - 'r-rcpp >=0.12.12' + - r-shiny + - r-shinybs + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-dt + - r-htmltools + - 'r-rcpp >=0.12.12' + - r-shiny + - r-shinybs + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'An interactive web application for quality control, filtering and trimming of FASTQ files. This user-friendly tool combines a pipeline for data processing based on Biostrings and ShortRead infrastructure, with a cutting-edge visual environment. Single-Read and Paired-End files can be locally processed. Diagnostic interactive plots (CG content, per-base sequence quality, etc.) are provided for both the input and output files.' + diff --git a/recipes/bioconductor-fastseg/build.sh b/recipes/bioconductor-fastseg/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fastseg/build.sh +++ b/recipes/bioconductor-fastseg/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fastseg/meta.yaml b/recipes/bioconductor-fastseg/meta.yaml index c5a3de89d271b..65616d8d50582 100644 --- a/recipes/bioconductor-fastseg/meta.yaml +++ b/recipes/bioconductor-fastseg/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "fastseg" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 33be8adf3cd52a4d12906d22b3fe48fe1368aecb8ed436d5f1182d68a28286fb + md5: f47179909801546c1b8cbadd9d487295 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: DNAcopy, oligo requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base build: - {{ compiler('c') }} @@ -39,9 +40,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'fastseg implements a very fast and efficient segmentation algorithm. It has similar functionality as DNACopy (Olshen and Venkatraman 2004), but is considerably faster and more flexible. fastseg can segment data from DNA microarrays and data from next generation sequencing for example to detect copy number segments. Further it can segment data from RNA microarrays like tiling arrays to identify transcripts. Most generally, it can segment data given as a matrix or as a vector. Various data formats can be used as input to fastseg like expression set objects for microarrays or GRanges for sequencing data. The segmentation criterion of fastseg is based on a statistical test in a Bayesian framework, namely the cyber t-test (Baldi 2001). The speed-up arises from the facts, that sampling is not necessary in for fastseg and that a dynamic programming approach is used for calculation of the segments'' first and higher order moments.' extra: identifiers: - biotools:fastseg + parent_recipe: + name: bioconductor-fastseg + path: recipes/bioconductor-fastseg + version: 1.26.0 + diff --git a/recipes/bioconductor-fcbf/build.sh b/recipes/bioconductor-fcbf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fcbf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fcbf/meta.yaml b/recipes/bioconductor-fcbf/meta.yaml new file mode 100644 index 0000000000000..6a5ccfd600c93 --- /dev/null +++ b/recipes/bioconductor-fcbf/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "FCBF" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: afb5852e392691116c6407141851044e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: caret, mlbench, SingleCellExperiment, knitr, rmarkdown, testthat, BiocManager +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridextra + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridextra +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package provides a simple R implementation for the Fast Correlation Based Filter described in Yu, L. and Liu, H.; Feature Selection for High-Dimensional Data: A Fast Correlation Based Filter Solution,Proc. 20th Intl. Conf. Mach. Learn. (ICML-2003), Washington DC, 2003 The current package is an intent to make easier for bioinformaticians to use FCBF for feature selection, especially regarding transcriptomic data.This implies discretizing expression (function discretize_exprs) before calculating the features that explain the class, but are not predictable by other features. The functions are implemented based on the algorithm of Yu and Liu, 2003 and Rajarshi Guha''s implementation from 13/05/2005 available (as of 26/08/2018) at http://www.rguha.net/code/R/fcbf.R .' + diff --git a/recipes/bioconductor-fccac/build.sh b/recipes/bioconductor-fccac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fccac/build.sh +++ b/recipes/bioconductor-fccac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fccac/meta.yaml b/recipes/bioconductor-fccac/meta.yaml index cbc30b34887c4..be97adbfc2835 100644 --- a/recipes/bioconductor-fccac/meta.yaml +++ b/recipes/bioconductor-fccac/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "fCCAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dbe5368f2130730abd567026a029f1343bbbb7da7ee75d195590506d9c5bfb1f + md5: 20e26204e5c9d0726a0a060b5c2e41cd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda - r-ggplot2 - r-rcolorbrewer run: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda - r-ggplot2 @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq).' + summary: 'An application of functional canonical correlation analysis to assess covariance of nucleic acid sequencing datasets such as chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). The package can be used as well with other types of sequencing data such as neMeRIP-seq (PMID: 29489750) or with single cell RNA-seq or epigenome data provided in bigWig format.' extra: identifiers: - biotools:fccac + parent_recipe: + name: bioconductor-fccac + path: recipes/bioconductor-fccac + version: 1.6.0 + diff --git a/recipes/bioconductor-fci/build.sh b/recipes/bioconductor-fci/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fci/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fci/meta.yaml b/recipes/bioconductor-fci/meta.yaml new file mode 100644 index 0000000000000..20ee266d011c6 --- /dev/null +++ b/recipes/bioconductor-fci/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.12.0" %} +{% set name = "fCI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a3c20a38535de3aeba64aa906ac0d37a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle +requirements: + host: + - r-base + - r-fnn + - r-gtools + - r-psych + - r-rgl + - r-venndiagram + - r-zoo + run: + - r-base + - r-fnn + - r-gtools + - r-psych + - r-rgl + - r-venndiagram + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: '(f-divergence Cutoff Index), is to find DEGs in the transcriptomic & proteomic data, and identify DEGs by computing the difference between the distribution of fold-changes for the control-control and remaining (non-differential) case-control gene expression ratio data. fCI provides several advantages compared to existing methods.' + diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml new file mode 100644 index 0000000000000..9a98a8912e91c --- /dev/null +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "FDb.FANTOM4.promoters.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 99a610eb895470e3d945acc5cfb3ebe6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, rtracklayer, matrixStats +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FANTOM4 promoters, liftOver''ed from hg18 to hg19, CpGs quantified' + diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh b/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh new file mode 100644 index 0000000000000..a12b17294b7e9 --- /dev/null +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.FANTOM4.promoters.hg19_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.fantom4.promoters.hg19/bioconductor-fdb.fantom4.promoters.hg19_1.0.0_src_all.tar.gz" +) +MD5="99a610eb895470e3d945acc5cfb3ebe6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fdb.fantom4.promoters.hg19/pre-unlink.sh b/recipes/bioconductor-fdb.fantom4.promoters.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..a6d1d433f0e2e --- /dev/null +++ b/recipes/bioconductor-fdb.fantom4.promoters.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.FANTOM4.promoters.hg19 diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml new file mode 100644 index 0000000000000..900fcb98dfc38 --- /dev/null +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.2.0" %} +{% set name = "FDb.InfiniumMethylation.hg18" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 95ceab50d0a7c3d417cee12fbe3defb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Compiled HumanMethylation27 and HumanMethylation450 annotations' + diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh new file mode 100644 index 0000000000000..2ff12a22bddb3 --- /dev/null +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg18_2.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg18/bioconductor-fdb.infiniummethylation.hg18_2.2.0_src_all.tar.gz" +) +MD5="95ceab50d0a7c3d417cee12fbe3defb3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg18/pre-unlink.sh b/recipes/bioconductor-fdb.infiniummethylation.hg18/pre-unlink.sh new file mode 100644 index 0000000000000..763c5dc1eee35 --- /dev/null +++ b/recipes/bioconductor-fdb.infiniummethylation.hg18/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.InfiniumMethylation.hg18 diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml index 4ee7d049e0ae4..7b669b972c24a 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/meta.yaml @@ -1,43 +1,49 @@ {% set version = "2.2.0" %} {% set name = "FDb.InfiniumMethylation.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 605aa3643588a2f40a942fa760b92662060a0dfedb26b4e4cd6f1a78b703093f + md5: b8b1abc599b9556b9fe9c6e824cb2697 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: FDb.UCSC.snp135common.hg19 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Compiled HumanMethylation27 and HumanMethylation450 annotations' - +extra: + parent_recipe: + name: bioconductor-fdb.infiniummethylation.hg19 + path: recipes/bioconductor-fdb.infiniummethylation.hg19 + version: 2.2.0 diff --git a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh index 75afe3b912650..ba59def2f0797 100644 --- a/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh +++ b/recipes/bioconductor-fdb.infiniummethylation.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" "https://bioarchive.galaxyproject.org/FDb.InfiniumMethylation.hg19_2.2.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-fdb.infiniummethylation.hg19/bioconductor-fdb.infiniummethylation.hg19_2.2.0_src_all.tar.gz" diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml new file mode 100644 index 0000000000000..7344bf3a0b899 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "FDb.UCSC.snp135common.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0cdca5fa595bb69464016ceb97635f78 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20111119 +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'makeFeatureDbFromUCSC cannot cope with this track, hence a package' + diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh new file mode 100644 index 0000000000000..56d6c7400a000 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.UCSC.snp135common.hg19_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp135common.hg19/bioconductor-fdb.ucsc.snp135common.hg19_1.0.0_src_all.tar.gz" +) +MD5="0cdca5fa595bb69464016ceb97635f78" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fdb.ucsc.snp135common.hg19/pre-unlink.sh b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..24f9c221ac848 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp135common.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.UCSC.snp135common.hg19 diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml new file mode 100644 index 0000000000000..87c7999eafba5 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.0.0" %} +{% set name = "FDb.UCSC.snp137common.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dac83f2d2f9ea9f033e50beac5c44838 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'makeFeatureDbFromUCSC cannot cope with this track, hence a package' + diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh new file mode 100644 index 0000000000000..b94795333fba5 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.UCSC.snp137common.hg19_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.snp137common.hg19/bioconductor-fdb.ucsc.snp137common.hg19_1.0.0_src_all.tar.gz" +) +MD5="dac83f2d2f9ea9f033e50beac5c44838" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fdb.ucsc.snp137common.hg19/pre-unlink.sh b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..dab8a80fa94ae --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.snp137common.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.UCSC.snp137common.hg19 diff --git a/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml new file mode 100644 index 0000000000000..4ce40cd9a1f8b --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.trnas/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.1" %} +{% set name = "FDb.UCSC.tRNAs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 77bfdadd4d9f995a72b001e4e41792fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as FeatureDb objects' + diff --git a/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh b/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh new file mode 100644 index 0000000000000..5303c7972f626 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.trnas/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FDb.UCSC.tRNAs_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/FDb.UCSC.tRNAs_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/FDb.UCSC.tRNAs_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fdb.ucsc.trnas/bioconductor-fdb.ucsc.trnas_1.0.1_src_all.tar.gz" +) +MD5="77bfdadd4d9f995a72b001e4e41792fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fdb.ucsc.trnas/pre-unlink.sh b/recipes/bioconductor-fdb.ucsc.trnas/pre-unlink.sh new file mode 100644 index 0000000000000..bc309e730c1f4 --- /dev/null +++ b/recipes/bioconductor-fdb.ucsc.trnas/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FDb.UCSC.tRNAs diff --git a/recipes/bioconductor-fdrame/build.sh b/recipes/bioconductor-fdrame/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fdrame/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fdrame/meta.yaml b/recipes/bioconductor-fdrame/meta.yaml new file mode 100644 index 0000000000000..68dc8c642ffa8 --- /dev/null +++ b/recipes/bioconductor-fdrame/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.54.0" %} +{% set name = "fdrame" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1cb9ad63d92d24dae60d42ba7ed28916 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains two main functions. The first is fdr.ma which takes normalized expression data array, experimental design and computes adjusted p-values It returns the fdr adjusted p-values and plots, according to the methods described in (Reiner, Yekutieli and Benjamini 2002). The second, is fdr.gui() which creates a simple graphic user interface to access fdr.ma' + diff --git a/recipes/bioconductor-fella/build.sh b/recipes/bioconductor-fella/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fella/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fella/meta.yaml b/recipes/bioconductor-fella/meta.yaml new file mode 100644 index 0000000000000..2261b28c279c8 --- /dev/null +++ b/recipes/bioconductor-fella/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.2.0" %} +{% set name = "FELLA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 57cc316a2cfa0eed827576e28c8e7fd6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: shiny, DT, magrittr, visNetwork, knitr, BiocStyle, rmarkdown, testthat, biomaRt, org.Hs.eg.db, org.Mm.eg.db, AnnotationDbi, GOSemSim +requirements: + host: + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - r-base + - r-igraph + - r-matrix + - r-plyr + run: + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - r-base + - r-igraph + - r-matrix + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Enrichment of metabolomics data using KEGG entries. Given a set of affected compounds, FELLA suggests affected reactions, enzymes, modules and pathways using label propagation in a knowledge model network. The resulting subnetwork can be visualised and exported.' + diff --git a/recipes/bioconductor-fem/build.sh b/recipes/bioconductor-fem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fem/meta.yaml b/recipes/bioconductor-fem/meta.yaml new file mode 100644 index 0000000000000..56167b72f82ab --- /dev/null +++ b/recipes/bioconductor-fem/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "3.10.0" %} +{% set name = "FEM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bdcb6f1671541b2849ed9ca57a974b9b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - r-corrplot + - r-igraph + - r-matrix + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - r-corrplot + - r-igraph + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'The FEM package performs a systems-level integrative analysis of DNA methylation and gene expression data. It seeks modules of functionally related genes which exhibit differential promoter DNA methylation and differential expression, where an inverse association between promoter DNA methylation and gene expression is assumed. For full details, see Jiao et al Bioinformatics 2014.' + diff --git a/recipes/bioconductor-ffpe/build.sh b/recipes/bioconductor-ffpe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ffpe/build.sh +++ b/recipes/bioconductor-ffpe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ffpe/conda_build_config.yaml b/recipes/bioconductor-ffpe/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-ffpe/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-ffpe/meta.yaml b/recipes/bioconductor-ffpe/meta.yaml index d11d5a2433cb6..b408593af6e07 100644 --- a/recipes/bioconductor-ffpe/meta.yaml +++ b/recipes/bioconductor-ffpe/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ffpe" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: efaabc3e9c8582c5827793c6c232679c4d62a96812fa996a0aeb8796e7b66fb5 + md5: 0854fb74a6463f5e5c6fd54a18ad20e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: genefilter, ffpeExampleData requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' - r-base - r-sfsmisc - r-ttr run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' - r-base - r-sfsmisc - r-ttr @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>2)' summary: 'Identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots).' extra: identifiers: - biotools:ffpe + parent_recipe: + name: bioconductor-ffpe + path: recipes/bioconductor-ffpe + version: 1.24.0 + diff --git a/recipes/bioconductor-ffpeexampledata/meta.yaml b/recipes/bioconductor-ffpeexampledata/meta.yaml new file mode 100644 index 0000000000000..4d29741b0bc74 --- /dev/null +++ b/recipes/bioconductor-ffpeexampledata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.20.0" %} +{% set name = "ffpeExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3e1855c53c4cef163383ef8921a86ab1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: genefilter, affy +requirements: + host: + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>2)' + summary: 'A subset of GSE17565 (April et al. 2009) containing 32 FFPE samples of Burkitts Lymphoma and Breast Adenocarcinoma, with a dilution series in technical duplicate.' + diff --git a/recipes/bioconductor-ffpeexampledata/post-link.sh b/recipes/bioconductor-ffpeexampledata/post-link.sh new file mode 100644 index 0000000000000..d8216c828de7f --- /dev/null +++ b/recipes/bioconductor-ffpeexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ffpeExampleData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ffpeExampleData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ffpeExampleData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ffpeexampledata/bioconductor-ffpeexampledata_1.20.0_src_all.tar.gz" +) +MD5="3e1855c53c4cef163383ef8921a86ab1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ffpeexampledata/pre-unlink.sh b/recipes/bioconductor-ffpeexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..8ae4beba50d13 --- /dev/null +++ b/recipes/bioconductor-ffpeexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ffpeExampleData diff --git a/recipes/bioconductor-fgnet/build.sh b/recipes/bioconductor-fgnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fgnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fgnet/meta.yaml b/recipes/bioconductor-fgnet/meta.yaml new file mode 100644 index 0000000000000..e424c3ed6ed55 --- /dev/null +++ b/recipes/bioconductor-fgnet/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "3.16.0" %} +{% set name = "FGNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8e0ffafc6f001f952cf23b176de7d099 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RCurl, RDAVIDWebService, gage, topGO, GO.db, KEGG.db, reactome.db, RUnit, BiocGenerics, org.Sc.sgd.db, knitr, rmarkdown, AnnotationDbi, RGtk2, BiocManager +requirements: + host: + - r-base + - r-hwriter + - 'r-igraph >=0.6' + - r-plotrix + - r-png + - r-r.utils + - r-rcolorbrewer + - r-reshape2 + - r-xml + run: + - r-base + - r-hwriter + - 'r-igraph >=0.6' + - r-plotrix + - r-png + - r-r.utils + - r-rcolorbrewer + - r-reshape2 + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Build and visualize functional gene and term networks from clustering of enrichment analyses in multiple annotation spaces. The package includes a graphical user interface (GUI) and functions to perform the functional enrichment analysis through DAVID, GeneTerm Linker, gage (GSEA) and topGO.' + diff --git a/recipes/bioconductor-fgsea/build.sh b/recipes/bioconductor-fgsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fgsea/build.sh +++ b/recipes/bioconductor-fgsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fgsea/meta.yaml b/recipes/bioconductor-fgsea/meta.yaml index 81558a5499645..660bf73b180d9 100644 --- a/recipes/bioconductor-fgsea/meta.yaml +++ b/recipes/bioconductor-fgsea/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "fgsea" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9ac57aceebf752f287ec94ed663d383ddf8ea1e7beb419c277b3f7f2d7d5c6c0 + md5: 1ede6d5cb80ae8f3832581da55ee5cc0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, reactome.db, AnnotationDbi, parallel, org.Mm.eg.db, limma, GEOquery +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-data.table - r-fastmatch @@ -27,7 +29,7 @@ requirements: - r-matrix - r-rcpp run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base - r-data.table - r-fastmatch @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENCE' summary: 'The package implements an algorithm for fast gene set enrichment analysis. Using the fast algorithm allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.' extra: identifiers: - biotools:fgsea - doi:10.1101/060012 + parent_recipe: + name: bioconductor-fgsea + path: recipes/bioconductor-fgsea + version: 1.6.0 + diff --git a/recipes/bioconductor-fibroeset/meta.yaml b/recipes/bioconductor-fibroeset/meta.yaml new file mode 100644 index 0000000000000..a7c4dd03915cd --- /dev/null +++ b/recipes/bioconductor-fibroeset/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "fibroEset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 62d8b288008e726bd897b0a7296aade1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'exprSet for Karaman et al. (2003) human, bonobo and gorilla fibroblasts data' + diff --git a/recipes/bioconductor-fibroeset/post-link.sh b/recipes/bioconductor-fibroeset/post-link.sh new file mode 100644 index 0000000000000..429da1db2d7c9 --- /dev/null +++ b/recipes/bioconductor-fibroeset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="fibroEset_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fibroEset_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/fibroEset_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fibroeset/bioconductor-fibroeset_1.24.0_src_all.tar.gz" +) +MD5="62d8b288008e726bd897b0a7296aade1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fibroeset/pre-unlink.sh b/recipes/bioconductor-fibroeset/pre-unlink.sh new file mode 100644 index 0000000000000..997a377a0523b --- /dev/null +++ b/recipes/bioconductor-fibroeset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ fibroEset diff --git a/recipes/bioconductor-findmyfriends/build.sh b/recipes/bioconductor-findmyfriends/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-findmyfriends/build.sh +++ b/recipes/bioconductor-findmyfriends/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-findmyfriends/meta.yaml b/recipes/bioconductor-findmyfriends/meta.yaml index a07a763899a12..f77c7344290e7 100644 --- a/recipes/bioconductor-findmyfriends/meta.yaml +++ b/recipes/bioconductor-findmyfriends/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "FindMyFriends" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f207cfb4e8836357b9acafb1c8d578a57fa5530498230568e931fa1a138f979b + md5: 1b49ddefa018ab07f89bc316d119f099 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, testthat, knitr, rmarkdown, reutils requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-kebabs >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-digest - r-dplyr @@ -37,13 +38,13 @@ requirements: - r-rcpp - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-kebabs >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-digest - r-dplyr @@ -63,10 +64,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'A framework for doing microbial comparative genomics in R. The main purpose of the package is assisting in the creation of pangenome matrices where genes from related organisms are grouped by similarity, as well as the analysis of these data. FindMyFriends provides many novel approaches to doing pangenome analysis and supports a gene grouping algorithm that scales linearly, thus making the creation of huge pangenomes feasible.' extra: identifiers: - biotools:findmyfriends - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-findmyfriends + path: recipes/bioconductor-findmyfriends + version: 1.10.0 + diff --git a/recipes/bioconductor-fis/meta.yaml b/recipes/bioconductor-fis/meta.yaml index e09b570e040c1..e24ac53ea669e 100644 --- a/recipes/bioconductor-fis/meta.yaml +++ b/recipes/bioconductor-fis/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "FIs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5079ed505952460d83859eb8c8c028cfff8abe25ab5dd645f5a2e7be08f1ddb4 + md5: b7e898f0a018f003f8268ed5b255049f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Data set containing two complete lists of identified functional interaction partners in Human. Data are derived from Reactome and BioGRID databases.' - +extra: + parent_recipe: + name: bioconductor-fis + path: recipes/bioconductor-fis + version: 1.8.0 diff --git a/recipes/bioconductor-fis/post-link.sh b/recipes/bioconductor-fis/post-link.sh index da643cb8bc422..6bc14e4a701c7 100644 --- a/recipes/bioconductor-fis/post-link.sh +++ b/recipes/bioconductor-fis/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FIs_1.8.0.tar.gz" +FN="FIs_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/FIs_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/FIs_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FIs_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/FIs_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fis/bioconductor-fis_1.10.0_src_all.tar.gz" ) -MD5="2724d2e77ed0d6583fc3cdb03586df39" +MD5="b7e898f0a018f003f8268ed5b255049f" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-fishalyser/build.sh b/recipes/bioconductor-fishalyser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fishalyser/build.sh +++ b/recipes/bioconductor-fishalyser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fishalyser/meta.yaml b/recipes/bioconductor-fishalyser/meta.yaml index 5706d907f07a1..a8aee0c54ced2 100644 --- a/recipes/bioconductor-fishalyser/meta.yaml +++ b/recipes/bioconductor-fishalyser/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "FISHalyseR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7d9538726a00d4a4659ca6bd01e7a74d977169355b796b7b21ae5143a9064ae4 + md5: 18f4ac8d3e1695713f0953102e3105f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' - r-abind - r-base run: - - 'bioconductor-ebimage >=4.22.1,<4.24.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' - r-abind - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'FISHalyseR provides functionality to process and analyse digital cell culture images, in particular to quantify FISH probes within nuclei. Furthermore, it extract the spatial location of each nucleus as well as each probe enabling spatial co-localisation analysis.' extra: identifiers: - biotools:fishalyser - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-fishalyser + path: recipes/bioconductor-fishalyser + version: 1.14.0 + diff --git a/recipes/bioconductor-fission/meta.yaml b/recipes/bioconductor-fission/meta.yaml new file mode 100644 index 0000000000000..e38e1a7bb4331 --- /dev/null +++ b/recipes/bioconductor-fission/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2.0" %} +{% set name = "fission" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9576468d0dd81fb3edc7e7b550e0dc86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package provides a RangedSummarizedExperiment object of read counts in genes for a time course RNA-Seq experiment of fission yeast (Schizosaccharomyces pombe) in response to oxidative stress (1M sorbitol treatment) at 0, 15, 30, 60, 120 and 180 mins. The samples are further divided between a wild-type group and a group with deletion of atf21. The read count matrix was prepared and provided by the author of the study: Leong HS, Dawson K, Wirth C, Li Y, Connolly Y, Smith DL, Wilkinson CR, Miller CJ. "A global non-coding RNA system modulates fission yeast protein levels in response to stress". Nat Commun 2014 May 23;5:3947. PMID: 24853205. GEO: GSE56761.' + diff --git a/recipes/bioconductor-fission/post-link.sh b/recipes/bioconductor-fission/post-link.sh new file mode 100644 index 0000000000000..f59abe1a67c66 --- /dev/null +++ b/recipes/bioconductor-fission/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="fission_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/fission_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/fission_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fission/bioconductor-fission_1.2.0_src_all.tar.gz" +) +MD5="9576468d0dd81fb3edc7e7b550e0dc86" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fission/pre-unlink.sh b/recipes/bioconductor-fission/pre-unlink.sh new file mode 100644 index 0000000000000..9d7ac30e33016 --- /dev/null +++ b/recipes/bioconductor-fission/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ fission diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml new file mode 100644 index 0000000000000..2c7d1a2ebf8d1 --- /dev/null +++ b/recipes/bioconductor-fitcons.ucsc.hg19/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.1" %} +{% set name = "fitCons.UCSC.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 53d954890ec9b91084664a10161ce391 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store UCSC fitCons fitness consequences scores version 1.01 for the human genome (hg19).' + diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh b/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh new file mode 100644 index 0000000000000..78f796e6774e6 --- /dev/null +++ b/recipes/bioconductor-fitcons.ucsc.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="fitCons.UCSC.hg19_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/fitCons.UCSC.hg19_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/fitCons.UCSC.hg19_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fitcons.ucsc.hg19/bioconductor-fitcons.ucsc.hg19_3.7.1_src_all.tar.gz" +) +MD5="53d954890ec9b91084664a10161ce391" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fitcons.ucsc.hg19/pre-unlink.sh b/recipes/bioconductor-fitcons.ucsc.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..c99b417aaf027 --- /dev/null +++ b/recipes/bioconductor-fitcons.ucsc.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ fitCons.UCSC.hg19 diff --git a/recipes/bioconductor-fithic/build.sh b/recipes/bioconductor-fithic/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fithic/build.sh +++ b/recipes/bioconductor-fithic/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fithic/meta.yaml b/recipes/bioconductor-fithic/meta.yaml index 8c235eefe57a0..74adc06980102 100644 --- a/recipes/bioconductor-fithic/meta.yaml +++ b/recipes/bioconductor-fithic/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FitHiC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd573c41219a8ed0d49be732f4e4ed90dc92c9864fe940d7dc35c46506c2841b + md5: e61cb471638915e53858418b543fe1af build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown requirements: host: - r-base @@ -35,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Fit-Hi-C is a tool for assigning statistical confidence estimates to intra-chromosomal contact maps produced by genome-wide genome architecture assays such as Hi-C.' extra: identifiers: - biotools:fithic - doi:10.1101/gr.160374 + parent_recipe: + name: bioconductor-fithic + path: recipes/bioconductor-fithic + version: 1.6.0 + diff --git a/recipes/bioconductor-flagme/build.sh b/recipes/bioconductor-flagme/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flagme/build.sh +++ b/recipes/bioconductor-flagme/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flagme/meta.yaml b/recipes/bioconductor-flagme/meta.yaml index 2b996f7691338..a4bd32d1913c2 100644 --- a/recipes/bioconductor-flagme/meta.yaml +++ b/recipes/bioconductor-flagme/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "flagme" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c60206b52cbe07a4442c39bf7a2ffe3d5f1cfec1cd1c24975460f2f8af429a7f + md5: 265d812a5d8cbd4de27f0d4da32b73ad build: number: 0 rpaths: @@ -18,17 +18,17 @@ build: - lib/ requirements: host: - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-gcspikelite >=1.18.0,<1.20.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-gcspikelite >=1.20.0,<1.21.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-gplots - r-mass - r-sparsem run: - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-gcspikelite >=1.18.0,<1.20.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-gcspikelite >=1.20.0,<1.21.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-gplots - r-mass @@ -40,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Fragment-level analysis of gas chromatography - mass spectrometry metabolomics data' extra: identifiers: - biotools:flagme - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flagme + path: recipes/bioconductor-flagme + version: 1.36.0 + diff --git a/recipes/bioconductor-fletcher2013a/meta.yaml b/recipes/bioconductor-fletcher2013a/meta.yaml new file mode 100644 index 0000000000000..04e80d1d01955 --- /dev/null +++ b/recipes/bioconductor-fletcher2013a/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.18.0" %} +{% set name = "Fletcher2013a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8fc3c9e06927fa7a6508ea42fee23dd7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-gplots + - r-venndiagram + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-gplots + - r-venndiagram + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package Fletcher2013a contains time-course gene expression data from MCF-7 cells treated under different experimental systems in order to perturb FGFR2 signalling. The data comes from Fletcher et al. (Nature Comms 4:2464, 2013) where further details about the background and the experimental design of the study can be found.' + diff --git a/recipes/bioconductor-fletcher2013a/post-link.sh b/recipes/bioconductor-fletcher2013a/post-link.sh new file mode 100644 index 0000000000000..cd38b663aaa9e --- /dev/null +++ b/recipes/bioconductor-fletcher2013a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Fletcher2013a_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Fletcher2013a_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Fletcher2013a_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fletcher2013a/bioconductor-fletcher2013a_1.18.0_src_all.tar.gz" +) +MD5="8fc3c9e06927fa7a6508ea42fee23dd7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fletcher2013a/pre-unlink.sh b/recipes/bioconductor-fletcher2013a/pre-unlink.sh new file mode 100644 index 0000000000000..b4b03bf16d8dd --- /dev/null +++ b/recipes/bioconductor-fletcher2013a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Fletcher2013a diff --git a/recipes/bioconductor-fletcher2013b/meta.yaml b/recipes/bioconductor-fletcher2013b/meta.yaml new file mode 100644 index 0000000000000..2a1fc73fef911 --- /dev/null +++ b/recipes/bioconductor-fletcher2013b/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.18.0" %} +{% set name = "Fletcher2013b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 02757b2d756e7d7fb48641ad9a81aaf4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-fletcher2013a >=1.18.0,<1.19.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - r-base + - r-igraph + - r-rcolorbrewer + run: + - 'bioconductor-fletcher2013a >=1.18.0,<1.19.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - r-base + - r-igraph + - r-rcolorbrewer + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package reproduces the systems biology analysis for the data in package Fletcher2013a using RTN.' + diff --git a/recipes/bioconductor-fletcher2013b/post-link.sh b/recipes/bioconductor-fletcher2013b/post-link.sh new file mode 100644 index 0000000000000..12fbdb6d8669e --- /dev/null +++ b/recipes/bioconductor-fletcher2013b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Fletcher2013b_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Fletcher2013b_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Fletcher2013b_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fletcher2013b/bioconductor-fletcher2013b_1.18.0_src_all.tar.gz" +) +MD5="02757b2d756e7d7fb48641ad9a81aaf4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fletcher2013b/pre-unlink.sh b/recipes/bioconductor-fletcher2013b/pre-unlink.sh new file mode 100644 index 0000000000000..e3b233ea19f3b --- /dev/null +++ b/recipes/bioconductor-fletcher2013b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Fletcher2013b diff --git a/recipes/bioconductor-flipflop/build.sh b/recipes/bioconductor-flipflop/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flipflop/build.sh +++ b/recipes/bioconductor-flipflop/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flipflop/meta.yaml b/recipes/bioconductor-flipflop/meta.yaml index 7e0acb4c786d9..bb2b5c3d53377 100644 --- a/recipes/bioconductor-flipflop/meta.yaml +++ b/recipes/bioconductor-flipflop/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flipflop" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ddc865bf10511537392a46a5c50735007deb20b55f0e647dce502b8364592084 + md5: 6d7199d947a60eb70e2ce165f468bb82 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: GenomicFeatures +# SystemRequirements: GNU make requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-matrix run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-matrix build: @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Flipflop discovers which isoforms of a gene are expressed in a given sample together with their abundances, based on RNA-Seq read data. It takes an alignment file in SAM format as input. It can also discover transcripts from several samples simultaneously, increasing statistical power.' extra: identifiers: - biotools:flipflop + parent_recipe: + name: bioconductor-flipflop + path: recipes/bioconductor-flipflop + version: 1.18.0 + diff --git a/recipes/bioconductor-flowai/build.sh b/recipes/bioconductor-flowai/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowai/build.sh +++ b/recipes/bioconductor-flowai/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowai/meta.yaml b/recipes/bioconductor-flowai/meta.yaml index b386b634a2b93..fe5e1e0e4d6f4 100644 --- a/recipes/bioconductor-flowai/meta.yaml +++ b/recipes/bioconductor-flowai/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.1" %} {% set name = "flowAI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7cfd063a85442eac9ebfc5a1aa5b8b8ee7687a36c42e59f519f884d5dec54e1d + md5: e4860065d21f61fafd653eb15ec5cb52 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, shiny requirements: host: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-changepoint - r-ggplot2 @@ -29,7 +31,7 @@ requirements: - r-rmarkdown - r-scales run: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-changepoint - r-ggplot2 @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package is able to perform an automatic or interactive quality control on FCS data acquired using flow cytometry instruments. By evaluating three different properties: 1) flow rate, 2) signal acquisition, 3) dynamic range, the quality control enables the detection and removal of anomalies.' extra: identifiers: - biotools:flowai - doi:10.1093/bioinformatics/btw191 + parent_recipe: + name: bioconductor-flowai + path: recipes/bioconductor-flowai + version: 1.10.1 + diff --git a/recipes/bioconductor-flowbeads/build.sh b/recipes/bioconductor-flowbeads/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowbeads/build.sh +++ b/recipes/bioconductor-flowbeads/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowbeads/meta.yaml b/recipes/bioconductor-flowbeads/meta.yaml index 85a8415836f4e..6a3d749c131b0 100644 --- a/recipes/bioconductor-flowbeads/meta.yaml +++ b/recipes/bioconductor-flowbeads/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowBeads" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 347e01ce4a32b3c1e91583912e9b5ec1e3dc4eaab7f4d7e9d360f6ff3e8cbef2 + md5: fc8ae810a91f127ff4ad0bbe8ae888ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: flowViz requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-knitr - r-rrcov - r-xtable run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-knitr - r-rrcov @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package extends flowCore to provide functionality specific to bead data. One of the goals of this package is to automate analysis of bead data for the purpose of normalisation.' extra: identifiers: - biotools:flowbeads - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flowbeads + path: recipes/bioconductor-flowbeads + version: 1.18.0 + diff --git a/recipes/bioconductor-flowbin/build.sh b/recipes/bioconductor-flowbin/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowbin/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowbin/meta.yaml b/recipes/bioconductor-flowbin/meta.yaml new file mode 100644 index 0000000000000..900021f43fbc5 --- /dev/null +++ b/recipes/bioconductor-flowbin/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.18.0" %} +{% set name = "flowBin" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4adf63836576460151cff9e5022bcbec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: parallel +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-class + - r-snow + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-class + - r-snow +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Software to combine flow cytometry data that has been multiplexed into multiple tubes with common markers between them, by establishing common bins across tubes in terms of the common markers, then determining expression within each tube for each bin in terms of the tube-specific markers.' + diff --git a/recipes/bioconductor-flowcatchr/build.sh b/recipes/bioconductor-flowcatchr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowcatchr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowcatchr/meta.yaml b/recipes/bioconductor-flowcatchr/meta.yaml new file mode 100644 index 0000000000000..4bb6f7d180877 --- /dev/null +++ b/recipes/bioconductor-flowcatchr/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.16.0" %} +{% set name = "flowcatchR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e6cce882873b92da15dcc28e0bff415d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: ImageMagick +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-abind + - r-base + - r-colorramps + - r-plotly + - r-shiny + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-abind + - r-base + - r-colorramps + - r-plotly + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'flowcatchR is a set of tools to analyze in vivo microscopy imaging data, focused on tracking flowing blood cells. It guides the steps from segmentation to calculation of features, filtering out particles not of interest, providing also a set of utilities to help checking the quality of the performed operations (e.g. how good the segmentation was). It allows investigating the issue of tracking flowing cells such as in blood vessels, to categorize the particles in flowing, rolling and adherent. This classification is applied in the study of phenomena such as hemostasis and study of thrombosis development. Moreover, flowcatchR presents an integrated workflow solution, based on the integration with a Shiny App and Jupyter notebooks, which is delivered alongside the package, and can enable fully reproducible bioimage analysis in the R environment.' + diff --git a/recipes/bioconductor-flowchic/build.sh b/recipes/bioconductor-flowchic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowchic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowchic/meta.yaml b/recipes/bioconductor-flowchic/meta.yaml new file mode 100644 index 0000000000000..03de49d9c1fbb --- /dev/null +++ b/recipes/bioconductor-flowchic/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.16.0" %} +{% set name = "flowCHIC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2ed608da9c12a446d191101b5bc30ee7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-hexbin + - r-vegan + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-ggplot2 + - r-hexbin + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A package to analyze flow cytometric data of complex microbial communities based on histogram images' + diff --git a/recipes/bioconductor-flowcl/build.sh b/recipes/bioconductor-flowcl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowcl/build.sh +++ b/recipes/bioconductor-flowcl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowcl/meta.yaml b/recipes/bioconductor-flowcl/meta.yaml index f2053dc36aabc..a6c5aab51b3e5 100644 --- a/recipes/bioconductor-flowcl/meta.yaml +++ b/recipes/bioconductor-flowcl/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.1" %} {% set name = "flowCL" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0b650e3bbca75e53a42f5933aa8f0cf9720ae1747d62479c11422cc8ba0f2a5e + md5: cb31d847de5e1c0582c3b12d778a1931 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-sparql run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-sparql test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Semantic labelling of flow cytometric cell populations.' extra: identifiers: - biotools:flowcl - doi:10.1093/bioinformatics/btu807 + parent_recipe: + name: bioconductor-flowcl + path: recipes/bioconductor-flowcl + version: 1.18.1 + diff --git a/recipes/bioconductor-flowclean/build.sh b/recipes/bioconductor-flowclean/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowclean/build.sh +++ b/recipes/bioconductor-flowclean/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowclean/meta.yaml b/recipes/bioconductor-flowclean/meta.yaml index cd94777c540c8..03f74063f2e60 100644 --- a/recipes/bioconductor-flowclean/meta.yaml +++ b/recipes/bioconductor-flowclean/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowClean" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 17dec0e2f27dd8e54c4d7e8777404824b89ff330fe5e4c2d2de395fc83cab488 + md5: 5aee35d8d33660b091d930a61da84b11 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: flowViz, grid, gridExtra requirements: host: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-bit - r-changepoint - r-sfsmisc run: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-bit - r-changepoint @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A quality control tool for flow cytometry data based on compositional data analysis.' extra: identifiers: - biotools:flowclean + parent_recipe: + name: bioconductor-flowclean + path: recipes/bioconductor-flowclean + version: 1.18.0 + diff --git a/recipes/bioconductor-flowclust/build.sh b/recipes/bioconductor-flowclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowclust/meta.yaml b/recipes/bioconductor-flowclust/meta.yaml new file mode 100644 index 0000000000000..904ddb74a6eff --- /dev/null +++ b/recipes/bioconductor-flowclust/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "3.20.0" %} +{% set name = "flowClust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a53bc9c6beaa0a76bb4023ade9b38116 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, flowWorkspace, flowWorkspaceData +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-clue + - r-corpcor + - r-ellipse + - r-mnormt + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-clue + - r-corpcor + - r-ellipse + - r-mnormt + build: + - {{ compiler('c') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Robust model-based clustering using a t-mixture model with Box-Cox transformation. Note: users should have GSL installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''.' + diff --git a/recipes/bioconductor-flowcore/build.sh b/recipes/bioconductor-flowcore/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowcore/build.sh +++ b/recipes/bioconductor-flowcore/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowcore/meta.yaml b/recipes/bioconductor-flowcore/meta.yaml index 7f59ce7fae3f6..a73ac02722de0 100644 --- a/recipes/bioconductor-flowcore/meta.yaml +++ b/recipes/bioconductor-flowcore/meta.yaml @@ -1,39 +1,43 @@ -{% set version = "1.46.2" %} +{% set version = "1.48.0" %} {% set name = "flowCore" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1430325fa5da6c57735b7b7a085868fe269d28dca7a7980ce20d21babdfa3403 + md5: 75951b12ee2eb1bf65c73a9b0dc8e77b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Rgraphviz, flowViz, flowStats, testthat, flowWorkspace, flowWorkspaceData, openCyto, knitr, ggcyto, gridExtra +# SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - 'r-bh >=1.65.0.1' - r-corpcor + - r-mass - r-matrixstats - r-rcpp - r-rrcov run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - 'r-bh >=1.65.0.1' - r-corpcor + - r-mass - r-matrixstats - r-rcpp - r-rrcov @@ -45,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides S4 data structures and basic functions to deal with flow cytometry data.' extra: identifiers: - biotools:flowcore - doi:10.1186/1471-2105-10-106 + parent_recipe: + name: bioconductor-flowcore + path: recipes/bioconductor-flowcore + version: 1.46.2 + diff --git a/recipes/bioconductor-flowcybar/build.sh b/recipes/bioconductor-flowcybar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowcybar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowcybar/meta.yaml b/recipes/bioconductor-flowcybar/meta.yaml new file mode 100644 index 0000000000000..c094899437e45 --- /dev/null +++ b/recipes/bioconductor-flowcybar/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "flowCyBar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9fb23129a64b85f512c8df306e7c4c5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-gplots + - r-vegan + run: + - r-base + - r-gplots + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A package to analyze flow cytometric data using gate information to follow population/community dynamics' + diff --git a/recipes/bioconductor-flowdensity/build.sh b/recipes/bioconductor-flowdensity/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowdensity/build.sh +++ b/recipes/bioconductor-flowdensity/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowdensity/meta.yaml b/recipes/bioconductor-flowdensity/meta.yaml index 35669c7cb48c6..42ccf081e01aa 100644 --- a/recipes/bioconductor-flowdensity/meta.yaml +++ b/recipes/bioconductor-flowdensity/meta.yaml @@ -1,51 +1,55 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "flowDensity" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0519b8fa0530cdc533f8443697c47afbda2854325a9b0bbba18c6e13feadfd0a + md5: 72b17847c69bdf4f5fcd079f286b3091 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# The geos dependency gets around an incompatible dependency somewhere + noarch: generic +# SystemRequirements: GEOS (>= 3.2.0);for building from source: GEOS from http://trac.osgeo.org/geos/; GEOS OSX frameworks built by William Kyngesburye at http://www.kyngchaos.com/ may be used for source installs on OSX. requirements: host: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - r-base - r-car - r-gplots - r-rfoc - r-rgeos - r-sp - - geos 3.6.2 run: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' - r-base - r-car - r-gplots - r-rfoc - r-rgeos - r-sp - - geos 3.6.2 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides tools for automated sequential gating analogous to the manual gating strategy based on the density of the data.' extra: identifiers: - biotools:flowdensity - doi:10.1093/bioinformatics/btu677 + parent_recipe: + name: bioconductor-flowdensity + path: recipes/bioconductor-flowdensity + version: 1.14.0 + diff --git a/recipes/bioconductor-flowfit/build.sh b/recipes/bioconductor-flowfit/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowfit/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowfit/meta.yaml b/recipes/bioconductor-flowfit/meta.yaml new file mode 100644 index 0000000000000..d305c855855d2 --- /dev/null +++ b/recipes/bioconductor-flowfit/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "flowFit" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 86ba9036cce3eeb3be973d321e947fca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: flowFitExampleData +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + - r-gplots + - r-kza + - r-minpack.lm + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + - r-gplots + - r-kza + - r-minpack.lm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package estimate the proliferation of a cell population in cell-tracking dye studies. The package uses an R implementation of the Levenberg-Marquardt algorithm (minpack.lm) to fit a set of peaks (corresponding to different generations of cells) over the proliferation-tracking dye distribution in a FACS experiment.' + diff --git a/recipes/bioconductor-flowfitexampledata/meta.yaml b/recipes/bioconductor-flowfitexampledata/meta.yaml new file mode 100644 index 0000000000000..8f31f2e28536e --- /dev/null +++ b/recipes/bioconductor-flowfitexampledata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "flowFitExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1ffa4e31d23b8df9f4df96504a893639 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Two dataset that can be used to run examples from the flowFit vignette and examples' + diff --git a/recipes/bioconductor-flowfitexampledata/post-link.sh b/recipes/bioconductor-flowfitexampledata/post-link.sh new file mode 100644 index 0000000000000..2b88b27a8aaa2 --- /dev/null +++ b/recipes/bioconductor-flowfitexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="flowFitExampleData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowFitExampleData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowFitExampleData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowfitexampledata/bioconductor-flowfitexampledata_1.18.0_src_all.tar.gz" +) +MD5="1ffa4e31d23b8df9f4df96504a893639" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowfitexampledata/pre-unlink.sh b/recipes/bioconductor-flowfitexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..0344904ca1c44 --- /dev/null +++ b/recipes/bioconductor-flowfitexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ flowFitExampleData diff --git a/recipes/bioconductor-flowfp/build.sh b/recipes/bioconductor-flowfp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowfp/build.sh +++ b/recipes/bioconductor-flowfp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowfp/meta.yaml b/recipes/bioconductor-flowfp/meta.yaml index 2bc030de362b9..348de7bb20be9 100644 --- a/recipes/bioconductor-flowfp/meta.yaml +++ b/recipes/bioconductor-flowfp/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "flowFP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 13eb62a9485c55e63c4fa957c86046872957cbcc8e01224f26c9165ebe2a5533 + md5: d3a2bfd5a4e4b74002838cabd1b26066 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' - r-base build: - {{ compiler('c') }} @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Fingerprint generation of flow cytometry data, used to facilitate the application of machine learning and datamining tools for flow cytometry.' extra: identifiers: - biotools:flowfp - doi:10.1155/2009/193947 + parent_recipe: + name: bioconductor-flowfp + path: recipes/bioconductor-flowfp + version: 1.38.0 + diff --git a/recipes/bioconductor-flowmap/build.sh b/recipes/bioconductor-flowmap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowmap/build.sh +++ b/recipes/bioconductor-flowmap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowmap/meta.yaml b/recipes/bioconductor-flowmap/meta.yaml index 7f860ad0d1a86..3786b1d57bc80 100644 --- a/recipes/bioconductor-flowmap/meta.yaml +++ b/recipes/bioconductor-flowmap/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "flowMap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0b7c51d7d4c2570f0d54ad6b761bae25b6a7ab75d8807d53d10ef0b8aabd813a + md5: cab65dfb9ca11db06ec0f2ea9dfb75e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr requirements: host: - 'r-abind >=1.4.0' @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'flowMap quantifies the similarity of cell populations across multiple flow cytometry samples using a nonparametric multivariate statistical test. The method is able to map cell populations of different size, shape, and proportion across multiple flow cytometry samples. The algorithm can be incorporate in any flow cytometry work flow that requires accurat quantification of similarity between cell populations.' extra: identifiers: - biotools:flowmap - doi:10.1002/cyto.a.22735 + parent_recipe: + name: bioconductor-flowmap + path: recipes/bioconductor-flowmap + version: 1.18.0 + diff --git a/recipes/bioconductor-flowmatch/build.sh b/recipes/bioconductor-flowmatch/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowmatch/build.sh +++ b/recipes/bioconductor-flowmatch/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowmatch/meta.yaml b/recipes/bioconductor-flowmatch/meta.yaml index a577f7b177d5f..b607b5d18ebb0 100644 --- a/recipes/bioconductor-flowmatch/meta.yaml +++ b/recipes/bioconductor-flowmatch/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "flowMatch" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 85065fbe032498519f789fe5dc82422de595e720ff99c01124875d772f96ced7 + md5: 7d6d3eea6d0f74416629b825d8bcd6a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: healthyFlowData requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.11.0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - 'r-rcpp >=0.11.0' build: @@ -35,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Matching cell populations and building meta-clusters and templates from a collection of FC samples.' extra: identifiers: - biotools:flowmatch - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flowmatch + path: recipes/bioconductor-flowmatch + version: 1.16.0 + diff --git a/recipes/bioconductor-flowmeans/build.sh b/recipes/bioconductor-flowmeans/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowmeans/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowmeans/meta.yaml b/recipes/bioconductor-flowmeans/meta.yaml new file mode 100644 index 0000000000000..a064c09aab51b --- /dev/null +++ b/recipes/bioconductor-flowmeans/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.42.0" %} +{% set name = "flowMeans" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 19389036944c6237feb203f969b5fcc6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-feature + - r-rrcov + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-feature + - r-rrcov +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Identifies cell populations in Flow Cytometry data using non-parametric clustering and segmented-regression-based change point detection. Note: R 2.11.0 or newer is required.' + diff --git a/recipes/bioconductor-flowmerge/build.sh b/recipes/bioconductor-flowmerge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowmerge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowmerge/meta.yaml b/recipes/bioconductor-flowmerge/meta.yaml new file mode 100644 index 0000000000000..cfc207caac432 --- /dev/null +++ b/recipes/bioconductor-flowmerge/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "2.30.0" %} +{% set name = "flowMerge" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2d009505f7e93f75d8e01843b63b889d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-feature + - r-foreach + - r-rrcov + - r-snow + run: + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-feature + - r-foreach + - r-rrcov + - r-snow +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Merging of mixture components for model-based automated gating of flow cytometry data using the flowClust framework. Note: users should have a working copy of flowClust 2.0 installed.' + diff --git a/recipes/bioconductor-flowpeaks/build.sh b/recipes/bioconductor-flowpeaks/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowpeaks/build.sh +++ b/recipes/bioconductor-flowpeaks/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowpeaks/meta.yaml b/recipes/bioconductor-flowpeaks/meta.yaml index 81c17bbd5261a..9a875598f8c49 100644 --- a/recipes/bioconductor-flowpeaks/meta.yaml +++ b/recipes/bioconductor-flowpeaks/meta.yaml @@ -1,39 +1,43 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "flowPeaks" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8db483f53772b770a424b7d570a6b13aa468b70170463f1b9aae7e3c96628e81 + md5: 17ad7d32c56c3c0482baff1230607047 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# SystemRequirements: gsl requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - make host: - r-base - - openblas run: - r-base - - openblas + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-1.0 summary: 'A fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.' extra: identifiers: - biotools:flowpeaks + parent_recipe: + name: bioconductor-flowpeaks + path: recipes/bioconductor-flowpeaks + version: 1.26.0 + diff --git a/recipes/bioconductor-flowploidy/build.sh b/recipes/bioconductor-flowploidy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowploidy/build.sh +++ b/recipes/bioconductor-flowploidy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowploidy/meta.yaml b/recipes/bioconductor-flowploidy/meta.yaml index edb3ec45ca667..cc638d088ec0c 100644 --- a/recipes/bioconductor-flowploidy/meta.yaml +++ b/recipes/bioconductor-flowploidy/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "flowPloidy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8e821b2d364401915e86ba3cfdced6f65373b7e1edd8e5a6aa6e08f211e1dcb3 + md5: 4866ee71a93962a34151e674a0a26895 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: flowPloidyData, testthat requirements: host: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-car - r-catools @@ -27,7 +29,7 @@ requirements: - r-rmarkdown - r-shiny run: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-car - r-catools @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Determine sample ploidy via flow cytometry histogram analysis. Reads Flow Cytometry Standard (FCS) files via the flowCore bioconductor package, and provides functions for determining the DNA ploidy of samples based on internal standards.' extra: identifiers: - biotools:flowploidy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-flowploidy + path: recipes/bioconductor-flowploidy + version: 1.6.0 + diff --git a/recipes/bioconductor-flowploidydata/meta.yaml b/recipes/bioconductor-flowploidydata/meta.yaml new file mode 100644 index 0000000000000..3ab1f2f651adf --- /dev/null +++ b/recipes/bioconductor-flowploidydata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.8.0" %} +{% set name = "flowPloidyData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 86881aa99d32cc1ce20304591cb599ab +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, flowCore +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'A collection of raw flow cytometry data for use in vignettes for the flowPloidy package.' + diff --git a/recipes/bioconductor-flowploidydata/post-link.sh b/recipes/bioconductor-flowploidydata/post-link.sh new file mode 100644 index 0000000000000..5a405567262a9 --- /dev/null +++ b/recipes/bioconductor-flowploidydata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="flowPloidyData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowPloidyData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowPloidyData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowploidydata/bioconductor-flowploidydata_1.8.0_src_all.tar.gz" +) +MD5="86881aa99d32cc1ce20304591cb599ab" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowploidydata/pre-unlink.sh b/recipes/bioconductor-flowploidydata/pre-unlink.sh new file mode 100644 index 0000000000000..8e45c7e3c1be1 --- /dev/null +++ b/recipes/bioconductor-flowploidydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ flowPloidyData diff --git a/recipes/bioconductor-flowplots/build.sh b/recipes/bioconductor-flowplots/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowplots/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowplots/meta.yaml b/recipes/bioconductor-flowplots/meta.yaml new file mode 100644 index 0000000000000..48262ebdb0b63 --- /dev/null +++ b/recipes/bioconductor-flowplots/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.30.0" %} +{% set name = "flowPlots" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 54e171f83d6699850b8149ebbc75e81e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: vcd +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Graphical displays with embedded statistical tests for gated ICS flow cytometry data, and a data class which stores "stacked" data and has methods for computing summary measures on stacked data, such as marginal and polyfunctional degree data.' + diff --git a/recipes/bioconductor-flowqb/build.sh b/recipes/bioconductor-flowqb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowqb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowqb/meta.yaml b/recipes/bioconductor-flowqb/meta.yaml new file mode 100644 index 0000000000000..847fe2ebd2eca --- /dev/null +++ b/recipes/bioconductor-flowqb/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.10.0" %} +{% set name = "flowQB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 128eaa3e9d221b47f45afcefd7577139 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: flowQBData, FlowRepositoryR, xlsx, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-extremevalues + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-extremevalues +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'flowQB is a fully automated R Bioconductor package to calculate automatically the detector efficiency (Q), optical background (B) and intrinsic CV of the beads.' + diff --git a/recipes/bioconductor-flowqbdata/meta.yaml b/recipes/bioconductor-flowqbdata/meta.yaml new file mode 100644 index 0000000000000..2e4b39b9e1ecb --- /dev/null +++ b/recipes/bioconductor-flowqbdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.8.0" %} +{% set name = "flowQBData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4692d5e5b2c714b9b1d55636c65b90d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: flowQB +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'The flowQBData package provides data files used as examples and for testing of the software provided in the flowQB package.' + diff --git a/recipes/bioconductor-flowqbdata/post-link.sh b/recipes/bioconductor-flowqbdata/post-link.sh new file mode 100644 index 0000000000000..13b3ba3f63116 --- /dev/null +++ b/recipes/bioconductor-flowqbdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="flowQBData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowQBData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowQBData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowqbdata/bioconductor-flowqbdata_1.8.0_src_all.tar.gz" +) +MD5="4692d5e5b2c714b9b1d55636c65b90d4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowqbdata/pre-unlink.sh b/recipes/bioconductor-flowqbdata/pre-unlink.sh new file mode 100644 index 0000000000000..c2d85cc1fc7e9 --- /dev/null +++ b/recipes/bioconductor-flowqbdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ flowQBData diff --git a/recipes/bioconductor-flowrepositoryr/build.sh b/recipes/bioconductor-flowrepositoryr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowrepositoryr/build.sh +++ b/recipes/bioconductor-flowrepositoryr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowrepositoryr/meta.yaml b/recipes/bioconductor-flowrepositoryr/meta.yaml index 549b4e6b3d21d..6a0dcbee43123 100644 --- a/recipes/bioconductor-flowrepositoryr/meta.yaml +++ b/recipes/bioconductor-flowrepositoryr/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "FlowRepositoryR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 085c20352fb3f41454cc211d377dfce3dc0f898b46c00a794db6e187a3d543bf + md5: 93c8d4c92bc54a491809e12f17a42ebc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, flowCore, methods requirements: host: - r-base @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides an interface to search and download data and annotations from FlowRepository (flowrepository.org). It uses the FlowRepository programming interface to communicate with a FlowRepository server.' extra: identifiers: - biotools:flowrepositoryr - doi:10.1002/cyto.a.22106 + parent_recipe: + name: bioconductor-flowrepositoryr + path: recipes/bioconductor-flowrepositoryr + version: 1.12.0 + diff --git a/recipes/bioconductor-flowsom/build.sh b/recipes/bioconductor-flowsom/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowsom/build.sh +++ b/recipes/bioconductor-flowsom/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowsom/meta.yaml b/recipes/bioconductor-flowsom/meta.yaml index 4c7a1e5e8175e..9b8aab381b48c 100644 --- a/recipes/bioconductor-flowsom/meta.yaml +++ b/recipes/bioconductor-flowsom/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "FlowSOM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 93f5ca235048ae643078ac61b56bc5cbe84628806847f40188178b094f2e4efe + md5: fc800e5ec3c9388466990a9ab44107bc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowutils >=1.44.0,<1.46.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowutils >=1.46.0,<1.47.0' - r-base - r-igraph - r-tsne - r-xml run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowutils >=1.44.0,<1.46.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowutils >=1.46.0,<1.47.0' - r-base - r-igraph - r-tsne @@ -42,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'FlowSOM offers visualization options for cytometry data, by using Self-Organizing Map clustering and Minimal Spanning Trees.' extra: identifiers: - biotools:flowsom - doi:10.1002/cyto.a.22625 + parent_recipe: + name: bioconductor-flowsom + path: recipes/bioconductor-flowsom + version: 1.12.0 + diff --git a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml index 36a4db41c6c9d..49a0bcb7ee331 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/meta.yaml +++ b/recipes/bioconductor-flowsorted.blood.450k/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "FlowSorted.Blood.450k" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c7c9d339d7e17f0569d7ea8dfefc4936f2506308c52e9516b35a57db6588ac75 + md5: de53e97b7b4dd6b5930d22cef0cf7a64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Raw data objects for the Illumina 450k DNA methylation microarrays, and an object depicting which CpGs on the array are associated with cell type.' - +extra: + parent_recipe: + name: bioconductor-flowsorted.blood.450k + path: recipes/bioconductor-flowsorted.blood.450k + version: 1.18.0 diff --git a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh index 5894150841ea4..00b542a759cb3 100644 --- a/recipes/bioconductor-flowsorted.blood.450k/post-link.sh +++ b/recipes/bioconductor-flowsorted.blood.450k/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="FlowSorted.Blood.450k_1.18.0.tar.gz" +FN="FlowSorted.Blood.450k_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/FlowSorted.Blood.450k_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.Blood.450k_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.Blood.450k_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.450k/bioconductor-flowsorted.blood.450k_1.20.0_src_all.tar.gz" ) -MD5="1d76f19de113f7b3fe1c12b0f7e63c39" +MD5="de53e97b7b4dd6b5930d22cef0cf7a64" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-flowsorted.blood.epic/meta.yaml b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml new file mode 100644 index 0000000000000..ac8dbc36d373b --- /dev/null +++ b/recipes/bioconductor-flowsorted.blood.epic/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "FlowSorted.Blood.EPIC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8d567155aab1d5b96ad468d0f0632acd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, EpiDISH, FlowSorted.Blood.450k(>= 1.0.1), FlowSorted.CordBlood.450k, FlowSorted.CordBloodNorway.450k, testthat, IlluminaHumanMethylation450kmanifest(>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19(>= 0.2.1), IlluminaHumanMethylationEPICanno.ilm10b2.hg19 +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-nlme + - r-quadprog + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-nlme + - r-quadprog + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Raw data objects to be used for blood cell proportion estimation in minfi and similar packages. The FlowSorted.Blood.EPIC object is based in samples assayed by Brock Christensen and colleagues; for details see Salas et al. 2018. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE110554.' + diff --git a/recipes/bioconductor-flowsorted.blood.epic/post-link.sh b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh new file mode 100644 index 0000000000000..73fbbc3d3ebae --- /dev/null +++ b/recipes/bioconductor-flowsorted.blood.epic/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FlowSorted.Blood.EPIC_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.Blood.EPIC_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.Blood.EPIC_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.blood.epic/bioconductor-flowsorted.blood.epic_1.0.0_src_all.tar.gz" +) +MD5="8d567155aab1d5b96ad468d0f0632acd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowsorted.blood.epic/pre-unlink.sh b/recipes/bioconductor-flowsorted.blood.epic/pre-unlink.sh new file mode 100644 index 0000000000000..f3e42914b0f6f --- /dev/null +++ b/recipes/bioconductor-flowsorted.blood.epic/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FlowSorted.Blood.EPIC diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml new file mode 100644 index 0000000000000..6b875dcec9758 --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordblood.450k/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.10.0" %} +{% set name = "FlowSorted.CordBlood.450k" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5a049ecac95e4b77ea0d497838edb2e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Raw data objects to be used for cord blood cell proportion estimation in minfi.' + diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh new file mode 100644 index 0000000000000..1c3e500ac45ed --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordblood.450k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FlowSorted.CordBlood.450k_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.CordBlood.450k_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.CordBlood.450k_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordblood.450k/bioconductor-flowsorted.cordblood.450k_1.10.0_src_all.tar.gz" +) +MD5="5a049ecac95e4b77ea0d497838edb2e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowsorted.cordblood.450k/pre-unlink.sh b/recipes/bioconductor-flowsorted.cordblood.450k/pre-unlink.sh new file mode 100644 index 0000000000000..45fac993dd418 --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordblood.450k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FlowSorted.CordBlood.450k diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml new file mode 100644 index 0000000000000..6153184cdba8c --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.8.0" %} +{% set name = "FlowSorted.CordBloodNorway.450k" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f8a375e9ed900e593e944cbd95f13750 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Raw data objects for the Illumina 450k DNA methylation microarrays, for cell type composition estimation.' + diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh new file mode 100644 index 0000000000000..a223416d99d8e --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.CordBloodNorway.450k_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.cordbloodnorway.450k/bioconductor-flowsorted.cordbloodnorway.450k_1.8.0_src_all.tar.gz" +) +MD5="f8a375e9ed900e593e944cbd95f13750" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowsorted.cordbloodnorway.450k/pre-unlink.sh b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/pre-unlink.sh new file mode 100644 index 0000000000000..25ccb1b7c9969 --- /dev/null +++ b/recipes/bioconductor-flowsorted.cordbloodnorway.450k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FlowSorted.CordBloodNorway.450k diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml new file mode 100644 index 0000000000000..8ae27298dad6b --- /dev/null +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "FlowSorted.DLPFC.450k" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de071e70f511a405aad3ee9b3196fd43 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Raw data objects for the Illumina 450k DNA methylation microarrays.' + diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh new file mode 100644 index 0000000000000..9c455116de7f5 --- /dev/null +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FlowSorted.DLPFC.450k_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FlowSorted.DLPFC.450k_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/FlowSorted.DLPFC.450k_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowsorted.dlpfc.450k/bioconductor-flowsorted.dlpfc.450k_1.18.0_src_all.tar.gz" +) +MD5="de071e70f511a405aad3ee9b3196fd43" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowsorted.dlpfc.450k/pre-unlink.sh b/recipes/bioconductor-flowsorted.dlpfc.450k/pre-unlink.sh new file mode 100644 index 0000000000000..509bc9e05e2e5 --- /dev/null +++ b/recipes/bioconductor-flowsorted.dlpfc.450k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FlowSorted.DLPFC.450k diff --git a/recipes/bioconductor-flowstats/build.sh b/recipes/bioconductor-flowstats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowstats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowstats/meta.yaml b/recipes/bioconductor-flowstats/meta.yaml new file mode 100644 index 0000000000000..13e552a244656 --- /dev/null +++ b/recipes/bioconductor-flowstats/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "3.40.0" %} +{% set name = "flowStats" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1d95d4729aafe8f21e32289373ff1aa3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xtable +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - r-base + - r-cluster + - 'r-fda >=2.2.6' + - r-kernsmooth + - r-ks + - r-lattice + - r-mass + - r-rcolorbrewer + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - r-base + - r-cluster + - 'r-fda >=2.2.6' + - r-kernsmooth + - r-ks + - r-lattice + - r-mass + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Methods and functionality to analyse flow data that is beyond the basic infrastructure provided by the flowCore package.' + diff --git a/recipes/bioconductor-flowtime/build.sh b/recipes/bioconductor-flowtime/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowtime/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowtime/meta.yaml b/recipes/bioconductor-flowtime/meta.yaml new file mode 100644 index 0000000000000..fd10d7533da6c --- /dev/null +++ b/recipes/bioconductor-flowtime/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.6.0" %} +{% set name = "flowTime" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6dc8563724ec85842899e6784f515be0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, flowViz, ggplot2, BiocGenerics, moments, stats +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-plyr + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package was developed for analysis of both dynamic and steady state experiments examining the function of gene regulatory networks in yeast (strain W303) expressing fluorescent reporter proteins using a BD Accuri C6 and SORP cytometers. However, the functions are for the most part general and may be adapted for analysis of other organisms using other flow cytometers. Functions in this package facilitate the annotation of flow cytometry data with experimental metadata, as is requisite for dissemination and general ease-of-use. Functions for creating, saving and loading gate sets are also included. In the past, we have typically generated summary statistics for each flowset for each timepoint and then annotated and analyzed these summary statistics. This method loses a great deal of the power that comes from the large amounts of individual cell data generated in flow cytometry, by essentially collapsing this data into a bulk measurement after subsetting. In addition to these summary functions, this package also contains functions to facilitate annotation and analysis of steady-state or time-lapse data utilizing all of the data collected from the thousands of individual cells in each sample.' + diff --git a/recipes/bioconductor-flowtrans/build.sh b/recipes/bioconductor-flowtrans/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowtrans/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowtrans/meta.yaml b/recipes/bioconductor-flowtrans/meta.yaml new file mode 100644 index 0000000000000..33db22b62d5e4 --- /dev/null +++ b/recipes/bioconductor-flowtrans/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.34.0" %} +{% set name = "flowTrans" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b5ebb0150ba77abab998b93e3a5cb255 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + run: + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Profile maximum likelihood estimation of parameters for flow cytometry data transformations.' + diff --git a/recipes/bioconductor-flowtype/build.sh b/recipes/bioconductor-flowtype/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowtype/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowtype/meta.yaml b/recipes/bioconductor-flowtype/meta.yaml new file mode 100644 index 0000000000000..ead499e2172fc --- /dev/null +++ b/recipes/bioconductor-flowtype/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "2.20.0" %} +{% set name = "flowType" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 75344927b4bf183166789555a40a2319 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: xtable +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowmeans >=1.42.0,<1.43.0' + - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - r-base + - 'r-bh >=1.51.0-3' + - 'r-rcpp >=0.10.4' + - r-rrcov + - r-sfsmisc + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowmeans >=1.42.0,<1.43.0' + - 'bioconductor-flowmerge >=2.30.0,<2.31.0' + - r-base + - 'r-bh >=1.51.0-3' + - 'r-rcpp >=0.10.4' + - r-rrcov + - r-sfsmisc + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Phenotyping Flow Cytometry Assays using multidimentional expansion of single dimentional partitions.' + diff --git a/recipes/bioconductor-flowutils/build.sh b/recipes/bioconductor-flowutils/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowutils/build.sh +++ b/recipes/bioconductor-flowutils/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowutils/meta.yaml b/recipes/bioconductor-flowutils/meta.yaml index 8a849f5f815df..03ff960d6df9a 100644 --- a/recipes/bioconductor-flowutils/meta.yaml +++ b/recipes/bioconductor-flowutils/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "flowUtils" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a8ad6718efcdf2eebef99632f0815eb9c58f2afef169edacde4416e301f4eba2 + md5: 78d2192acdbf334af073d596172d403d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: gatingMLData requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-corpcor - r-runit - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-corpcor - r-runit @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides utilities for flow cytometry data.' extra: identifiers: - biotools:flowutils - doi:10.1186/1471-2105-10-145 + parent_recipe: + name: bioconductor-flowutils + path: recipes/bioconductor-flowutils + version: 1.44.0 + diff --git a/recipes/bioconductor-flowviz/build.sh b/recipes/bioconductor-flowviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowviz/build.sh +++ b/recipes/bioconductor-flowviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowviz/meta.yaml b/recipes/bioconductor-flowviz/meta.yaml index d2a05ed07f30a..6d79bdce4ae86 100644 --- a/recipes/bioconductor-flowviz/meta.yaml +++ b/recipes/bioconductor-flowviz/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "flowViz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 82dae08a9eb73f4468e6303627764f1a6b616f8a17d166ae9b75ada1f1459bca + md5: 9d2171980c5a0fb9aec05c807e797e2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: colorspace, flowStats,knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-hexbin - r-idpmisc @@ -29,8 +31,8 @@ requirements: - r-mass - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' - r-base - r-hexbin - r-idpmisc @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides visualization tools for flow cytometry data.' extra: identifiers: - biotools:flowviz - doi:10.1093/bioinformatics/btn021 + parent_recipe: + name: bioconductor-flowviz + path: recipes/bioconductor-flowviz + version: 1.44.0 + diff --git a/recipes/bioconductor-flowvs/build.sh b/recipes/bioconductor-flowvs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-flowvs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowvs/meta.yaml b/recipes/bioconductor-flowvs/meta.yaml new file mode 100644 index 0000000000000..7929193779e78 --- /dev/null +++ b/recipes/bioconductor-flowvs/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.14.0" %} +{% set name = "flowVS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11621c551d9f8e4688c0861206ee2564 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, vsn, +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Per-channel variance stabilization from a collection of flow cytometry samples by Bertlett test for homogeneity of variances. The approach is applicable to microarrays data as well.' + diff --git a/recipes/bioconductor-flowworkspace/build.sh b/recipes/bioconductor-flowworkspace/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-flowworkspace/build.sh +++ b/recipes/bioconductor-flowworkspace/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-flowworkspace/meta.yaml b/recipes/bioconductor-flowworkspace/meta.yaml index 5429d35930cff..c71b6f0ed7a83 100644 --- a/recipes/bioconductor-flowworkspace/meta.yaml +++ b/recipes/bioconductor-flowworkspace/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "3.28.2" %} +{% set version = "3.30.1" %} {% set name = "flowWorkspace" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 64f60df146a17b9ef0f4935a3db3fcabc31820aa4da61fc7408fb1c0d19a46a8 + md5: 60dc049334c3137bd95abfc28c87f366 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, flowWorkspaceData, knitr, ggcyto, parallel +# SystemRequirements: xml2, GNU make, C++11 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-cytolib >=1.2.0,<1.4.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cytolib >=1.4.0,<1.5.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' - r-base - 'r-bh >=1.62.0-1' - r-data.table @@ -42,16 +44,16 @@ requirements: - r-stringr - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-cytolib >=1.2.0,<1.4.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rprotobuflib >=1.2.0,<1.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cytolib >=1.4.0,<1.5.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rprotobuflib >=1.4.0,<1.5.0' - r-base - 'r-bh >=1.62.0-1' - r-data.table @@ -74,10 +76,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.' extra: identifiers: - biotools:flowworkspace - doi:10.1186/1471-2105-13-252 + parent_recipe: + name: bioconductor-flowworkspace + path: recipes/bioconductor-flowworkspace + version: 3.28.2 + diff --git a/recipes/bioconductor-flowworkspacedata/meta.yaml b/recipes/bioconductor-flowworkspacedata/meta.yaml new file mode 100644 index 0000000000000..5022171efb946 --- /dev/null +++ b/recipes/bioconductor-flowworkspacedata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.18.0" %} +{% set name = "flowWorkspaceData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 67cd786b29a27ccdbb1b1c423bfce42d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'The necessary external data to run the flowWorkspace and openCyto vignette is found in this package.' + diff --git a/recipes/bioconductor-flowworkspacedata/post-link.sh b/recipes/bioconductor-flowworkspacedata/post-link.sh new file mode 100644 index 0000000000000..fbc81bdd768dd --- /dev/null +++ b/recipes/bioconductor-flowworkspacedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="flowWorkspaceData_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/flowWorkspaceData_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/flowWorkspaceData_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-flowworkspacedata/bioconductor-flowworkspacedata_2.18.0_src_all.tar.gz" +) +MD5="67cd786b29a27ccdbb1b1c423bfce42d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-flowworkspacedata/pre-unlink.sh b/recipes/bioconductor-flowworkspacedata/pre-unlink.sh new file mode 100644 index 0000000000000..20f21deb52888 --- /dev/null +++ b/recipes/bioconductor-flowworkspacedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ flowWorkspaceData diff --git a/recipes/bioconductor-fly.db0/meta.yaml b/recipes/bioconductor-fly.db0/meta.yaml new file mode 100644 index 0000000000000..4d3a76998d629 --- /dev/null +++ b/recipes/bioconductor-fly.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "fly.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5158fc82a6d73d7ca2f20010e7f18149 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for fly, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-fly.db0/post-link.sh b/recipes/bioconductor-fly.db0/post-link.sh new file mode 100644 index 0000000000000..2bc220aa32ed5 --- /dev/null +++ b/recipes/bioconductor-fly.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="fly.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/fly.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/fly.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-fly.db0/bioconductor-fly.db0_3.7.1_src_all.tar.gz" +) +MD5="5158fc82a6d73d7ca2f20010e7f18149" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-fly.db0/pre-unlink.sh b/recipes/bioconductor-fly.db0/pre-unlink.sh new file mode 100644 index 0000000000000..a43344c23b868 --- /dev/null +++ b/recipes/bioconductor-fly.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ fly.db0 diff --git a/recipes/bioconductor-fmcsr/build.sh b/recipes/bioconductor-fmcsr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-fmcsr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fmcsr/meta.yaml b/recipes/bioconductor-fmcsr/meta.yaml new file mode 100644 index 0000000000000..53378a4e42a4f --- /dev/null +++ b/recipes/bioconductor-fmcsr/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.24.0" %} +{% set name = "fmcsR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 62865bc0fa2c4ac4a6f437220ff05e8e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, knitcitations, knitrBootstrap +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - r-runit + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - r-runit + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The fmcsR package introduces an efficient maximum common substructure (MCS) algorithms combined with a novel matching strategy that allows for atom and/or bond mismatches in the substructures shared among two small molecules. The resulting flexible MCSs (FMCSs) are often larger than strict MCSs, resulting in the identification of more common features in their source structures, as well as a higher sensitivity in finding compounds with weak structural similarities. The fmcsR package provides several utilities to use the FMCS algorithm for pairwise compound comparisons, structure similarity searching and clustering.' + diff --git a/recipes/bioconductor-focalcall/build.sh b/recipes/bioconductor-focalcall/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-focalcall/build.sh +++ b/recipes/bioconductor-focalcall/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-focalcall/meta.yaml b/recipes/bioconductor-focalcall/meta.yaml index 64a3a08bae4b7..5c443072164be 100644 --- a/recipes/bioconductor-focalcall/meta.yaml +++ b/recipes/bioconductor-focalcall/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "focalCall" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: db49bbc1b715ca304f5dfa2429c1e736d410d9193735d2d91f79be220bcd96aa + md5: b19052a468311959ee34805929344404 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' - r-base run: - - 'bioconductor-cghcall >=2.42.0,<2.44.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Detection of genomic focal aberrations in high-resolution DNA copy number data' extra: identifiers: - biotools:focalcall - doi:10.4137/cin.s19519 + parent_recipe: + name: bioconductor-focalcall + path: recipes/bioconductor-focalcall + version: 1.14.0 + diff --git a/recipes/bioconductor-foldgo/build.sh b/recipes/bioconductor-foldgo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-foldgo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-foldgo/meta.yaml b/recipes/bioconductor-foldgo/meta.yaml new file mode 100644 index 0000000000000..dbcbdc696caa6 --- /dev/null +++ b/recipes/bioconductor-foldgo/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.1" %} +{% set name = "FoldGO" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 48dac3b597db9819387033f7f5030e60 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, devtools, kableExtra +requirements: + host: + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - 'r-tidyr >=0.8.0' + run: + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - 'r-tidyr >=0.8.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'FoldGO is a package designed to annotate gene sets derived from expression experiments and identify fold-change-specific GO terms.' + diff --git a/recipes/bioconductor-fourcseq/build.sh b/recipes/bioconductor-fourcseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-fourcseq/build.sh +++ b/recipes/bioconductor-fourcseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-fourcseq/conda_build_config.yaml b/recipes/bioconductor-fourcseq/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-fourcseq/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-fourcseq/meta.yaml b/recipes/bioconductor-fourcseq/meta.yaml index 297d31995c898..e2249f0882658 100644 --- a/recipes/bioconductor-fourcseq/meta.yaml +++ b/recipes/bioconductor-fourcseq/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "FourCSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 662cc98cd7609dfbd5a27abb608a0b9e860d3a255bb70657ce1bce8f5167802c + md5: 53c2a29adaf6ec73c43ccb06f633a330 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, TxDb.Dmelanogaster.UCSC.dm3.ensGene requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-fda - r-ggplot2 @@ -35,15 +37,15 @@ requirements: - r-matrix - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-fda - r-ggplot2 @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'FourCSeq is an R package dedicated to the analysis of (multiplexed) 4C sequencing data. The package provides a pipeline to detect specific interactions between DNA elements and identify differential interactions between conditions. The statistical analysis in R starts with individual bam files for each sample as inputs. To obtain these files, the package contains a python script (extdata/python/demultiplex.py) to demultiplex libraries and trim off primer sequences. With a standard alignment software the required bam files can be then be generated.' extra: identifiers: - biotools:fourcseq + parent_recipe: + name: bioconductor-fourcseq + path: recipes/bioconductor-fourcseq + version: 1.14.0 + diff --git a/recipes/bioconductor-frgepistasis/build.sh b/recipes/bioconductor-frgepistasis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-frgepistasis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-frgepistasis/meta.yaml b/recipes/bioconductor-frgepistasis/meta.yaml new file mode 100644 index 0000000000000..d8d7128bfa4c9 --- /dev/null +++ b/recipes/bioconductor-frgepistasis/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.18.0" %} +{% set name = "FRGEpistasis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 69714b75285540f4339872f28b55ca84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-fda + - r-mass + run: + - r-base + - r-fda + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A Tool for Epistasis Analysis Based on Functional Regression Model' + diff --git a/recipes/bioconductor-frma/build.sh b/recipes/bioconductor-frma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-frma/build.sh +++ b/recipes/bioconductor-frma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-frma/conda_build_config.yaml b/recipes/bioconductor-frma/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-frma/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-frma/meta.yaml b/recipes/bioconductor-frma/meta.yaml index 8266a972793cd..3daf0fbbc7060 100644 --- a/recipes/bioconductor-frma/meta.yaml +++ b/recipes/bioconductor-frma/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "frma" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5ef83662a1d9afb45cd41edb14628b89f6d6daf14f33c4406ee22beb1c6231dd + md5: b37d6b5a88ba58da47c33d6d7f09b93a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-mass run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-mass @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Preprocessing and analysis for single microarrays and microarray batches.' extra: identifiers: - biotools:frma + parent_recipe: + name: bioconductor-frma + path: recipes/bioconductor-frma + version: 1.32.0 + diff --git a/recipes/bioconductor-frmaexampledata/meta.yaml b/recipes/bioconductor-frmaexampledata/meta.yaml new file mode 100644 index 0000000000000..e87a5eab3f57b --- /dev/null +++ b/recipes/bioconductor-frmaexampledata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "frmaExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d4faf0fddd05a0522bb832c1569b052d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data files used by the examples in frma and frmaTools packages' + diff --git a/recipes/bioconductor-frmaexampledata/post-link.sh b/recipes/bioconductor-frmaexampledata/post-link.sh new file mode 100644 index 0000000000000..d1796dbd5fd69 --- /dev/null +++ b/recipes/bioconductor-frmaexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="frmaExampleData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/frmaExampleData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/frmaExampleData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-frmaexampledata/bioconductor-frmaexampledata_1.18.0_src_all.tar.gz" +) +MD5="d4faf0fddd05a0522bb832c1569b052d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-frmaexampledata/pre-unlink.sh b/recipes/bioconductor-frmaexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..75530530045d5 --- /dev/null +++ b/recipes/bioconductor-frmaexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ frmaExampleData diff --git a/recipes/bioconductor-frmatools/build.sh b/recipes/bioconductor-frmatools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-frmatools/build.sh +++ b/recipes/bioconductor-frmatools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-frmatools/conda_build_config.yaml b/recipes/bioconductor-frmatools/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-frmatools/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-frmatools/meta.yaml b/recipes/bioconductor-frmatools/meta.yaml index 4a3a1adf39c31..0f695c23ba05b 100644 --- a/recipes/bioconductor-frmatools/meta.yaml +++ b/recipes/bioconductor-frmatools/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "frmaTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 83a5daa041637f4d20320f9950e9ff063196ba18d477c7bd529e769b25c3bfac + md5: a62d9d619c2495c994c3ef00f8d44708 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: oligo, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, frma, affyPLM, hgu133aprobe, hgu133atagprobe, hgu133plus2probe, hgu133acdf, hgu133atagcdf, hgu133plus2cdf, hgu133afrmavecs, frmaExampleData requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Tools for advanced use of the frma package.' extra: identifiers: - biotools:frmatools + parent_recipe: + name: bioconductor-frmatools + path: recipes/bioconductor-frmatools + version: 1.32.0 + diff --git a/recipes/bioconductor-funchip/build.sh b/recipes/bioconductor-funchip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-funchip/build.sh +++ b/recipes/bioconductor-funchip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-funchip/meta.yaml b/recipes/bioconductor-funchip/meta.yaml index c6d062d583772..6037f7f60a750 100644 --- a/recipes/bioconductor-funchip/meta.yaml +++ b/recipes/bioconductor-funchip/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "FunChIP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 70dd6f3e1087b69c47731a95805791f6bfba7cef2e786ab43efb0986fc284b16 + md5: c8c104f2587cb6dad1645d758e3ef9f2 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-doparallel - r-fda @@ -30,10 +30,10 @@ requirements: - r-rcpp - r-shiny run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-doparallel - r-fda @@ -49,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Preprocessing and smoothing of ChIP-Seq peaks and efficient implementation of the k-mean alignment algorithm to classify them.' extra: identifiers: - biotools:funchip - doi:10.1093/bioinformatics/btx201 + parent_recipe: + name: bioconductor-funchip + path: recipes/bioconductor-funchip + version: 1.6.0 + diff --git a/recipes/bioconductor-funcisnp.data/meta.yaml b/recipes/bioconductor-funcisnp.data/meta.yaml new file mode 100644 index 0000000000000..f5f1263acf769 --- /dev/null +++ b/recipes/bioconductor-funcisnp.data/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.18.0" %} +{% set name = "FunciSNP.data" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d92989e8bb3e92138d3a597266fd0770 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + run: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Data sets needed for FunciSNP to integrate information from GWAS, 1000genomes and chromatin feature, in order to identify functional SNP in coding or non-coding regions.' + diff --git a/recipes/bioconductor-funcisnp.data/post-link.sh b/recipes/bioconductor-funcisnp.data/post-link.sh new file mode 100644 index 0000000000000..5d620a1bde67d --- /dev/null +++ b/recipes/bioconductor-funcisnp.data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="FunciSNP.data_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/FunciSNP.data_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/FunciSNP.data_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-funcisnp.data/bioconductor-funcisnp.data_1.18.0_src_all.tar.gz" +) +MD5="d92989e8bb3e92138d3a597266fd0770" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-funcisnp.data/pre-unlink.sh b/recipes/bioconductor-funcisnp.data/pre-unlink.sh new file mode 100644 index 0000000000000..8848b74c4b6b9 --- /dev/null +++ b/recipes/bioconductor-funcisnp.data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ FunciSNP.data diff --git a/recipes/bioconductor-funcisnp/build.sh b/recipes/bioconductor-funcisnp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-funcisnp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-funcisnp/meta.yaml b/recipes/bioconductor-funcisnp/meta.yaml new file mode 100644 index 0000000000000..4d3225458f8d2 --- /dev/null +++ b/recipes/bioconductor-funcisnp/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.26.0" %} +{% set name = "FunciSNP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e55399c304732cc26e706341e659018c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Hs.eg.db +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-funcisnp.data >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-ggplot2 >=0.9.0' + - r-plyr + - 'r-reshape >=0.8.4' + - r-scales + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-funcisnp.data >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-ggplot2 >=0.9.0' + - r-plyr + - 'r-reshape >=0.8.4' + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'FunciSNP integrates information from GWAS, 1000genomes and chromatin feature to identify functional SNP in coding or non-coding regions.' + diff --git a/recipes/bioconductor-funtoonorm/build.sh b/recipes/bioconductor-funtoonorm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-funtoonorm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-funtoonorm/meta.yaml b/recipes/bioconductor-funtoonorm/meta.yaml new file mode 100644 index 0000000000000..7d01724a1960a --- /dev/null +++ b/recipes/bioconductor-funtoonorm/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "funtooNorm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c580cc3077ad762b790f4ccbc1ca9de8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: prettydoc, minfiData, knitr, rmarkdown +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - r-matrixstats + - r-pls + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - r-matrixstats + - r-pls +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides a function to normalize Illumina Infinium Human Methylation 450 BeadChip (Illumina 450K), correcting for tissue and/or cell type.' + diff --git a/recipes/bioconductor-furrowseg/meta.yaml b/recipes/bioconductor-furrowseg/meta.yaml new file mode 100644 index 0000000000000..fcab9d0a4dfb8 --- /dev/null +++ b/recipes/bioconductor-furrowseg/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.10.0" %} +{% set name = "furrowSeg" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dc60909e3fe7d7b517d4aaa5693fbe83 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, ggplot2, knitr +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-abind + - r-base + - r-dplyr + - r-locfit + - r-tiff + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-abind + - r-base + - r-dplyr + - r-locfit + - r-tiff + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Image feature data and analysis codes for the Guglielmi, Barry et al. paper describing the application of an optogenetics tools to disrupt Drosophila embryo furrowing.' + diff --git a/recipes/bioconductor-furrowseg/post-link.sh b/recipes/bioconductor-furrowseg/post-link.sh new file mode 100644 index 0000000000000..1d398f03d3df9 --- /dev/null +++ b/recipes/bioconductor-furrowseg/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="furrowSeg_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/furrowSeg_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/furrowSeg_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-furrowseg/bioconductor-furrowseg_1.10.0_src_all.tar.gz" +) +MD5="dc60909e3fe7d7b517d4aaa5693fbe83" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-furrowseg/pre-unlink.sh b/recipes/bioconductor-furrowseg/pre-unlink.sh new file mode 100644 index 0000000000000..eaf6fa7cad276 --- /dev/null +++ b/recipes/bioconductor-furrowseg/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ furrowSeg diff --git a/recipes/bioconductor-ga4ghclient/build.sh b/recipes/bioconductor-ga4ghclient/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ga4ghclient/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ga4ghclient/meta.yaml b/recipes/bioconductor-ga4ghclient/meta.yaml new file mode 100644 index 0000000000000..41435097f8847 --- /dev/null +++ b/recipes/bioconductor-ga4ghclient/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "GA4GHclient" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f69a308636d5abd8d6c3e071e0182437 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationDbi, BiocStyle, DT, knitr, org.Hs.eg.db, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-dplyr + - r-httr + - r-jsonlite + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-dplyr + - r-httr + - r-jsonlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'GA4GHclient provides an easy way to access public data servers through Global Alliance for Genomics and Health (GA4GH) genomics API. It provides low-level access to GA4GH API and translates response data into Bioconductor-based class objects.' + diff --git a/recipes/bioconductor-ga4ghshiny/build.sh b/recipes/bioconductor-ga4ghshiny/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ga4ghshiny/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ga4ghshiny/meta.yaml b/recipes/bioconductor-ga4ghshiny/meta.yaml new file mode 100644 index 0000000000000..39a62032f93f3 --- /dev/null +++ b/recipes/bioconductor-ga4ghshiny/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.0" %} +{% set name = "GA4GHshiny" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5798bf389bc3818bb6508788039afce7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, org.Hs.eg.db, knitr, rmarkdown, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ga4ghclient >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-dt + - r-openxlsx + - r-purrr + - r-shiny + - r-shinyjs + - r-shinythemes + - r-tidyr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ga4ghclient >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-dt + - r-openxlsx + - r-purrr + - r-shiny + - r-shinyjs + - r-shinythemes + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'GA4GHshiny package provides an easy way to interact with data servers based on Global Alliance for Genomics and Health (GA4GH) genomics API through a Shiny application. It also integrates with Beacon Network.' + diff --git a/recipes/bioconductor-gaga/build.sh b/recipes/bioconductor-gaga/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gaga/build.sh +++ b/recipes/bioconductor-gaga/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gaga/meta.yaml b/recipes/bioconductor-gaga/meta.yaml index b93ff17147b05..5cb653540eaba 100644 --- a/recipes/bioconductor-gaga/meta.yaml +++ b/recipes/bioconductor-gaga/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "gaga" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4e2b1eb0cbb1b5ea9310c67acb4d117563fafb49a6e691ac9cc7a4c770bdd66e + md5: 02a50757de096f09c77607ef82c646b3 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - r-base - r-coda - r-mgcv run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' - r-base - r-coda - r-mgcv @@ -36,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Implements the GaGa model for high-throughput data analysis, including differential expression analysis, supervised gene clustering and classification. Additionally, it performs sequential sample size calculations using the GaGa and LNNGV models (the latter from EBarrays package).' extra: identifiers: - biotools:gaga - doi:10.1214/09-aoas244 + parent_recipe: + name: bioconductor-gaga + path: recipes/bioconductor-gaga + version: 2.26.0 + diff --git a/recipes/bioconductor-gage/build.sh b/recipes/bioconductor-gage/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gage/build.sh +++ b/recipes/bioconductor-gage/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gage/meta.yaml b/recipes/bioconductor-gage/meta.yaml index a39f359a1fcc1..03ae136a61bc4 100644 --- a/recipes/bioconductor-gage/meta.yaml +++ b/recipes/bioconductor-gage/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "gage" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c288e3e38d470edc6fe1e6c2dd7f65f101641256aed5c90d09eed2937cc76c48 + md5: 2f57d55ae9a703d93f8205f19e900c5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pathview, gageData, GO.db, org.Hs.eg.db, hgu133a.db, GSEABase, Rsamtools, GenomicAlignments, TxDb.Hsapiens.UCSC.hg19.knownGene, DESeq, DESeq2, edgeR, limma requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'GAGE is a published method for gene set (enrichment or GSEA) or pathway analysis. GAGE is generally applicable independent of microarray or RNA-Seq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity, and consistently achieves superior performance over other frequently used methods. In gage package, we provide functions for basic GAGE analysis, result processing and presentation. We have also built pipeline routines for of multiple GAGE analyses in a batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources/studies. In addition, we provide demo microarray data and commonly used gene set data based on KEGG pathways and GO terms. These funtions and data are also useful for gene set analysis using other methods.' extra: identifiers: - biotools:gage + parent_recipe: + name: bioconductor-gage + path: recipes/bioconductor-gage + version: 2.30.0 + diff --git a/recipes/bioconductor-gagedata/meta.yaml b/recipes/bioconductor-gagedata/meta.yaml index 3379e18da789f..72a3500f1b2b4 100644 --- a/recipes/bioconductor-gagedata/meta.yaml +++ b/recipes/bioconductor-gagedata/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "gageData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 324e57f4d685af00eb7892ecc418ce4e6cae3254e9d42d91639d57b28dc5ad1d + md5: d483527aa3d7520e62154c90057f7d23 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: gage, pathview, genefilter requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2.0)' summary: 'This is a supportive data package for the software package, gage. However, the data supplied here are also useful for gene set or pathway analysis or microarray data analysis in general. In this package, we provide two demo microarray dataset: GSE16873 (a breast cancer dataset from GEO) and BMP6 (originally published as an demo dataset for GAGE, also registered as GSE13604 in GEO). This package also includes commonly used gene set data based on KEGG pathways and GO terms for major research species, including human, mouse, rat and budding yeast. Mapping data between common gene IDs for budding yeast are also included.' - +extra: + parent_recipe: + name: bioconductor-gagedata + path: recipes/bioconductor-gagedata + version: 2.18.0 diff --git a/recipes/bioconductor-gagedata/post-link.sh b/recipes/bioconductor-gagedata/post-link.sh index 957670c2d0e97..c25427fe26941 100644 --- a/recipes/bioconductor-gagedata/post-link.sh +++ b/recipes/bioconductor-gagedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gageData_2.18.0.tar.gz" +FN="gageData_2.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/gageData_2.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/gageData_2.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gageData_2.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/gageData_2.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gagedata/bioconductor-gagedata_2.20.0_src_all.tar.gz" ) -MD5="1a08b3bb2a8944fa982488f998659c65" +MD5="d483527aa3d7520e62154c90057f7d23" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-gaggle/build.sh b/recipes/bioconductor-gaggle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gaggle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gaggle/meta.yaml b/recipes/bioconductor-gaggle/meta.yaml new file mode 100644 index 0000000000000..b5c9d0c8a259e --- /dev/null +++ b/recipes/bioconductor-gaggle/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.50.0" %} +{% set name = "gaggle" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0941a1c5621659082664ba61b3e33a61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - 'r-rjava >=0.4' + - 'r-runit >=0.4.17' + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - 'r-rjava >=0.4' + - 'r-runit >=0.4.17' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL version 2 or newer' + summary: 'This package contains functions enabling data exchange between R and Gaggle enabled bioinformatics software, including Cytoscape, Firegoose and Gaggle Genome Browser.' + diff --git a/recipes/bioconductor-gaia/build.sh b/recipes/bioconductor-gaia/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gaia/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gaia/meta.yaml b/recipes/bioconductor-gaia/meta.yaml new file mode 100644 index 0000000000000..66b7c5949c6d0 --- /dev/null +++ b/recipes/bioconductor-gaia/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "2.26.0" %} +{% set name = "gaia" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e4d353ce4c66796d457f0a54189ed840 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package allows to assess the statistical significance of chromosomal aberrations.' + diff --git a/recipes/bioconductor-gaprediction/build.sh b/recipes/bioconductor-gaprediction/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gaprediction/build.sh +++ b/recipes/bioconductor-gaprediction/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gaprediction/meta.yaml b/recipes/bioconductor-gaprediction/meta.yaml index a83ba8454edec..ac832c2dd8bbd 100644 --- a/recipes/bioconductor-gaprediction/meta.yaml +++ b/recipes/bioconductor-gaprediction/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "GAprediction" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 59d07415ce04e694aa7fdf9c870679f9d8a077efc306860d6c05ef68fe95922d + md5: b8446cfccb0b45f63fc64b4cd4fc67b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: "[GAprediction] predicts gestational age using Illumina HumanMethylation450 CpG data." extra: identifiers: - biotools:gaprediction - doi:10.1186/s13059-016-1063-4 + parent_recipe: + name: bioconductor-gaprediction + path: recipes/bioconductor-gaprediction + version: 1.6.0 + diff --git a/recipes/bioconductor-garfield/build.sh b/recipes/bioconductor-garfield/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-garfield/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-garfield/meta.yaml b/recipes/bioconductor-garfield/meta.yaml new file mode 100644 index 0000000000000..5cf399aa58e94 --- /dev/null +++ b/recipes/bioconductor-garfield/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "garfield" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a32182358d9332b323393b06db079a20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'GARFIELD is a non-parametric functional enrichment analysis approach described in the paper GARFIELD: GWAS analysis of regulatory or functional information enrichment with LD correction. Briefly, it is a method that leverages GWAS findings with regulatory or functional annotations (primarily from ENCODE and Roadmap epigenomics data) to find features relevant to a phenotype of interest. It performs greedy pruning of GWAS SNPs (LD r2 > 0.1) and then annotates them based on functional information overlap. Next, it quantifies Fold Enrichment (FE) at various GWAS significance cutoffs and assesses them by permutation testing, while matching for minor allele frequency, distance to nearest transcription start site and number of LD proxies (r2 > 0.8).' + diff --git a/recipes/bioconductor-gars/build.sh b/recipes/bioconductor-gars/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gars/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gars/meta.yaml b/recipes/bioconductor-gars/meta.yaml new file mode 100644 index 0000000000000..1c94778bd5eab --- /dev/null +++ b/recipes/bioconductor-gars/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "GARS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 682be28045f9dab362947bae60f43b76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-damirseq >=1.6.0,<1.7.0' + - 'bioconductor-mlseq >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-ggplot2 + run: + - 'bioconductor-damirseq >=1.6.0,<1.7.0' + - 'bioconductor-mlseq >=2.0.0,<2.1.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Feature selection aims to identify and remove redundant, irrelevant and noisy variables from high-dimensional datasets. Selecting informative features affects the subsequent classification and regression analyses by improving their overall performances. Several methods have been proposed to perform feature selection: most of them relies on univariate statistics, correlation, entropy measurements or the usage of backward/forward regressions. Herein, we propose an efficient, robust and fast method that adopts stochastic optimization approaches for high-dimensional. GARS is an innovative implementation of a genetic algorithm that selects robust features in high-dimensional and challenging datasets.' + diff --git a/recipes/bioconductor-gaschyhs/meta.yaml b/recipes/bioconductor-gaschyhs/meta.yaml new file mode 100644 index 0000000000000..6f8cdddf039c9 --- /dev/null +++ b/recipes/bioconductor-gaschyhs/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "gaschYHS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c6348bdc5404d69a6c6e4726478d2e62 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Data from PMID 11102521' + diff --git a/recipes/bioconductor-gaschyhs/post-link.sh b/recipes/bioconductor-gaschyhs/post-link.sh new file mode 100644 index 0000000000000..04fc385ee47a9 --- /dev/null +++ b/recipes/bioconductor-gaschyhs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="gaschYHS_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gaschYHS_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/gaschYHS_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gaschyhs/bioconductor-gaschyhs_1.20.0_src_all.tar.gz" +) +MD5="c6348bdc5404d69a6c6e4726478d2e62" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gaschyhs/pre-unlink.sh b/recipes/bioconductor-gaschyhs/pre-unlink.sh new file mode 100644 index 0000000000000..7ca20d920eb06 --- /dev/null +++ b/recipes/bioconductor-gaschyhs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gaschYHS diff --git a/recipes/bioconductor-gatefinder/build.sh b/recipes/bioconductor-gatefinder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gatefinder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gatefinder/meta.yaml b/recipes/bioconductor-gatefinder/meta.yaml new file mode 100644 index 0000000000000..2bc06363740e3 --- /dev/null +++ b/recipes/bioconductor-gatefinder/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "GateFinder" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 72c29a720bc9634230ca614f8cd47619 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, flowUtils, BiocGenerics +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - r-base + - r-diptest + - r-mvoutlier + - r-splancs + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowfp >=1.40.0,<1.41.0' + - r-base + - r-diptest + - r-mvoutlier + - r-splancs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Given a vector of cluster memberships for a cell population, identifies a sequence of gates (polygon filters on 2D scatter plots) for isolation of that cell type.' + diff --git a/recipes/bioconductor-gatingmldata/meta.yaml b/recipes/bioconductor-gatingmldata/meta.yaml new file mode 100644 index 0000000000000..51b66eb20160f --- /dev/null +++ b/recipes/bioconductor-gatingmldata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.22.0" %} +{% set name = "gatingMLData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ea5dc27900b34bcf1588ec22100f1d95 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: flowUtils +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Test data and XML files for testing compliance of the flowUtils/flowCore packages with Gating-ML (1.5 and 2.0) standards.' + diff --git a/recipes/bioconductor-gatingmldata/post-link.sh b/recipes/bioconductor-gatingmldata/post-link.sh new file mode 100644 index 0000000000000..663c264881652 --- /dev/null +++ b/recipes/bioconductor-gatingmldata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="gatingMLData_2.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gatingMLData_2.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/gatingMLData_2.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gatingmldata/bioconductor-gatingmldata_2.22.0_src_all.tar.gz" +) +MD5="ea5dc27900b34bcf1588ec22100f1d95" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gatingmldata/pre-unlink.sh b/recipes/bioconductor-gatingmldata/pre-unlink.sh new file mode 100644 index 0000000000000..eed4e20abe52e --- /dev/null +++ b/recipes/bioconductor-gatingmldata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gatingMLData diff --git a/recipes/bioconductor-gcapc/build.sh b/recipes/bioconductor-gcapc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gcapc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcapc/meta.yaml b/recipes/bioconductor-gcapc/meta.yaml new file mode 100644 index 0000000000000..38ea00db785eb --- /dev/null +++ b/recipes/bioconductor-gcapc/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "gcapc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ac19d863951e0b659a1d4605aafeb1c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-mass + - r-matrixstats + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-mass + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Peak calling for ChIP-seq data with consideration of potential GC bias in sequencing reads. GC bias is first estimated with generalized linear mixture models using effective GC strategy, then applied into peak significance estimation.' + diff --git a/recipes/bioconductor-gcatest/build.sh b/recipes/bioconductor-gcatest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gcatest/build.sh +++ b/recipes/bioconductor-gcatest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcatest/meta.yaml b/recipes/bioconductor-gcatest/meta.yaml index b37a68867b7eb..00613102cb8fd 100644 --- a/recipes/bioconductor-gcatest/meta.yaml +++ b/recipes/bioconductor-gcatest/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "gcatest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 086839540cad6878c3bd874e3010f92f4f6b3d6348cb142c035f61f1f686f0ea + md5: 4fdd3965d7db773c137fbd281f34d6e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, ggplot2 requirements: host: - - 'bioconductor-lfa >=1.10.0,<1.12.0' + - 'bioconductor-lfa >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-lfa >=1.10.0,<1.12.0' + - 'bioconductor-lfa >=1.12.0,<1.13.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'GCAT is an association test for genome wide association studies that controls for population structure under a general class of trait. models.' extra: identifiers: - biotools:gcatest - doi:10.1101/012682 + parent_recipe: + name: bioconductor-gcatest + path: recipes/bioconductor-gcatest + version: 1.10.0 + diff --git a/recipes/bioconductor-gcmap/build.sh b/recipes/bioconductor-gcmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gcmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcmap/meta.yaml b/recipes/bioconductor-gcmap/meta.yaml new file mode 100644 index 0000000000000..ab1d955ccef89 --- /dev/null +++ b/recipes/bioconductor-gcmap/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.26.0" %} +{% set name = "gCMAP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3753b67183a2d0c21be53cf900eda12a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, KEGG.db, reactome.db, RUnit, GO.db, mgsa +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bigmemoryextras >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsealm >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-bigmemory + - 'r-matrix >=1.0.9' + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-bigmemoryextras >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsealm >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-bigmemory + - 'r-matrix >=1.0.9' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The gCMAP package provides a toolkit for comparing differential gene expression profiles through gene set enrichment analysis. Starting from normalized microarray or RNA-seq gene expression values (stored in lists of ExpressionSet and CountDataSet objects) the package performs differential expression analysis using the limma or DESeq packages. Supplying a simple list of gene identifiers, global differential expression profiles or data from complete experiments as input, users can use a unified set of several well-known gene set enrichment analysis methods to retrieve experiments with similar changes in gene expression. To take into account the directionality of gene expression changes, gCMAPQuery introduces the SignedGeneSet class, directly extending GeneSet from the GSEABase package. To increase performance of large queries, multiple gene sets are stored as sparse incidence matrices within CMAPCollection eSets. gCMAP offers implementations of 1. Fisher''s exact test (Fisher, J R Stat Soc, 1922) 2. The "connectivity map" method (Lamb et al, Science, 2006) 3. Parametric and non-parametric t-statistic summaries (Jiang & Gentleman, Bioinformatics, 2007) and 4. Wilcoxon / Mann-Whitney rank sum statistics (Wilcoxon, Biometrics Bulletin, 1945) as well as wrappers for the 5. camera (Wu & Smyth, Nucleic Acid Res, 2012) 6. mroast and romer (Wu et al, Bioinformatics, 2010) functions from the limma package and 7. wraps the gsea method from the mgsa package (Bauer et al, NAR, 2010). All methods return CMAPResult objects, an S4 class inheriting from AnnotatedDataFrame, containing enrichment statistics as well as annotation data and providing simple high-level summary plots.' + diff --git a/recipes/bioconductor-gcmapweb/build.sh b/recipes/bioconductor-gcmapweb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gcmapweb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcmapweb/meta.yaml b/recipes/bioconductor-gcmapweb/meta.yaml new file mode 100644 index 0000000000000..f7ea7d1567e53 --- /dev/null +++ b/recipes/bioconductor-gcmapweb/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.22.0" %} +{% set name = "gCMAPWeb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2d2b869ba468ba3932dc14580d96f88f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: affy, ArrayExpress, hgfocus.db, hgu133a.db, mgug4104a.db, org.Hs.eg.db, org.Mm.eg.db, RUnit +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcmap >=1.26.0,<1.27.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-brew + - r-hwriter + - r-rook + - r-yaml + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcmap >=1.26.0,<1.27.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-brew + - r-hwriter + - r-rook + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The gCMAPWeb R package provides a graphical user interface for the gCMAP package. gCMAPWeb uses the Rook package and can be used either on a local machine, leveraging R''s internal web server, or run on a dedicated rApache web server installation. gCMAPWeb allows users to search their own data sources and instructions to generate reference datasets from public repositories are included with the package. The package supports three common types of analyses, specifically queries with 1. one or two sets of query gene identifiers, whose members are expected to show changes in gene expression in a consistent direction. For example, an up-regulated gene set might contain genes activated by a transcription factor, a down-regulated geneset targets repressed by the same factor. 2. a single set of query gene identifiers, whose members are expected to show divergent differential expression (non-directional query). For example, members of a particular signaling pathway, some of which may be up- some down-regulated in response to a stimulus. 3. a query with the complete results of a differential expression profiling experiment. For example, gene identifiers and z-scores from a previous perturbation experiment. gCMAPWeb accepts three types of identifiers: EntreIds, gene Symbols and microarray probe ids and can be configured to work with any species supported by Bioconductor. For each query submission, significantly similar reference datasets will be identified and reported in graphical and tabular form.' + diff --git a/recipes/bioconductor-gcrisprtools/build.sh b/recipes/bioconductor-gcrisprtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gcrisprtools/build.sh +++ b/recipes/bioconductor-gcrisprtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcrisprtools/meta.yaml b/recipes/bioconductor-gcrisprtools/meta.yaml index 2a31cf0e06783..3f7824867863e 100644 --- a/recipes/bioconductor-gcrisprtools/meta.yaml +++ b/recipes/bioconductor-gcrisprtools/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "gCrisprTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0f7c1b5244d9b0aa5ef83d791ca2f6d2d1f03b26e54f42178df4a2460c9d7430 + md5: 1c5860fdfdf165520493eecf72540ce8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: edgeR, knitr, grid, AnnotationDbi, org.Mm.eg.db, org.Hs.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-panther.db >=1.0.4,<1.2.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-panther.db >=1.0.0,<1.1.0' - r-base - r-ggplot2 - r-rmarkdown - r-robustrankaggreg run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-panther.db >=1.0.4,<1.2.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-panther.db >=1.0.0,<1.1.0' - r-base - r-ggplot2 - r-rmarkdown @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Set of tools for evaluating pooled high-throughput screening experiments, typically employing CRISPR/Cas9 or shRNA expression cassettes. Contains methods for interrogating library and cassette behavior within an experiment, identifying differentially abundant cassettes, aggregating signals to identify candidate targets for empirical validation, hypothesis testing, and comprehensive reporting.' extra: identifiers: - biotools:gcrisprtools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gcrisprtools + path: recipes/bioconductor-gcrisprtools + version: 1.8.0 + diff --git a/recipes/bioconductor-gcrma/build.sh b/recipes/bioconductor-gcrma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gcrma/build.sh +++ b/recipes/bioconductor-gcrma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gcrma/conda_build_config.yaml b/recipes/bioconductor-gcrma/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-gcrma/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-gcrma/meta.yaml b/recipes/bioconductor-gcrma/meta.yaml index 7a84db87751a7..945290c8a17de 100644 --- a/recipes/bioconductor-gcrma/meta.yaml +++ b/recipes/bioconductor-gcrma/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "gcrma" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e1310d019392319f8d4384653deab6122d1db1c0d8594b8e10c874e7ba2f8291 + md5: 413897a1c3888e7ee57ee6c5f238934c build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affydata, tools, splines, hgu95av2cdf, hgu95av2probe requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base + - r-biocmanager run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base + - r-biocmanager build: - {{ compiler('c') }} - make @@ -40,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Background adjustment using sequence information' extra: identifiers: - biotools:gcrma - doi:10.1186/1471-2105-9-452 + parent_recipe: + name: bioconductor-gcrma + path: recipes/bioconductor-gcrma + version: 2.52.0 + diff --git a/recipes/bioconductor-gcspikelite/meta.yaml b/recipes/bioconductor-gcspikelite/meta.yaml index 0d30edceea609..f32e532bf3882 100644 --- a/recipes/bioconductor-gcspikelite/meta.yaml +++ b/recipes/bioconductor-gcspikelite/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "gcspikelite" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2c0c76a8b6682fc9d49fcea473d01c64a7183c83fd08c02d567f10f74308db2c + md5: d365d11462a9a1ed68634ff8e9e0cfa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'Spike-in data for GC/MS data and methods within flagme' - +extra: + parent_recipe: + name: bioconductor-gcspikelite + path: recipes/bioconductor-gcspikelite + version: 1.18.0 diff --git a/recipes/bioconductor-gcspikelite/post-link.sh b/recipes/bioconductor-gcspikelite/post-link.sh index 7799e2a3fabf4..43f3c952bc38e 100644 --- a/recipes/bioconductor-gcspikelite/post-link.sh +++ b/recipes/bioconductor-gcspikelite/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="gcspikelite_1.18.0.tar.gz" +FN="gcspikelite_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/gcspikelite_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/gcspikelite_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gcspikelite_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/gcspikelite_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gcspikelite/bioconductor-gcspikelite_1.20.0_src_all.tar.gz" ) -MD5="27f20c8a5b7e2f9e68fef3bac7813225" +MD5="d365d11462a9a1ed68634ff8e9e0cfa4" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-gdcrnatools/build.sh b/recipes/bioconductor-gdcrnatools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdcrnatools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdcrnatools/meta.yaml b/recipes/bioconductor-gdcrnatools/meta.yaml new file mode 100644 index 0000000000000..efc9c13989db8 --- /dev/null +++ b/recipes/bioconductor-gdcrnatools/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.2.0" %} +{% set name = "GDCRNATools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e702d575672f68f5b46c0ec7f872442d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - r-base + - r-dt + - r-ggplot2 + - r-gplots + - r-jsonlite + - r-rjson + - r-shiny + - r-survival + - r-survminer + - r-xml + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - r-base + - r-dt + - r-ggplot2 + - r-gplots + - r-jsonlite + - r-rjson + - r-shiny + - r-survival + - r-survminer + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This is an easy-to-use package for downloading, organizing, and integrative analyzing RNA expression data in GDC with an emphasis on deciphering the lncRNA-mRNA related ceRNA regulatory network in cancer. Three databases of lncRNA-miRNA interactions including spongeScan, starBase, and miRcode, as well as three databases of mRNA-miRNA interactions including miRTarBase, starBase, and miRcode are incorporated into the package for ceRNAs network construction. limma, edgeR, and DESeq2 can be used to identify differentially expressed genes/miRNAs. Functional enrichment analyses including GO, KEGG, and DO can be performed based on the clusterProfiler and DO packages. Both univariate CoxPH and KM survival analyses of multiple genes can be implemented in the package. Besides some routine visualization functions such as volcano plot, bar plot, and KM plot, a few simply shiny apps are developed to facilitate visualization of results on a local webpage.' + diff --git a/recipes/bioconductor-gdsarray/build.sh b/recipes/bioconductor-gdsarray/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gdsarray/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdsarray/meta.yaml b/recipes/bioconductor-gdsarray/meta.yaml new file mode 100644 index 0000000000000..69279e97f035e --- /dev/null +++ b/recipes/bioconductor-gdsarray/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "GDSArray" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6c3b4ae29009e0e1bf5c6cee249a25a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, BiocStyle, BiocManager +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'GDS files are widely used to represent genotyping or sequence data. The GDSArray package implements the `GDSArray` class to represent nodes in GDS files in a matrix-like representation that allows easy manipulation (e.g., subsetting, mathematical transformation) in _R_. The data remains on disk until needed, so that very large files can be processed.' + diff --git a/recipes/bioconductor-gdsfmt/build.sh b/recipes/bioconductor-gdsfmt/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gdsfmt/build.sh +++ b/recipes/bioconductor-gdsfmt/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gdsfmt/meta.yaml b/recipes/bioconductor-gdsfmt/meta.yaml index f23f4c9b51073..3edc7ffe286f1 100644 --- a/recipes/bioconductor-gdsfmt/meta.yaml +++ b/recipes/bioconductor-gdsfmt/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "gdsfmt" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ead9c16e1b3089eaca20a9509cd273e414fec10baeda10188954e37c849bef03 + md5: 7538626e88124c3fc733b67512f7179d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, digest, crayon, RUnit, knitr, BiocGenerics requirements: host: - r-base @@ -29,8 +30,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'This package provides a high-level R interface to CoreArray Genomic Data Structure (GDS) data files, which are portable across platforms with hierarchical structure to store multiple scalable array-oriented data sets with metadata information. It is suited for large-scale datasets, especially for data which are much larger than the available random-access memory. The gdsfmt package offers the efficient operations specifically designed for integers of less than 8 bits, since a diploid genotype, like single-nucleotide polymorphism (SNP), usually occupies fewer bits than a byte. Data compression and decompression are available with relatively efficient random access. It is also allowed to read a GDS file in parallel with multiple R processes supported by the package parallel.' - +extra: + parent_recipe: + name: bioconductor-gdsfmt + path: recipes/bioconductor-gdsfmt + version: 1.16.0 diff --git a/recipes/bioconductor-geecc/build.sh b/recipes/bioconductor-geecc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geecc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geecc/meta.yaml b/recipes/bioconductor-geecc/meta.yaml new file mode 100644 index 0000000000000..551adf95de8b5 --- /dev/null +++ b/recipes/bioconductor-geecc/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.16.0" %} +{% set name = "geecc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2599b369944d75ec0eea0969f6686923 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: hgu133plus2.db, GO.db, AnnotationDbi +# SystemRequirements: Rcpp +requirements: + host: + - r-base + - r-gplots + - 'r-hypergea >=1.3.0' + - r-mass + - 'r-rcpp >=0.11.3' + run: + - r-base + - r-gplots + - 'r-hypergea >=1.3.0' + - r-mass + - 'r-rcpp >=0.11.3' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Use log-linear models to perform hypergeometric and chi-squared tests for gene set enrichments for two (based on contingency tables) or three categories (contingency cubes). Categories can be differentially expressed genes, GO terms, sequence length, GC content, chromosomal position, phylostrata, divergence-strata, ....' + diff --git a/recipes/bioconductor-gem/build.sh b/recipes/bioconductor-gem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gem/meta.yaml b/recipes/bioconductor-gem/meta.yaml new file mode 100644 index 0000000000000..6f5336e43be8b --- /dev/null +++ b/recipes/bioconductor-gem/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.8.0" %} +{% set name = "GEM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06d08b08b90d67d3bfd976aef192dc52 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, testthat, BiocGenerics +requirements: + host: + - r-base + - r-ggplot2 + run: + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools for analyzing EWAS, methQTL and GxE genome widely.' + diff --git a/recipes/bioconductor-genarise/build.sh b/recipes/bioconductor-genarise/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genarise/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genarise/meta.yaml b/recipes/bioconductor-genarise/meta.yaml new file mode 100644 index 0000000000000..6c0b2f104e4a0 --- /dev/null +++ b/recipes/bioconductor-genarise/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.58.0" %} +{% set name = "genArise" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4b848ac87c655ce850a42af452508f99 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-locfit + - r-tkrplot + - r-xtable + run: + - r-base + - r-locfit + - r-tkrplot + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'genArise is an easy to use tool for dual color microarray data. Its GUI-Tk based environment let any non-experienced user performs a basic, but not simple, data analysis just following a wizard. In addition it provides some tools for the developer.' + diff --git a/recipes/bioconductor-genbankr/build.sh b/recipes/bioconductor-genbankr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genbankr/build.sh +++ b/recipes/bioconductor-genbankr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genbankr/meta.yaml b/recipes/bioconductor-genbankr/meta.yaml index 2751ef4abd9df..7af1401c5e586 100644 --- a/recipes/bioconductor-genbankr/meta.yaml +++ b/recipes/bioconductor-genbankr/meta.yaml @@ -1,54 +1,61 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "genbankr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bea0a9dbf0c5cccd4668fc1cbee3a45d447604d304a339e17a5bc97eb0458160 + md5: 3eb9b0da2de16e06cbf5adcf518b27ac build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, rentrez, knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Reads Genbank files.' extra: identifiers: - biotools:genbankr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genbankr + path: recipes/bioconductor-genbankr + version: 1.8.0 + diff --git a/recipes/bioconductor-geneaccord/build.sh b/recipes/bioconductor-geneaccord/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneaccord/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneaccord/meta.yaml b/recipes/bioconductor-geneaccord/meta.yaml new file mode 100644 index 0000000000000..4a14e1a1da938 --- /dev/null +++ b/recipes/bioconductor-geneaccord/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "GeneAccord" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 20327d63683336b7ae0f47d9757727b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: assertthat, BiocStyle, devtools, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-catools + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-gtools + - r-magrittr + - r-maxlik + - r-rcolorbrewer + - r-reshape2 + - r-tibble + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-catools + - r-dplyr + - r-ggplot2 + - r-ggpubr + - r-gtools + - r-magrittr + - r-maxlik + - r-rcolorbrewer + - r-reshape2 + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'A statistical framework to examine the combinations of clones that co-exist in tumors. More precisely, the algorithm finds pairs of genes that are mutated in the same tumor but in different clones, i.e. their subclonal mutation profiles are mutually exclusive. We refer to this as clonally exclusive. It means that the mutations occurred in different branches of the tumor phylogeny, indicating parallel evolution of the clones. Our statistical framework assesses whether a pattern of clonal exclusivity occurs more often than expected by chance alone across a cohort of patients. The required input data are the mutated gene-to-clone assignments from a cohort of cancer patients, which were obtained by running phylogenetic tree inference methods. Reconstructing the evolutionary history of a tumor and detecting the clones is challenging. For nondeterministic algorithms, repeated tree inference runs may lead to slightly different mutation-to-clone assignments. Therefore, our algorithm was designed to allow the input of multiple gene-to-clone assignments per patient. They may have been generated by repeatedly performing the tree inference, or by sampling from the posterior distribution of trees. The tree inference methods designate the mutations to individual clones. The mutations can then be mapped to genes or pathways. Hence our statistical framework can be applied on the gene level, or on the pathway level to detect clonally exclusive pairs of pathways. If a pair is significantly clonally exclusive, it points towards the fact that this specific clone configuration confers a selective advantage, possibly through synergies between the clones with these mutations.' + diff --git a/recipes/bioconductor-geneanswers/build.sh b/recipes/bioconductor-geneanswers/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneanswers/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneanswers/meta.yaml b/recipes/bioconductor-geneanswers/meta.yaml new file mode 100644 index 0000000000000..227fe81b544be --- /dev/null +++ b/recipes/bioconductor-geneanswers/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "2.24.0" %} +{% set name = "GeneAnswers" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0d3cf555819cf8b8d71029082abc33e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GO.db, KEGG.db, reactome.db, biomaRt, AnnotationDbi, org.Hs.eg.db, org.Rn.eg.db, org.Mm.eg.db, org.Dm.eg.db, graph +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-downloader + - r-igraph + - r-mass + - r-rcolorbrewer + - r-rcurl + - r-rsqlite + - r-xml + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-downloader + - r-igraph + - r-mass + - r-rcolorbrewer + - r-rcurl + - r-rsqlite + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'GeneAnswers provides an integrated tool for biological or medical interpretation of the given one or more groups of genes by means of statistical test.' + diff --git a/recipes/bioconductor-geneattribution/build.sh b/recipes/bioconductor-geneattribution/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneattribution/build.sh +++ b/recipes/bioconductor-geneattribution/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneattribution/meta.yaml b/recipes/bioconductor-geneattribution/meta.yaml index 1e943bea91893..956b3de14db15 100644 --- a/recipes/bioconductor-geneattribution/meta.yaml +++ b/recipes/bioconductor-geneattribution/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "geneAttribution" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 656c60c15d52ba20403c2811de777a4b5c2d37531bb0f29547ed6a962b85a317 + md5: f789b0c41a0d5bcce055f113b718d583 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg38.knownGene, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Identification of the most likely gene or genes through which variation at a given genomic locus in the human genome acts. The most basic functionality assumes that the closer gene is to the input locus, the more likely the gene is to be causative. Additionally, any empirical data that links genomic regions to genes (e.g. eQTL or genome conformation data) can be used if it is supplied in the UCSC .BED file format.' extra: identifiers: - biotools:geneattribution - doi:10.1093/bioinformatics/btw698 + parent_recipe: + name: bioconductor-geneattribution + path: recipes/bioconductor-geneattribution + version: 1.6.0 + diff --git a/recipes/bioconductor-genebreak/build.sh b/recipes/bioconductor-genebreak/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genebreak/build.sh +++ b/recipes/bioconductor-genebreak/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genebreak/meta.yaml b/recipes/bioconductor-genebreak/meta.yaml index 07f0b3bffcf30..bc98de079d832 100644 --- a/recipes/bioconductor-genebreak/meta.yaml +++ b/recipes/bioconductor-genebreak/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GeneBreak" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f22d56049037084772dca16d73619d9773a96fdef44f1eab716cd772281ec511 + md5: 6210aae2a4a0e02205f7fcb10831f943 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Recurrent breakpoint gene detection on copy number aberration profiles.' extra: identifiers: - biotools:genebreak - doi:10.12688/f1000research.9259.1 + parent_recipe: + name: bioconductor-genebreak + path: recipes/bioconductor-genebreak + version: 1.10.0 + diff --git a/recipes/bioconductor-geneclassifiers/build.sh b/recipes/bioconductor-geneclassifiers/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneclassifiers/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneclassifiers/meta.yaml b/recipes/bioconductor-geneclassifiers/meta.yaml new file mode 100644 index 0000000000000..22fa21219908a --- /dev/null +++ b/recipes/bioconductor-geneclassifiers/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.6.0" %} +{% set name = "geneClassifiers" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2af1e841e8a184c21b9d0d1c6907d376 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This packages aims for easy accessible application of classifiers which have been published in literature using an ExpressionSet as input.' + diff --git a/recipes/bioconductor-geneexpressionsignature/build.sh b/recipes/bioconductor-geneexpressionsignature/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneexpressionsignature/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneexpressionsignature/meta.yaml b/recipes/bioconductor-geneexpressionsignature/meta.yaml new file mode 100644 index 0000000000000..cc1406088fc6e --- /dev/null +++ b/recipes/bioconductor-geneexpressionsignature/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.28.0" %} +{% set name = "GeneExpressionSignature" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00e1e0a915a2a1455f65c1dd159427cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: apcluster,GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-pgsea >=1.56.0,<1.57.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-pgsea >=1.56.0,<1.57.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package gives the implementations of the gene expression signature and its distance to each. Gene expression signature is represented as a list of genes whose expression is correlated with a biological state of interest. And its distance is defined using a nonparametric, rank-based pattern-matching strategy based on the Kolmogorov-Smirnov statistic. Gene expression signature and its distance can be used to detect similarities among the signatures of drugs, diseases, and biological states of interest.' + diff --git a/recipes/bioconductor-genefilter/build.sh b/recipes/bioconductor-genefilter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genefilter/build.sh +++ b/recipes/bioconductor-genefilter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genefilter/meta.yaml b/recipes/bioconductor-genefilter/meta.yaml index f40d24026656e..f76cf94979dcd 100644 --- a/recipes/bioconductor-genefilter/meta.yaml +++ b/recipes/bioconductor-genefilter/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.62.0" %} +{% set version = "1.64.0" %} {% set name = "genefilter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11ab26d789c6ee644545d5b371a263fc4dbacb839f850a64e7b25e2d80738092 + md5: 88bde15c167b64adeaeb6396a4adafed build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: class, hgu95av2.db, tkWidgets, ALL, ROC, DESeq, pasilla, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-survival build: @@ -40,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Some basic functions for filtering genes' + summary: 'Some basic functions for filtering genes.' extra: identifiers: - biotools:genefilter - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genefilter + path: recipes/bioconductor-genefilter + version: 1.62.0 + diff --git a/recipes/bioconductor-genefu/build.sh b/recipes/bioconductor-genefu/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genefu/build.sh +++ b/recipes/bioconductor-genefu/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genefu/meta.yaml b/recipes/bioconductor-genefu/meta.yaml index 42fb3fa96a70d..6f871b132794d 100644 --- a/recipes/bioconductor-genefu/meta.yaml +++ b/recipes/bioconductor-genefu/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "genefu" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c18c62048f4038d94a2fc15cbce8decfb3ac3791e64d72668344429f3aa7c7d2 + md5: 26fd028d750b137edebcdbf8966c0324 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GeneMeta, breastCancerVDX, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerUNT, breastCancerNKI, rmeta, Biobase, xtable, knitr, caret, survival requirements: host: - - 'bioconductor-aims >=1.12.0,<1.14.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-survcomp >=1.30.0,<1.32.0' + - 'bioconductor-aims >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-survcomp >=1.32.0,<1.33.0' - r-amap - r-base - r-ic10 - r-mclust run: - - 'bioconductor-aims >=1.12.0,<1.14.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-survcomp >=1.30.0,<1.32.0' + - 'bioconductor-aims >=1.14.0,<1.15.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-survcomp >=1.32.0,<1.33.0' - r-amap - r-base - r-ic10 @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Description: This package contains functions implementing various tasks usually required by gene expression analysis, especially in breast cancer studies: gene mapping between different microarray platforms, identification of molecular subtypes, implementation of published gene signatures, gene selection, and survival analysis.' extra: identifiers: - biotools:genefu - doi:10.1093/bioinformatics/btv693 + parent_recipe: + name: bioconductor-genefu + path: recipes/bioconductor-genefu + version: 2.12.0 + diff --git a/recipes/bioconductor-genega/build.sh b/recipes/bioconductor-genega/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genega/build.sh +++ b/recipes/bioconductor-genega/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genega/meta.yaml b/recipes/bioconductor-genega/meta.yaml index 4a4eedfa2b2f1..2b0b99c0f0068 100644 --- a/recipes/bioconductor-genega/meta.yaml +++ b/recipes/bioconductor-genega/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "GeneGA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 79f1b800ee88be9a9c6b337d4a965d54c7b2c84c942ea1e52f5e7331de84b48e + md5: 4d664e7a6933501a3286da527d3f306c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL version 2' summary: 'R based Genetic algorithm for gene expression optimization by considering both mRNA secondary structure and codon usage bias, GeneGA includes the information of highly expressed genes of almost 200 genomes. Meanwhile, Vienna RNA Package is needed to ensure GeneGA to function properly.' extra: identifiers: - biotools:genega - doi:10.1186/1748-7188-6-26 + parent_recipe: + name: bioconductor-genega + path: recipes/bioconductor-genega + version: 1.30.0 + diff --git a/recipes/bioconductor-genegeneinter/build.sh b/recipes/bioconductor-genegeneinter/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genegeneinter/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genegeneinter/meta.yaml b/recipes/bioconductor-genegeneinter/meta.yaml new file mode 100644 index 0000000000000..ab227e81ed466 --- /dev/null +++ b/recipes/bioconductor-genegeneinter/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.8.0" %} +{% set name = "GeneGeneInteR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aa36bdccea1e40711a5ed4b583c8e602 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-factominer + - r-igraph + - r-kernlab + - r-mvtnorm + - r-plspm + - r-rioja + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggtools >=5.18.0,<5.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - r-data.table + - r-factominer + - r-igraph + - r-kernlab + - r-mvtnorm + - r-plspm + - r-rioja +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The aim of this package is to propose several methods for testing gene-gene interaction in case-control association studies. Such a test can be done by aggregating SNP-SNP interaction tests performed at the SNP level (SSI) or by using gene-gene multidimensionnal methods (GGI) methods. The package also proposes tools for a graphic display of the results.' + diff --git a/recipes/bioconductor-genelendatabase/meta.yaml b/recipes/bioconductor-genelendatabase/meta.yaml index ff1aa1ae1cec9..b74abd93168d3 100644 --- a/recipes/bioconductor-genelendatabase/meta.yaml +++ b/recipes/bioconductor-genelendatabase/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "geneLenDataBase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 454972055f675858c2cc2ec2ccf85e5ac387ead26d04a62b09fbac398aadb51e + md5: 6bb5df37b2b3472202006a767123ac34 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Length of mRNA transcripts for a number of genomes and gene ID formats, largely based on UCSC table browser' - +extra: + parent_recipe: + name: bioconductor-genelendatabase + path: recipes/bioconductor-genelendatabase + version: 1.16.0 diff --git a/recipes/bioconductor-genelendatabase/post-link.sh b/recipes/bioconductor-genelendatabase/post-link.sh index 8616f3b604c0b..90871542d0e8b 100644 --- a/recipes/bioconductor-genelendatabase/post-link.sh +++ b/recipes/bioconductor-genelendatabase/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="geneLenDataBase_1.16.0.tar.gz" +FN="geneLenDataBase_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/geneLenDataBase_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/geneLenDataBase_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geneLenDataBase_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/geneLenDataBase_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genelendatabase/bioconductor-genelendatabase_1.18.0_src_all.tar.gz" ) -MD5="aa23db3bc55f6d20e42e66a47a99f065" +MD5="6bb5df37b2b3472202006a767123ac34" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-genemeta/build.sh b/recipes/bioconductor-genemeta/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genemeta/build.sh +++ b/recipes/bioconductor-genemeta/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genemeta/meta.yaml b/recipes/bioconductor-genemeta/meta.yaml index bdf8e20884154..bbda7f1c356b7 100644 --- a/recipes/bioconductor-genemeta/meta.yaml +++ b/recipes/bioconductor-genemeta/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "GeneMeta" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a7f42a9e65043449c0c877bb133bff9ff23bf932e750480af135bc5c9f64ee02 + md5: f6cc399bae052e2cbeb38d2bcbe3cd10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A collection of meta-analysis tools for analysing high throughput experimental data' extra: identifiers: - biotools:genemeta - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genemeta + path: recipes/bioconductor-genemeta + version: 1.52.0 + diff --git a/recipes/bioconductor-genenetworkbuilder/build.sh b/recipes/bioconductor-genenetworkbuilder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genenetworkbuilder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genenetworkbuilder/meta.yaml b/recipes/bioconductor-genenetworkbuilder/meta.yaml new file mode 100644 index 0000000000000..a63849f82f42c --- /dev/null +++ b/recipes/bioconductor-genenetworkbuilder/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.24.0" %} +{% set name = "GeneNetworkBuilder" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c13d1b3bf1eaf22d2bc50c75ce245e6c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics, RBGL, knitr, simpIntLists, shiny, STRINGdb +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-htmlwidgets + - r-plyr + - 'r-rcpp >=0.9.13' + - r-rjson + - r-xml + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-htmlwidgets + - r-plyr + - 'r-rcpp >=0.9.13' + - r-rjson + - r-xml + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Appliation for discovering direct or indirect targets of transcription factors using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, GeneNetworkBuilder generates a regulatory network of the TF.' + diff --git a/recipes/bioconductor-geneoverlap/build.sh b/recipes/bioconductor-geneoverlap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneoverlap/build.sh +++ b/recipes/bioconductor-geneoverlap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneoverlap/meta.yaml b/recipes/bioconductor-geneoverlap/meta.yaml index d75a3c55a161b..c2aeee3ef6102 100644 --- a/recipes/bioconductor-geneoverlap/meta.yaml +++ b/recipes/bioconductor-geneoverlap/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GeneOverlap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3f753a59517641e56586e0c19d6657ecdc07b446cb5fa9a21e361c2a83c6b092 + md5: dd4b8465cdd86f717727612caef4f1af build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Test two sets of gene lists and visualize the results.' extra: identifiers: - biotools:geneoverlap - doi:10.1167/iovs.16-20618 + parent_recipe: + name: bioconductor-geneoverlap + path: recipes/bioconductor-geneoverlap + version: 1.16.0 + diff --git a/recipes/bioconductor-geneplast.data.string.v91/meta.yaml b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml new file mode 100644 index 0000000000000..c709c0c4eac15 --- /dev/null +++ b/recipes/bioconductor-geneplast.data.string.v91/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.99.6" %} +{% set name = "geneplast.data.string.v91" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 86433f8489d9228c5ed73e2b75a55398 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package geneplast.data.string.v91 contains input data used in the analysis pipelines available in the geneplast package.' + diff --git a/recipes/bioconductor-geneplast.data.string.v91/post-link.sh b/recipes/bioconductor-geneplast.data.string.v91/post-link.sh new file mode 100644 index 0000000000000..914e1e5611b42 --- /dev/null +++ b/recipes/bioconductor-geneplast.data.string.v91/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="geneplast.data.string.v91_0.99.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/geneplast.data.string.v91_0.99.6.tar.gz" + "https://bioarchive.galaxyproject.org/geneplast.data.string.v91_0.99.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geneplast.data.string.v91/bioconductor-geneplast.data.string.v91_0.99.6_src_all.tar.gz" +) +MD5="86433f8489d9228c5ed73e2b75a55398" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-geneplast.data.string.v91/pre-unlink.sh b/recipes/bioconductor-geneplast.data.string.v91/pre-unlink.sh new file mode 100644 index 0000000000000..2c6a3aaf6062a --- /dev/null +++ b/recipes/bioconductor-geneplast.data.string.v91/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ geneplast.data.string.v91 diff --git a/recipes/bioconductor-geneplast/build.sh b/recipes/bioconductor-geneplast/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneplast/build.sh +++ b/recipes/bioconductor-geneplast/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneplast/meta.yaml b/recipes/bioconductor-geneplast/meta.yaml index 804e6c7c6633b..d17c73447a434 100644 --- a/recipes/bioconductor-geneplast/meta.yaml +++ b/recipes/bioconductor-geneplast/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "geneplast" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cf9d190319d5ca34aa62075a92ba53c6b173b0903557741c91b6737d56fbdccf + md5: bcdbc3f90a41dc19ce54893cbc0cf1b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RTN, RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown requirements: host: - r-ape @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Geneplast is designed for evolutionary and plasticity analysis based on orthologous groups distribution in a given species tree. It uses Shannon information theory and orthologs abundance to estimate the Evolutionary Plasticity Index. Additionally, it implements the Bridge algorithm to determine the evolutionary root of a given gene based on its orthologs distribution.' extra: identifiers: - biotools:geneplast - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geneplast + path: recipes/bioconductor-geneplast + version: 1.6.2 + diff --git a/recipes/bioconductor-geneplotter/build.sh b/recipes/bioconductor-geneplotter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneplotter/build.sh +++ b/recipes/bioconductor-geneplotter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneplotter/meta.yaml b/recipes/bioconductor-geneplotter/meta.yaml index ca8f864c45e34..21c93d4992ee7 100644 --- a/recipes/bioconductor-geneplotter/meta.yaml +++ b/recipes/bioconductor-geneplotter/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "geneplotter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0f74be95c4a699b654e0db4b39992f8e183dab8a1dbdf90025f4abf83a12af14 + md5: 077d06670401f046e762f770a0815a25 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz, fibroEset, hgu95av2.db, hu6800.db, hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-lattice - r-rcolorbrewer @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions for plotting genomic data' extra: identifiers: - biotools:geneplotter - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geneplotter + path: recipes/bioconductor-geneplotter + version: 1.58.0 + diff --git a/recipes/bioconductor-generecommender/build.sh b/recipes/bioconductor-generecommender/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-generecommender/build.sh +++ b/recipes/bioconductor-generecommender/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-generecommender/meta.yaml b/recipes/bioconductor-generecommender/meta.yaml index 35698131bc27d..7f04ec0147b5d 100644 --- a/recipes/bioconductor-generecommender/meta.yaml +++ b/recipes/bioconductor-generecommender/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "geneRecommender" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 61cce313de9cdd28769654e1e289c6d1975679246889bfc9fa6209120c097372 + md5: fa33e09ffa3ace8332c399d2d48728a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains a targeted clustering algorithm for the analysis of microarray data. The algorithm can aid in the discovery of new genes with similar functions to a given list of genes already known to have closely related functions.' extra: identifiers: - biotools:generecommender - doi:10.1101/gr.1125403 + parent_recipe: + name: bioconductor-generecommender + path: recipes/bioconductor-generecommender + version: 1.52.0 + diff --git a/recipes/bioconductor-generegionscan/build.sh b/recipes/bioconductor-generegionscan/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-generegionscan/build.sh +++ b/recipes/bioconductor-generegionscan/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-generegionscan/meta.yaml b/recipes/bioconductor-generegionscan/meta.yaml index ddbfea66ea8a8..ef4649df09ddc 100644 --- a/recipes/bioconductor-generegionscan/meta.yaml +++ b/recipes/bioconductor-generegionscan/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "GeneRegionScan" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: faaf1a6202015008281ba459467a914897fd7766485e1a329bf192314cbec9a2 + md5: 2260cef9b94226c671ee7b49585b48c2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome, affy, AnnotationDbi requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcolorbrewer test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package with focus on analysis of discrete regions of the genome. This package is useful for investigation of one or a few genes using Affymetrix data, since it will extract probe level data using the Affymetrix Power Tools application and wrap these data into a ProbeLevelSet. A ProbeLevelSet directly extends the expressionSet, but includes additional information about the sequence of each probe and the probe set it is derived from. The package includes a number of functions used for plotting these probe level data as a function of location along sequences of mRNA-strands. This can be used for analysis of variable splicing, and is especially well suited for use with exon-array data.' extra: identifiers: - biotools:generegionscan + parent_recipe: + name: bioconductor-generegionscan + path: recipes/bioconductor-generegionscan + version: 1.36.0 + diff --git a/recipes/bioconductor-generxcluster/build.sh b/recipes/bioconductor-generxcluster/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-generxcluster/build.sh +++ b/recipes/bioconductor-generxcluster/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-generxcluster/meta.yaml b/recipes/bioconductor-generxcluster/meta.yaml index 0a25d52005350..569c70411799c 100644 --- a/recipes/bioconductor-generxcluster/meta.yaml +++ b/recipes/bioconductor-generxcluster/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "geneRxCluster" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 574b94248242e36998d7c5aaa9e6cb33cd361dbf8074ed0ae94d977d0f099f05 + md5: 8d1ada8668cffaf687eb24c1313cf667 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base build: - {{ compiler('c') }} @@ -32,9 +33,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detect Differential Clustering of Genomic Sites such as gene therapy integrations. The package provides some functions for exploring genomic insertion sites originating from two different sources. Possibly, the two sources are two different gene therapy vectors. Vectors are preferred that target sensitive regions less frequently, motivating the search for localized clusters of insertions and comparison of the clusters formed by integration of different vectors. Scan statistics allow the discovery of spatial differences in clustering and calculation of False Discovery Rates (FDRs) providing statistical methods for comparing retroviral vectors. A scan statistic for comparing two vectors using multiple window widths to detect clustering differentials and compute FDRs is implemented here.' extra: identifiers: - biotools:generxcluster + parent_recipe: + name: bioconductor-generxcluster + path: recipes/bioconductor-generxcluster + version: 1.16.0 + diff --git a/recipes/bioconductor-geneselectmmd/build.sh b/recipes/bioconductor-geneselectmmd/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneselectmmd/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneselectmmd/meta.yaml b/recipes/bioconductor-geneselectmmd/meta.yaml new file mode 100644 index 0000000000000..ce6357ac0ff9f --- /dev/null +++ b/recipes/bioconductor-geneselectmmd/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "2.26.0" %} +{% set name = "GeneSelectMMD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d3e9c106d9ae273e16d315dc1e37f123 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ALL +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-mass + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-mass + - r-survival + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Gene selection based on a mixture of marginal distributions' + diff --git a/recipes/bioconductor-geneselector/build.sh b/recipes/bioconductor-geneselector/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneselector/build.sh +++ b/recipes/bioconductor-geneselector/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneselector/meta.yaml b/recipes/bioconductor-geneselector/meta.yaml index 1b340eefe96c5..cd2009964a352 100644 --- a/recipes/bioconductor-geneselector/meta.yaml +++ b/recipes/bioconductor-geneselector/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "2.30.0" %} +{% set version = "2.32.0" %} {% set name = "GeneSelector" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ed67f869d7835022929e2ce13173833340f7b4a1930e8acdb9cb69350f7a124 + md5: d33abf828afc8bb90576ee93daf62701 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: multtest, siggenes, samr, limma requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-samr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-samr build: @@ -38,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The term ''GeneSelector'' refers to a filter selecting those genes which are consistently identified as differentially expressed using various statistical procedures. ''Selected'' genes are those present at the top of the list in various ranking methods (currently 14). In addition, the stability of the findings can be taken into account in the final ranking by examining perturbed versions of the original data set, e.g. by leaving samples, swapping class labels, generating bootstrap replicates or adding noise. Given multiple ranked lists, one can use aggregation methods in order to find a synthesis.' extra: identifiers: - biotools:geneselector - doi:10.1093/bib/bbp034 + parent_recipe: + name: bioconductor-geneselector + path: recipes/bioconductor-geneselector + version: 2.30.0 + diff --git a/recipes/bioconductor-genesis/build.sh b/recipes/bioconductor-genesis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genesis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genesis/meta.yaml b/recipes/bioconductor-genesis/meta.yaml new file mode 100644 index 0000000000000..20df0a83b5a20 --- /dev/null +++ b/recipes/bioconductor-genesis/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "2.12.0" %} +{% set name = "GENESIS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a0cf436a8357cd15fdaec5c6c8b7574b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: CompQuadForm, poibin, survey, testthat, knitr, rmarkdown, GWASdata, ggplot2, GGally, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-seqvartools >=1.20.0,<1.21.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-dplyr + - r-foreach + - r-igraph + - r-matrix + - r-reshape2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - 'bioconductor-seqvartools >=1.20.0,<1.21.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-dplyr + - r-foreach + - r-igraph + - r-matrix + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The GENESIS package provides methodology for estimating, inferring, and accounting for population and pedigree structure in genetic analyses. The current implementation provides functions to perform PC-AiR (Conomos et al., 2015, Gen Epi) and PC-Relate (Conomos et al., 2016, AJHG). PC-AiR performs a Principal Components Analysis on genome-wide SNP data for the detection of population structure in a sample that may contain known or cryptic relatedness. Unlike standard PCA, PC-AiR accounts for relatedness in the sample to provide accurate ancestry inference that is not confounded by family structure. PC-Relate uses ancestry representative principal components to adjust for population structure/ancestry and accurately estimate measures of recent genetic relatedness such as kinship coefficients, IBD sharing probabilities, and inbreeding coefficients. Additionally, functions are provided to perform efficient variance component estimation and mixed model association testing for both quantitative and binary phenotypes.' + diff --git a/recipes/bioconductor-genestructuretools/build.sh b/recipes/bioconductor-genestructuretools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genestructuretools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genestructuretools/meta.yaml b/recipes/bioconductor-genestructuretools/meta.yaml new file mode 100644 index 0000000000000..6147b3f3bddc7 --- /dev/null +++ b/recipes/bioconductor-genestructuretools/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "GeneStructureTools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: df6de751d9ef353cd61d4e51488f0c5e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-plyr + - r-stringdist + - r-stringr + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-plyr + - r-stringdist + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'GeneStructureTools can be used to create in silico alternative splicing events, and analyse potential effects this has on functional gene products.' + diff --git a/recipes/bioconductor-genetclassifier/build.sh b/recipes/bioconductor-genetclassifier/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genetclassifier/build.sh +++ b/recipes/bioconductor-genetclassifier/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genetclassifier/meta.yaml b/recipes/bioconductor-genetclassifier/meta.yaml index bd899a425720a..2635eaf786674 100644 --- a/recipes/bioconductor-genetclassifier/meta.yaml +++ b/recipes/bioconductor-genetclassifier/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "geNetClassifier" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d620749f5f4e436bce373d0b1832e6ca8dc95708644549a8f8b6530078179dd3 + md5: 7ed135e01c9a31922be170711651ed12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: leukemiasEset, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - - 'bioconductor-minet >=3.38.0,<3.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' - r-base - r-e1071 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ebarrays >=2.44.0,<2.46.0' - - 'bioconductor-minet >=3.38.0,<3.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ebarrays >=2.46.0,<2.47.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' - r-base - r-e1071 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Comprehensive package to automatically train and validate a multi-class SVM classifier based on gene expression data. Provides transparent selection of gene markers, their coexpression networks, and an interface to query the classifier.' extra: identifiers: - biotools:genetclassifier + parent_recipe: + name: bioconductor-genetclassifier + path: recipes/bioconductor-genetclassifier + version: 1.20.0 + diff --git a/recipes/bioconductor-geneticsdesign/build.sh b/recipes/bioconductor-geneticsdesign/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geneticsdesign/build.sh +++ b/recipes/bioconductor-geneticsdesign/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneticsdesign/meta.yaml b/recipes/bioconductor-geneticsdesign/meta.yaml index 6d65fa8ef6d79..a002676773d6c 100644 --- a/recipes/bioconductor-geneticsdesign/meta.yaml +++ b/recipes/bioconductor-geneticsdesign/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "GeneticsDesign" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d49bf0c3bcb0840eca83f74b21d521467cfdfae96c7f0d665cb48e9d66a1dbc3 + md5: c1cc329cd3f43602ab706b0988a01ae7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains functions useful for designing genetics studies, including power and sample-size calculations.' extra: identifiers: - biotools:geneticsdesign - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geneticsdesign + path: recipes/bioconductor-geneticsdesign + version: 1.48.0 + diff --git a/recipes/bioconductor-geneticsped/build.sh b/recipes/bioconductor-geneticsped/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-geneticsped/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geneticsped/meta.yaml b/recipes/bioconductor-geneticsped/meta.yaml new file mode 100644 index 0000000000000..45e82afb50a3f --- /dev/null +++ b/recipes/bioconductor-geneticsped/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.44.0" %} +{% set name = "GeneticsPed" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 596538e0ee1818d212af9d5e61296166 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, gtools +requirements: + host: + - r-base + - r-gdata + - r-genetics + - r-mass + run: + - r-base + - r-gdata + - r-genetics + - r-mass + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - {{ compiler('fortran') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.1) | file LICENSE' + summary: 'Classes and methods for handling pedigree data. It also includes functions to calculate genetic relationship measures as relationship and inbreeding coefficients and other utilities. Note that package is not yet stable. Use it with care!' + diff --git a/recipes/bioconductor-genextender/build.sh b/recipes/bioconductor-genextender/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genextender/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genextender/meta.yaml b/recipes/bioconductor-genextender/meta.yaml new file mode 100644 index 0000000000000..59cddcaab9d51 --- /dev/null +++ b/recipes/bioconductor-genextender/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.8.0" %} +{% set name = "geneXtendeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 967c99eb692b4bff278ddd7d808b1806 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat, org.Ag.eg.db, org.Bt.eg.db, org.Ce.eg.db, org.Cf.eg.db, org.Dm.eg.db, org.Dr.eg.db, org.Gg.eg.db, org.Hs.eg.db, org.Mm.eg.db, org.Pt.eg.db, org.Sc.sgd.db, org.Ss.eg.db, org.Xl.eg.db, rtracklayer +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-dplyr + - r-networkd3 + - r-rcolorbrewer + - r-snowballc + - r-tm + - r-wordcloud + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-dplyr + - r-networkd3 + - r-rcolorbrewer + - r-snowballc + - r-tm + - r-wordcloud + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring relative differences in annotating ChIP-seq peak sets to variable-length gene bodies. In contrast to prior techniques, geneXtendeR considers peak annotations beyond just the closest gene, allowing users to see peak summary statistics for the first-closest gene, second-closest gene, ..., n-closest gene whilst ranking the output according to biologically relevant events and iteratively comparing the fidelity of peak-to-gene overlap across a user-defined range of upstream and downstream extensions on the original boundaries of each gene''s coordinates. Since different ChIP-seq peak callers produce different differentially enriched peaks with a large variance in peak length distribution and total peak count, annotating peak lists with their nearest genes can often be a noisy process. As such, the goal of geneXtendeR is to robustly link differentially enriched peaks with their respective genes, thereby aiding experimental follow-up and validation in designing primers for a set of prospective gene candidates during qPCR.' + diff --git a/recipes/bioconductor-genie3/build.sh b/recipes/bioconductor-genie3/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genie3/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genie3/meta.yaml b/recipes/bioconductor-genie3/meta.yaml new file mode 100644 index 0000000000000..5e1c1117a7a23 --- /dev/null +++ b/recipes/bioconductor-genie3/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.4.0" %} +{% set name = "GENIE3" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 861a6efb940089ee2e1baec76a59afa4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, foreach, doRNG, doParallel, Biobase, SummarizedExperiment, testthat, methods +requirements: + host: + - r-base + - r-reshape2 + run: + - r-base + - r-reshape2 + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package implements the GENIE3 algorithm for inferring gene regulatory networks from expression data.' + diff --git a/recipes/bioconductor-genocn/build.sh b/recipes/bioconductor-genocn/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genocn/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genocn/meta.yaml b/recipes/bioconductor-genocn/meta.yaml new file mode 100644 index 0000000000000..c4c3cd4b4f4de --- /dev/null +++ b/recipes/bioconductor-genocn/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.34.0" %} +{% set name = "genoCN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7b95b4cd827c5f41d1b35f5537be32f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Simultaneous identification of copy number states and genotype calls for regions of either copy number variations or copy number aberrations' + diff --git a/recipes/bioconductor-genogam/build.sh b/recipes/bioconductor-genogam/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genogam/build.sh +++ b/recipes/bioconductor-genogam/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genogam/meta.yaml b/recipes/bioconductor-genogam/meta.yaml index d0893db772164..4945fcfd6e499 100644 --- a/recipes/bioconductor-genogam/meta.yaml +++ b/recipes/bioconductor-genogam/meta.yaml @@ -1,62 +1,82 @@ -{% set version = "1.8.0" %} +{% set version = "2.0.1" %} {% set name = "GenoGAM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dac8591de7ba5396e9c2461df9aeea1c4172a15b9d92509b28c9760e7cf89981 + md5: a342d97707be1c0da6173cbeccbd47e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, chipseq (>= 1.21.2), LSD (>= 3.0.0), genefilter (>= 1.54.2), ggplot2 (>= 2.1.0), testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' - - 'r-mgcv >=1.8' - - 'r-reshape2 >=1.4.1' + - 'r-matrix >=1.2-8' + - 'r-rcpp >=0.12.14' + - r-rcpparmadillo + - 'r-sparseinv >=0.1.1' run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - 'r-data.table >=1.9.4' - 'r-futile.logger >=1.4.1' - - 'r-mgcv >=1.8' - - 'r-reshape2 >=1.4.1' + - 'r-matrix >=1.2-8' + - 'r-rcpp >=0.12.14' + - r-rcpparmadillo + - 'r-sparseinv >=0.1.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package allows statistical analysis of genome-wide data with smooth functions using generalized additive models based on the implementation from the R-package ''mgcv''. It provides methods for the statistical analysis of ChIP-Seq data including inference of protein occupancy, and pointwise and region-wise differential analysis. Estimation of dispersion and smoothing parameters is performed by cross-validation. Scaling of generalized additive model fitting to whole chromosomes is achieved by parallelization over overlapping genomic intervals.' extra: identifiers: - biotools:genogam - doi:10.1093/bioinformatics/btx150 + parent_recipe: + name: bioconductor-genogam + path: recipes/bioconductor-genogam + version: 1.8.0 + diff --git a/recipes/bioconductor-genomation/build.sh b/recipes/bioconductor-genomation/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomation/build.sh +++ b/recipes/bioconductor-genomation/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomation/meta.yaml b/recipes/bioconductor-genomation/meta.yaml index e7c3b4b1a49d3..ae8b4283e7ffb 100644 --- a/recipes/bioconductor-genomation/meta.yaml +++ b/recipes/bioconductor-genomation/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "genomation" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3747df788cc3535f593bcf11fa535b2cb30ccf062509bf1972f75880b36fb5ed + md5: b5adfde48396a2fd9ffd760e880690f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocGenerics, genomationData, knitr, RColorBrewer, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqpattern >=1.12.0,<1.14.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqpattern >=1.14.0,<1.15.0' - r-base - r-data.table - r-ggplot2 @@ -41,17 +42,17 @@ requirements: - r-reshape2 - r-runit run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqpattern >=1.12.0,<1.14.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqpattern >=1.14.0,<1.15.0' - r-base - r-data.table - r-ggplot2 @@ -71,9 +72,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.' extra: identifiers: - biotools:genomation + parent_recipe: + name: bioconductor-genomation + path: recipes/bioconductor-genomation + version: 1.12.0 + diff --git a/recipes/bioconductor-genomationdata/meta.yaml b/recipes/bioconductor-genomationdata/meta.yaml new file mode 100644 index 0000000000000..296fc359bfcf2 --- /dev/null +++ b/recipes/bioconductor-genomationdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "genomationData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c0a8b50d7fbe4e4179d172ce02204bf6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The package contains Chip Seq, Methylation and Cage data, downloaded from Encode' + diff --git a/recipes/bioconductor-genomationdata/post-link.sh b/recipes/bioconductor-genomationdata/post-link.sh new file mode 100644 index 0000000000000..b562ebef54849 --- /dev/null +++ b/recipes/bioconductor-genomationdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="genomationData_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/genomationData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/genomationData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomationdata/bioconductor-genomationdata_1.14.0_src_all.tar.gz" +) +MD5="c0a8b50d7fbe4e4179d172ce02204bf6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-genomationdata/pre-unlink.sh b/recipes/bioconductor-genomationdata/pre-unlink.sh new file mode 100644 index 0000000000000..e1f8e7c2e3835 --- /dev/null +++ b/recipes/bioconductor-genomationdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ genomationData diff --git a/recipes/bioconductor-genomegraphs/build.sh b/recipes/bioconductor-genomegraphs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomegraphs/build.sh +++ b/recipes/bioconductor-genomegraphs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomegraphs/meta.yaml b/recipes/bioconductor-genomegraphs/meta.yaml index 8c64faecc630c..1a22328692682 100644 --- a/recipes/bioconductor-genomegraphs/meta.yaml +++ b/recipes/bioconductor-genomegraphs/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "GenomeGraphs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8d5ed29b87f30da2d4d03fc31606500e3734f020e647d986fb40234a0cc5b73b + md5: 7be8b00de248fe8b5b73d43d17c9ea7a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.' + summary: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. GenomeGraphs uses the biomaRt package to perform live annotation queries to Ensembl and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data. Another strength of GenomeGraphs is to plot different data types such as array CGH, gene expression, sequencing and other data, together in one plot using the same genome coordinate system.' extra: identifiers: - biotools:genomegraphs - doi:10.1186/1471-2105-10-2 + parent_recipe: + name: bioconductor-genomegraphs + path: recipes/bioconductor-genomegraphs + version: 1.40.0 + diff --git a/recipes/bioconductor-genomeinfodb/build.sh b/recipes/bioconductor-genomeinfodb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomeinfodb/build.sh +++ b/recipes/bioconductor-genomeinfodb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomeinfodb/meta.yaml b/recipes/bioconductor-genomeinfodb/meta.yaml index 397ebb2c160d8..06df2a6b077cd 100644 --- a/recipes/bioconductor-genomeinfodb/meta.yaml +++ b/recipes/bioconductor-genomeinfodb/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "GenomeInfoDb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4d3cfacef3abf26241cb180b3a52ba053b45a85a794858613cb8d6e615c4167a + md5: b680b6c792d677f90541bdfdd0eb0bfb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GenomicRanges, Rsamtools, GenomicAlignments, BSgenome, GenomicFeatures, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Celegans.UCSC.ce2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Dmelanogaster.UCSC.dm3.ensGene, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodbdata >=1.1.0,<1.3.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcurl run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodbdata >=1.1.0,<1.3.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcurl test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Contains data and functions that define and allow translation between different chromosome sequence naming conventions (e.g., "chr1" versus "1"), including a function that attempts to place sequence names in their natural, rather than lexicographic, order.' extra: identifiers: - biotools:genomeinfodb - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genomeinfodb + path: recipes/bioconductor-genomeinfodb + version: 1.16.0 + diff --git a/recipes/bioconductor-genomeinfodbdata/meta.yaml b/recipes/bioconductor-genomeinfodbdata/meta.yaml index 88b7f5bf80d78..788e20b1ab7aa 100644 --- a/recipes/bioconductor-genomeinfodbdata/meta.yaml +++ b/recipes/bioconductor-genomeinfodbdata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.1.0" %} +{% set version = "1.2.0" %} {% set name = "GenomeInfoDbData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6efdca22839c90d455843bdab7c0ecb5d48e3b6c2f7b4882d3210a6bbad4304c + md5: 8fdbaf72a91aa676a3d521f0f307f10b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Files for mapping between NCBI taxonomy ID and species. Used by functions in the GenomeInfoDb package.' - +extra: + parent_recipe: + name: bioconductor-genomeinfodbdata + path: recipes/bioconductor-genomeinfodbdata + version: 1.1.0 diff --git a/recipes/bioconductor-genomeinfodbdata/post-link.sh b/recipes/bioconductor-genomeinfodbdata/post-link.sh index 1c0228a1c3abe..a974e47e62ffa 100644 --- a/recipes/bioconductor-genomeinfodbdata/post-link.sh +++ b/recipes/bioconductor-genomeinfodbdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GenomeInfoDbData_1.1.0.tar.gz" +FN="GenomeInfoDbData_1.2.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GenomeInfoDbData_1.1.0.tar.gz" - "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.1.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.1.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GenomeInfoDbData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/GenomeInfoDbData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomeinfodbdata/bioconductor-genomeinfodbdata_1.2.0_src_all.tar.gz" ) -MD5="e7fe0694dc065ebe8a7474d9b7afca63" +MD5="8fdbaf72a91aa676a3d521f0f307f10b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-genomeintervals/build.sh b/recipes/bioconductor-genomeintervals/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomeintervals/build.sh +++ b/recipes/bioconductor-genomeintervals/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomeintervals/meta.yaml b/recipes/bioconductor-genomeintervals/meta.yaml index 9f96fdf864682..57d605664d9ff 100644 --- a/recipes/bioconductor-genomeintervals/meta.yaml +++ b/recipes/bioconductor-genomeintervals/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "genomeIntervals" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d4d500f022255abd214723f690d278ce00b3c4582b694d4452f61c350259420f + md5: 4944f98e184cd5b015136453854d8bad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-intervals >=0.14.0' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-intervals >=0.14.0' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: ' This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package ''girafe''.' + summary: 'This package defines classes for representing genomic intervals and provides functions and methods for working with these. Note: The package provides the basic infrastructure for and is enhanced by the package ''girafe''.' extra: identifiers: - biotools:genomeintervals - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genomeintervals + path: recipes/bioconductor-genomeintervals + version: 1.36.0 + diff --git a/recipes/bioconductor-genomes/build.sh b/recipes/bioconductor-genomes/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genomes/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomes/meta.yaml b/recipes/bioconductor-genomes/meta.yaml new file mode 100644 index 0000000000000..27e2a195c36bb --- /dev/null +++ b/recipes/bioconductor-genomes/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.12.0" %} +{% set name = "genomes" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 725ed613b762b70263f03f55a1792cd4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-curl + - r-readr + run: + - r-base + - r-curl + - r-readr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Download genome and assembly reports from NCBI' + diff --git a/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml new file mode 100644 index 0000000000000..a3479e9f06524 --- /dev/null +++ b/recipes/bioconductor-genomewidesnp5crlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.6" %} +{% set name = "genomewidesnp5Crlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cc24140cd17758b8e09f4fe6c931526a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for fast genotyping Affymetrix GenomeWideSnp_5 arrays using the ''crlmm'' package. Annotation build is hg19.' + diff --git a/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh b/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh new file mode 100644 index 0000000000000..0185d129605b1 --- /dev/null +++ b/recipes/bioconductor-genomewidesnp5crlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="genomewidesnp5Crlmm_1.0.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/genomewidesnp5Crlmm_1.0.6.tar.gz" + "https://bioarchive.galaxyproject.org/genomewidesnp5Crlmm_1.0.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp5crlmm/bioconductor-genomewidesnp5crlmm_1.0.6_src_all.tar.gz" +) +MD5="cc24140cd17758b8e09f4fe6c931526a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-genomewidesnp5crlmm/pre-unlink.sh b/recipes/bioconductor-genomewidesnp5crlmm/pre-unlink.sh new file mode 100644 index 0000000000000..0c94b224c4619 --- /dev/null +++ b/recipes/bioconductor-genomewidesnp5crlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ genomewidesnp5Crlmm diff --git a/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml new file mode 100644 index 0000000000000..816a4d2060ac3 --- /dev/null +++ b/recipes/bioconductor-genomewidesnp6crlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.7" %} +{% set name = "genomewidesnp6Crlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 13dd5aef3d814524896f2f3013beb78b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for fast genotyping Affymetrix GenomeWideSnp_6 arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh b/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh new file mode 100644 index 0000000000000..b86df4588d0c7 --- /dev/null +++ b/recipes/bioconductor-genomewidesnp6crlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="genomewidesnp6Crlmm_1.0.7.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/genomewidesnp6Crlmm_1.0.7.tar.gz" + "https://bioarchive.galaxyproject.org/genomewidesnp6Crlmm_1.0.7.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-genomewidesnp6crlmm/bioconductor-genomewidesnp6crlmm_1.0.7_src_all.tar.gz" +) +MD5="13dd5aef3d814524896f2f3013beb78b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-genomewidesnp6crlmm/pre-unlink.sh b/recipes/bioconductor-genomewidesnp6crlmm/pre-unlink.sh new file mode 100644 index 0000000000000..0dce3e6d5c72e --- /dev/null +++ b/recipes/bioconductor-genomewidesnp6crlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ genomewidesnp6Crlmm diff --git a/recipes/bioconductor-genomicalignments/build.sh b/recipes/bioconductor-genomicalignments/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicalignments/build.sh +++ b/recipes/bioconductor-genomicalignments/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicalignments/meta.yaml b/recipes/bioconductor-genomicalignments/meta.yaml index da770863630f3..bb9f3d83734e5 100644 --- a/recipes/bioconductor-genomicalignments/meta.yaml +++ b/recipes/bioconductor-genomicalignments/meta.yaml @@ -1,43 +1,44 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GenomicAlignments" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5c31ea7deaf17c3ea3a66fe41dfce754b5495f65a28be7860042ae392d13f102 + md5: 9054ced6f29df68b28bc3241e8fc644a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: ShortRead, rtracklayer, BSgenome, GenomicFeatures, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Hsapiens.UCSC.hg19, DESeq2, edgeR, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base build: - {{ compiler('c') }} @@ -46,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides efficient containers for storing and manipulating short genomic alignments (typically obtained by aligning short reads to a reference genome). This includes read counting, computing the coverage, junction detection, and working with the nucleotide content of the alignments.' extra: identifiers: - biotools:genomicalignments + parent_recipe: + name: bioconductor-genomicalignments + path: recipes/bioconductor-genomicalignments + version: 1.16.0 + diff --git a/recipes/bioconductor-genomicdatacommons/build.sh b/recipes/bioconductor-genomicdatacommons/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicdatacommons/build.sh +++ b/recipes/bioconductor-genomicdatacommons/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicdatacommons/meta.yaml b/recipes/bioconductor-genomicdatacommons/meta.yaml index 8e1c5df614f8c..4c24d9d3e9681 100644 --- a/recipes/bioconductor-genomicdatacommons/meta.yaml +++ b/recipes/bioconductor-genomicdatacommons/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "GenomicDataCommons" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2b4259874fc3507fb81712e750c5aba8311abf913a78125ba39defee883aae7b + md5: 390615fd4999a0564cea10c4242c878e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, DT, testthat, listviewer, ggplot2, GenomicAlignments, Rsamtools requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dplyr - r-httr @@ -32,10 +34,10 @@ requirements: - r-readr - r-xml2 run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dplyr - r-httr @@ -49,8 +51,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Programmatically access the NIH / NCI Genomic Data Commons RESTful service.' - +extra: + parent_recipe: + name: bioconductor-genomicdatacommons + path: recipes/bioconductor-genomicdatacommons + version: 1.4.3 diff --git a/recipes/bioconductor-genomicfeatures/build.sh b/recipes/bioconductor-genomicfeatures/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicfeatures/build.sh +++ b/recipes/bioconductor-genomicfeatures/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicfeatures/meta.yaml b/recipes/bioconductor-genomicfeatures/meta.yaml index fd2ebffc05029..dc9c71d563d33 100644 --- a/recipes/bioconductor-genomicfeatures/meta.yaml +++ b/recipes/bioconductor-genomicfeatures/meta.yaml @@ -1,50 +1,52 @@ -{% set version = "1.32.3" %} +{% set version = "1.34.1" %} {% set name = "GenomicFeatures" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 081592aee639cbc730fc10e309d41012b97193a0ee5100f0d3dc0f186391f91a + md5: b227cf5cd1a3cbabc3df6381060234ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RMariaDB, org.Mm.eg.db, org.Hs.eg.db, BSgenome, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.17), BSgenome.Celegans.UCSC.ce2, BSgenome.Dmelanogaster.UCSC.dm3 (>= 1.3.17), mirbase.db, FDb.UCSC.tRNAs, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Dmelanogaster.UCSC.dm3.ensGene (>= 2.7.1), TxDb.Mmusculus.UCSC.mm10.knownGene, TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts, TxDb.Hsapiens.UCSC.hg38.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh38, Rsamtools, pasillaBamSubset (>= 0.0.5), GenomicAlignments (>= 1.15.7), ensembldb, RUnit, BiocStyle, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dbi - r-rcurl - 'r-rsqlite >=2.0' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dbi - r-rcurl @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of tools and methods for making and manipulating transcript centric annotations. With these tools the user can easily download the genomic locations of the transcripts, exons and cds of a given organism, from either the UCSC Genome Browser or a BioMart database (more sources will be supported in the future). This information is then stored in a local database that keeps track of the relationship between transcripts, exons, cds and genes. Flexible methods are provided for extracting the desired features in a convenient format.' extra: identifiers: - biotools:genomicfeatures + parent_recipe: + name: bioconductor-genomicfeatures + path: recipes/bioconductor-genomicfeatures + version: 1.32.3 + diff --git a/recipes/bioconductor-genomicfiles/build.sh b/recipes/bioconductor-genomicfiles/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicfiles/build.sh +++ b/recipes/bioconductor-genomicfiles/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicfiles/meta.yaml b/recipes/bioconductor-genomicfiles/meta.yaml index 06890911958dc..c0c2ab670cdf2 100644 --- a/recipes/bioconductor-genomicfiles/meta.yaml +++ b/recipes/bioconductor-genomicfiles/meta.yaml @@ -1,56 +1,63 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GenomicFiles" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b8ebf3927dafb3d9144042a357981aeb9841efbc53acf912f532bff859c11a2e + md5: 2776040839b95869d3c9686fedb8144a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, RUnit, genefilter, deepSNV, RNAseqData.HNRNPC.bam.chr14, Biostrings, Homo.sapiens requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides infrastructure for parallel computations distributed ''by file'' or ''by range''. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.' extra: identifiers: - biotools:genomicfiles - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genomicfiles + path: recipes/bioconductor-genomicfiles + version: 1.16.0 + diff --git a/recipes/bioconductor-genomicinteractions/build.sh b/recipes/bioconductor-genomicinteractions/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicinteractions/build.sh +++ b/recipes/bioconductor-genomicinteractions/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicinteractions/conda_build_config.yaml b/recipes/bioconductor-genomicinteractions/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-genomicinteractions/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-genomicinteractions/meta.yaml b/recipes/bioconductor-genomicinteractions/meta.yaml index c62c5de64acb3..baeab481c7c64 100644 --- a/recipes/bioconductor-genomicinteractions/meta.yaml +++ b/recipes/bioconductor-genomicinteractions/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GenomicInteractions" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 58e0ba4203e9d0481bf1a2c8570eccf5c1233bc7d0c724b4b96701d9f37dca32 + md5: c1beef4055b4d2e6cd2ccba99b7f331b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-dplyr @@ -36,16 +38,16 @@ requirements: - r-igraph - r-stringr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-dplyr @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R package for handling Genomic interaction data, such as ChIA-PET/Hi-C, annotating genomic features with interaction information and producing various plots / statistics.' extra: identifiers: - biotools:genomicinteractions - doi:10.1186/s12864-015-2140-x + parent_recipe: + name: bioconductor-genomicinteractions + path: recipes/bioconductor-genomicinteractions + version: 1.14.0 + diff --git a/recipes/bioconductor-genomicranges/build.sh b/recipes/bioconductor-genomicranges/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicranges/build.sh +++ b/recipes/bioconductor-genomicranges/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicranges/meta.yaml b/recipes/bioconductor-genomicranges/meta.yaml index 3a8088ebe24ed..b861fecd91ae8 100644 --- a/recipes/bioconductor-genomicranges/meta.yaml +++ b/recipes/bioconductor-genomicranges/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.32.7" %} +{% set version = "1.34.0" %} {% set name = "GenomicRanges" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3dfb5943567056c4e4908b85113b9fea3b36c3bd5b9961044ab3e6a5b42205d2 + md5: efe660c341dcd0c0b07d2e9086b63434 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Matrix, Biobase, AnnotationDbi, annotate, Biostrings (>= 2.25.3), SummarizedExperiment (>= 0.1.5), Rsamtools (>= 1.13.53), GenomicAlignments, rtracklayer, BSgenome, GenomicFeatures, Gviz, VariantAnnotation, AnnotationHub, DESeq2, DEXSeq, edgeR, KEGGgraph, RNAseqData.HNRNPC.bam.chr14, pasillaBamSubset, KEGG.db, hgu95av2.db, hgu95av2probe, BSgenome.Scerevisiae.UCSC.sacCer2, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, TxDb.Athaliana.BioMart.plantsmart22, TxDb.Dmelanogaster.UCSC.dm3.ensGene, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, RUnit, digest, knitr, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ability to efficiently represent and manipulate genomic annotations and alignments is playing a central role when it comes to analyzing high-throughput sequencing data (a.k.a. NGS data). The GenomicRanges package defines general purpose containers for storing and manipulating genomic intervals and variables defined along a genome. More specialized containers for representing and manipulating short alignments against a reference genome, or a matrix-like summarization of an experiment, are defined in the GenomicAlignments and SummarizedExperiment packages, respectively. Both packages build on top of the GenomicRanges infrastructure.' extra: identifiers: - biotools:genomicranges + parent_recipe: + name: bioconductor-genomicranges + path: recipes/bioconductor-genomicranges + version: 1.32.7 + diff --git a/recipes/bioconductor-genomicscores/build.sh b/recipes/bioconductor-genomicscores/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomicscores/build.sh +++ b/recipes/bioconductor-genomicscores/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomicscores/conda_build_config.yaml b/recipes/bioconductor-genomicscores/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-genomicscores/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-genomicscores/meta.yaml b/recipes/bioconductor-genomicscores/meta.yaml index 0d7251ab91405..7541d7cefb792 100644 --- a/recipes/bioconductor-genomicscores/meta.yaml +++ b/recipes/bioconductor-genomicscores/meta.yaml @@ -1,50 +1,58 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.0" %} {% set name = "GenomicScores" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: db91e995ca16bc45bb36987eed0e2eb921c4190d272061fbbf454d5c61836575 + md5: 002dca8198727b7629cf69f5b17b6240 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19, phastCons100way.UCSC.hg19, MafDb.1Kgenomes.phase1.hs37d5, SNPlocs.Hsapiens.dbSNP144.GRCh37, VariantAnnotation, TxDb.Hsapiens.UCSC.hg19.knownGene, gwascat, RColorBrewer requirements: host: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-xml run: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provide infrastructure to store and access genomewide position-specific scores within R and Bioconductor.' +extra: + parent_recipe: + name: bioconductor-genomicscores + path: recipes/bioconductor-genomicscores + version: 1.4.1 + diff --git a/recipes/bioconductor-genomictuples/build.sh b/recipes/bioconductor-genomictuples/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genomictuples/build.sh +++ b/recipes/bioconductor-genomictuples/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genomictuples/meta.yaml b/recipes/bioconductor-genomictuples/meta.yaml index b58fdef4e38ad..abfb320b0c272 100644 --- a/recipes/bioconductor-genomictuples/meta.yaml +++ b/recipes/bioconductor-genomictuples/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.14.1" %} +{% set version = "1.16.0" %} {% set name = "GenomicTuples" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 95f5e2e9be0502a57e524894089027f5061bbb2a408fc78288ddf71d7faab5f0 + md5: 9b7b5ed8d0fbd6a214f5556b2c38a4b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - 'r-rcpp >=0.11.2' @@ -43,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'GenomicTuples defines general purpose containers for storing genomic tuples. It aims to provide functionality for tuples of genomic co-ordinates that are analogous to those available for genomic ranges in the GenomicRanges Bioconductor package.' extra: identifiers: - biotools:genomictuples - doi:10.21105/joss.00020 + parent_recipe: + name: bioconductor-genomictuples + path: recipes/bioconductor-genomictuples + version: 1.14.1 + diff --git a/recipes/bioconductor-genominator/build.sh b/recipes/bioconductor-genominator/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genominator/build.sh +++ b/recipes/bioconductor-genominator/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genominator/meta.yaml b/recipes/bioconductor-genominator/meta.yaml index cc94c665012fd..1e5ecf8bf9c06 100644 --- a/recipes/bioconductor-genominator/meta.yaml +++ b/recipes/bioconductor-genominator/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "Genominator" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b1e8f89947dee843d4194acdf4e614277ef415aebfe350a5a2a71e25e70130b2 + md5: a787b87c5fee3feaea76a0151ccdee50 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, ShortRead, yeastRNASeq requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-dbi >=0.2-5' - r-rsqlite run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-dbi >=0.2-5' - r-rsqlite @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for storing, accessing, analyzing and visualizing genomic data.' extra: identifiers: - biotools:genominator - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genominator + path: recipes/bioconductor-genominator + version: 1.34.0 + diff --git a/recipes/bioconductor-genoset/build.sh b/recipes/bioconductor-genoset/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genoset/build.sh +++ b/recipes/bioconductor-genoset/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genoset/meta.yaml b/recipes/bioconductor-genoset/meta.yaml index 7b8afb9c06159..eb78b02ca9264 100644 --- a/recipes/bioconductor-genoset/meta.yaml +++ b/recipes/bioconductor-genoset/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "genoset" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6313ba101617a192ffc7066b3fccf4b564760f918838c5b53cb53e3faf3d33b8 + md5: 68336a575e2390f041edb49ed5b68477 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, BiocStyle, rmarkdown, DNAcopy, stats, BSgenome, Biostrings requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base build: - {{ compiler('c') }} @@ -40,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'GenoSet provides an extension of the RangedSummarizedExperiment class with additional API features. This class provides convenient and fast methods for working with segmented genomic data. Additionally, GenoSet provides the class RleDataFrame which stores runs of data along the genome for multiple samples and provides very fast summaries of arbitrary row sets (regions of the genome).' extra: identifiers: - biotools:genoset - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-genoset + path: recipes/bioconductor-genoset + version: 1.36.0 + diff --git a/recipes/bioconductor-genotypeeval/build.sh b/recipes/bioconductor-genotypeeval/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genotypeeval/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genotypeeval/meta.yaml b/recipes/bioconductor-genotypeeval/meta.yaml new file mode 100644 index 0000000000000..02d10822274a6 --- /dev/null +++ b/recipes/bioconductor-genotypeeval/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.14.0" %} +{% set name = "genotypeeval" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d8c0444b34549730384bdad50312d814 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rmarkdown, testthat, SNPlocs.Hsapiens.dbSNP141.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Takes in a gVCF or VCF and reports metrics to assess quality of calls.' + diff --git a/recipes/bioconductor-genphen/build.sh b/recipes/bioconductor-genphen/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-genphen/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genphen/meta.yaml b/recipes/bioconductor-genphen/meta.yaml new file mode 100644 index 0000000000000..ed8ed4e1b0268 --- /dev/null +++ b/recipes/bioconductor-genphen/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.10.0" %} +{% set name = "genphen" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c7be09e60a56d52fcdffa12b85b6e028 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-doparallel + - r-e1071 + - r-foreach + - r-ranger + - r-rstan + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-doparallel + - r-e1071 + - r-foreach + - r-ranger + - r-rstan + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Genetic association studies are an essential tool for studying the relationship between genotypes and phenotypes. With genphen we can quantify the association between genotypes and phenotypes using a hybrid method which uses statistical learning techniques such as random forest and support vector machines, and Bayesian inference using hierarchical models.' + diff --git a/recipes/bioconductor-genrank/build.sh b/recipes/bioconductor-genrank/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genrank/build.sh +++ b/recipes/bioconductor-genrank/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genrank/meta.yaml b/recipes/bioconductor-genrank/meta.yaml index 08fefa82c49eb..222d422e5471f 100644 --- a/recipes/bioconductor-genrank/meta.yaml +++ b/recipes/bioconductor-genrank/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GenRank" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9a61a6085c797dc11682740c9b98583709058facdd0048a2a97c4347e80252f0 + md5: 68b7b5b4ad252221ec675ee9f40e0037 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-survcomp >=1.30.0,<1.32.0' + - 'bioconductor-survcomp >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-reshape2 run: - - 'bioconductor-survcomp >=1.30.0,<1.32.0' + - 'bioconductor-survcomp >=1.32.0,<1.33.0' - r-base - r-matrixstats - r-reshape2 @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Methods for ranking genes based on convergent evidence obtained from multiple independent evidence layers. This package adapts three methods that are popular for meta-analysis.' extra: identifiers: - biotools:genrank - doi:10.12688/f1000research.11223.1 + parent_recipe: + name: bioconductor-genrank + path: recipes/bioconductor-genrank + version: 1.8.0 + diff --git a/recipes/bioconductor-genvisr/build.sh b/recipes/bioconductor-genvisr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-genvisr/build.sh +++ b/recipes/bioconductor-genvisr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-genvisr/meta.yaml b/recipes/bioconductor-genvisr/meta.yaml index bdf4932acea4c..0100b55c5a378 100644 --- a/recipes/bioconductor-genvisr/meta.yaml +++ b/recipes/bioconductor-genvisr/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.1" %} {% set name = "GenVisR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 575d7f8a0c316661b6ff290c36a37006e62c20f1393675e85f93b86a1327b7b4 + md5: 5d3227cc62984bf83ee35b0931b81555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, knitr, RMySQL, roxygen2, testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, rmarkdown, vdiffr, formatR, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - r-dbi @@ -42,17 +44,17 @@ requirements: - r-scales - r-viridis run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - r-dbi @@ -69,9 +71,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Produce highly customizable publication quality graphics for genomic data primarily at the cohort level.' extra: identifiers: - biotools:genvisr + parent_recipe: + name: bioconductor-genvisr + path: recipes/bioconductor-genvisr + version: 1.12.1 + diff --git a/recipes/bioconductor-geometadb/build.sh b/recipes/bioconductor-geometadb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geometadb/build.sh +++ b/recipes/bioconductor-geometadb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geometadb/meta.yaml b/recipes/bioconductor-geometadb/meta.yaml index 71c7503258e56..277b1c68be2ca 100644 --- a/recipes/bioconductor-geometadb/meta.yaml +++ b/recipes/bioconductor-geometadb/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GEOmetadb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6aa42745ede4b84d337454db584ff0c8881edc288d9efe55b6f23d372be03656 + md5: 9c85e98fb9e4f41fa76e8bac68ff4d35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, dplyr, tm, wordcloud requirements: host: - - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' - r-base - r-rsqlite run: - - 'bioconductor-geoquery >=2.48.0,<2.50.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' - r-base - r-rsqlite test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The NCBI Gene Expression Omnibus (GEO) represents the largest public repository of microarray data. However, finding data of interest can be challenging using current tools. GEOmetadb is an attempt to make access to the metadata associated with samples, platforms, and datasets much more feasible. This is accomplished by parsing all the NCBI GEO metadata into a SQLite database that can be stored and queried locally. GEOmetadb is simply a thin wrapper around the SQLite database along with associated documentation. Finally, the SQLite database is updated regularly as new data is added to GEO and can be downloaded at will for the most up-to-date metadata. GEOmetadb paper: http://bioinformatics.oxfordjournals.org/cgi/content/short/24/23/2798 .' extra: identifiers: - biotools:geometadb + parent_recipe: + name: bioconductor-geometadb + path: recipes/bioconductor-geometadb + version: 1.42.0 + diff --git a/recipes/bioconductor-geoquery/build.sh b/recipes/bioconductor-geoquery/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geoquery/build.sh +++ b/recipes/bioconductor-geoquery/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geoquery/meta.yaml b/recipes/bioconductor-geoquery/meta.yaml index e067c3fd6cb43..c12c926d292b9 100644 --- a/recipes/bioconductor-geoquery/meta.yaml +++ b/recipes/bioconductor-geoquery/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "2.48.0" %} +{% set version = "2.50.0" %} {% set name = "GEOquery" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8a1edf0e93f9da2561210bb709807cb8d848c1f68603b7cccc6c2c21161fb622 + md5: 4d161559db4839c1601d1f4ca53c3332 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocGenerics, testthat, covr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-httr @@ -28,8 +30,8 @@ requirements: - r-tidyr - r-xml2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-httr @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The NCBI Gene Expression Omnibus (GEO) is a public repository of microarray data. Given the rich and varied nature of this resource, it is only natural to want to apply BioConductor tools to these data. GEOquery is the bridge between GEO and BioConductor.' extra: identifiers: - biotools:geoquery + parent_recipe: + name: bioconductor-geoquery + path: recipes/bioconductor-geoquery + version: 2.48.0 + diff --git a/recipes/bioconductor-geosubmission/build.sh b/recipes/bioconductor-geosubmission/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-geosubmission/build.sh +++ b/recipes/bioconductor-geosubmission/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-geosubmission/conda_build_config.yaml b/recipes/bioconductor-geosubmission/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-geosubmission/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-geosubmission/meta.yaml b/recipes/bioconductor-geosubmission/meta.yaml index eca6a270fbc16..1e64433e553d3 100644 --- a/recipes/bioconductor-geosubmission/meta.yaml +++ b/recipes/bioconductor-geosubmission/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "GEOsubmission" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 14e7be69f386b0f7b97d0b36fe275cd13379363a1324e48d28e9ef2242509170 + md5: 54b2359778553d53725c9974f1cda515 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Helps to easily submit a microarray dataset and the associated sample information to GEO by preparing a single file for upload (direct deposit).' extra: identifiers: - biotools:geosubmission - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-geosubmission + path: recipes/bioconductor-geosubmission + version: 1.32.0 + diff --git a/recipes/bioconductor-gep2pep/build.sh b/recipes/bioconductor-gep2pep/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gep2pep/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gep2pep/meta.yaml b/recipes/bioconductor-gep2pep/meta.yaml new file mode 100644 index 0000000000000..399ba00737555 --- /dev/null +++ b/recipes/bioconductor-gep2pep/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "gep2pep" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fd48276c9acea753df8d96b68a5b5ab0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: WriteXLS, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-base + - r-digest + - r-foreach + - r-iterators + - 'r-repo >=2.1.1' + - r-xml + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-base + - r-digest + - r-foreach + - r-iterators + - 'r-repo >=2.1.1' + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Pathway Expression Profiles (PEPs) are based on the expression of pathways (defined as sets of genes) as opposed to individual genes. This package converts gene expression profiles to PEPs and performs enrichment analysis of both pathways and experimental conditions, such as "drug set enrichment analysis" and "gene2drug" drug discovery analysis respectively.' + diff --git a/recipes/bioconductor-gesper/build.sh b/recipes/bioconductor-gesper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gesper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gesper/meta.yaml b/recipes/bioconductor-gesper/meta.yaml new file mode 100644 index 0000000000000..8895942bf37d3 --- /dev/null +++ b/recipes/bioconductor-gesper/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.14.0" %} +{% set name = "gespeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d646d9eae2ab8798944be04aed1fa303 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-glmnet + - r-matrix + - r-reshape2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-glmnet + - r-matrix + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Estimates gene-specific phenotypes from off-target confounded RNAi screens. The phenotype of each siRNA is modeled based on on-targeted and off-targeted genes, using a regularized linear regression model.' + diff --git a/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml new file mode 100644 index 0000000000000..53c8bc70796f2 --- /dev/null +++ b/recipes/bioconductor-geuvadistranscriptexpr/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "GeuvadisTranscriptExpr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e7df5c58da3c1e58245c8b0d12263735 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, rtracklayer, GenomicRanges, Rsamtools, VariantAnnotation, tools, BiocStyle, knitr, testthat +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Provides transcript expression and bi-allelic genotypes corresponding to the chromosome 19 for CEU individuals from the GEUVADIS project, Lappalainen et al.' + diff --git a/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh new file mode 100644 index 0000000000000..ddcc63ee69362 --- /dev/null +++ b/recipes/bioconductor-geuvadistranscriptexpr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GeuvadisTranscriptExpr_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GeuvadisTranscriptExpr_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/GeuvadisTranscriptExpr_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvadistranscriptexpr/bioconductor-geuvadistranscriptexpr_1.10.0_src_all.tar.gz" +) +MD5="e7df5c58da3c1e58245c8b0d12263735" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-geuvadistranscriptexpr/pre-unlink.sh b/recipes/bioconductor-geuvadistranscriptexpr/pre-unlink.sh new file mode 100644 index 0000000000000..1f1b1a6bbc357 --- /dev/null +++ b/recipes/bioconductor-geuvadistranscriptexpr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GeuvadisTranscriptExpr diff --git a/recipes/bioconductor-geuvpack/meta.yaml b/recipes/bioconductor-geuvpack/meta.yaml new file mode 100644 index 0000000000000..054fc78590ba5 --- /dev/null +++ b/recipes/bioconductor-geuvpack/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.14.0" %} +{% set name = "geuvPack" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0fddefe9a5285b6545e39af655ef2502 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FPKM from GEUVADIS, annotated to gencode regions' + diff --git a/recipes/bioconductor-geuvpack/post-link.sh b/recipes/bioconductor-geuvpack/post-link.sh new file mode 100644 index 0000000000000..27215be2a17f6 --- /dev/null +++ b/recipes/bioconductor-geuvpack/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="geuvPack_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geuvPack_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/geuvPack_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvpack/bioconductor-geuvpack_1.14.0_src_all.tar.gz" +) +MD5="0fddefe9a5285b6545e39af655ef2502" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-geuvpack/pre-unlink.sh b/recipes/bioconductor-geuvpack/pre-unlink.sh new file mode 100644 index 0000000000000..8064c89fff54e --- /dev/null +++ b/recipes/bioconductor-geuvpack/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ geuvPack diff --git a/recipes/bioconductor-geuvstore2/meta.yaml b/recipes/bioconductor-geuvstore2/meta.yaml new file mode 100644 index 0000000000000..4b678c202fc4d --- /dev/null +++ b/recipes/bioconductor-geuvstore2/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.12.0" %} +{% set name = "geuvStore2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4a979fce43756a969ef30510fc7edd7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Homo.sapiens, knitr (>= 1.7), rmarkdown +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - r-base + - r-batchjobs + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - r-base + - r-batchjobs + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'demonstrate storage discipline for eQTL enumerations and analyses based on a selection of GEUVADIS results' + diff --git a/recipes/bioconductor-geuvstore2/post-link.sh b/recipes/bioconductor-geuvstore2/post-link.sh new file mode 100644 index 0000000000000..2fc765b3a909f --- /dev/null +++ b/recipes/bioconductor-geuvstore2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="geuvStore2_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/geuvStore2_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/geuvStore2_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-geuvstore2/bioconductor-geuvstore2_1.12.0_src_all.tar.gz" +) +MD5="4a979fce43756a969ef30510fc7edd7f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-geuvstore2/pre-unlink.sh b/recipes/bioconductor-geuvstore2/pre-unlink.sh new file mode 100644 index 0000000000000..3df07848c5b85 --- /dev/null +++ b/recipes/bioconductor-geuvstore2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ geuvStore2 diff --git a/recipes/bioconductor-gewist/build.sh b/recipes/bioconductor-gewist/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gewist/build.sh +++ b/recipes/bioconductor-gewist/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gewist/meta.yaml b/recipes/bioconductor-gewist/meta.yaml index 33795f86de50a..3da9a77fa5885 100644 --- a/recipes/bioconductor-gewist/meta.yaml +++ b/recipes/bioconductor-gewist/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "GEWIST" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 20f0beb921758bdcfa4b1accbb9d7cca053082ff2622e46568377937e7d3a58e + md5: d056905b8d6521e06a936955e8fdab08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This ''GEWIST'' package provides statistical tools to efficiently optimize SNP prioritization for gene-gene and gene-environment interactions.' extra: identifiers: - biotools:gewist - doi:10.1002/gepi.20624 + parent_recipe: + name: bioconductor-gewist + path: recipes/bioconductor-gewist + version: 1.24.0 + diff --git a/recipes/bioconductor-ggbase/build.sh b/recipes/bioconductor-ggbase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ggbase/build.sh +++ b/recipes/bioconductor-ggbase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggbase/meta.yaml b/recipes/bioconductor-ggbase/meta.yaml index 0b6e9b1988f3c..97155cac51a9f 100644 --- a/recipes/bioconductor-ggbase/meta.yaml +++ b/recipes/bioconductor-ggbase/meta.yaml @@ -1,47 +1,49 @@ -{% set version = "3.42.0" %} +{% set version = "3.44.0" %} {% set name = "GGBase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7cb06de6feb0dcbda0dc2a2f9f03a54344777ac7c981359edaae7c359006bfdf + md5: 126306447c411a4c114df4a7f83fdce7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GGtools, illuminaHumanv1.db, knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-snpstats >=1.30.0,<1.32.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-digest - r-matrix run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-snpstats >=1.30.0,<1.32.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-digest - r-matrix @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: infrastructure extra: identifiers: - biotools:ggbase - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ggbase + path: recipes/bioconductor-ggbase + version: 3.42.0 + diff --git a/recipes/bioconductor-ggbio/build.sh b/recipes/bioconductor-ggbio/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ggbio/build.sh +++ b/recipes/bioconductor-ggbio/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggbio/conda_build_config.yaml b/recipes/bioconductor-ggbio/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-ggbio/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-ggbio/meta.yaml b/recipes/bioconductor-ggbio/meta.yaml index 0718a0b3635fd..4e27ee449d09e 100644 --- a/recipes/bioconductor-ggbio/meta.yaml +++ b/recipes/bioconductor-ggbio/meta.yaml @@ -1,42 +1,44 @@ -{% set version = "1.28.5" %} +{% set version = "1.30.0" %} {% set name = "ggbio" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4d901925bc46118cc1135883b18ee1bf97617c48a7d2411d218e33ef00d942a7 + md5: fff6ae2022a12bfc785903fa9f64e7a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: vsn, BSgenome.Hsapiens.UCSC.hg19, Homo.sapiens, TxDb.Hsapiens.UCSC.hg19.knownGene, chipseq, TxDb.Mmusculus.UCSC.mm9.knownGene, knitr, BiocStyle, testthat, EnsDb.Hsapiens.v75, tinytex requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -47,25 +49,25 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggally - 'r-ggplot2 >=1.0.0' @@ -79,9 +81,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ggbio package extends and specializes the grammar of graphics for biological data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries.' extra: identifiers: - biotools:ggbio + parent_recipe: + name: bioconductor-ggbio + path: recipes/bioconductor-ggbio + version: 1.28.5 + diff --git a/recipes/bioconductor-ggcyto/build.sh b/recipes/bioconductor-ggcyto/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ggcyto/build.sh +++ b/recipes/bioconductor-ggcyto/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggcyto/meta.yaml b/recipes/bioconductor-ggcyto/meta.yaml index 60eeaf4190f1f..9abbf230e1f9a 100644 --- a/recipes/bioconductor-ggcyto/meta.yaml +++ b/recipes/bioconductor-ggcyto/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "ggcyto" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 481774bcc1f99f4dfb3feb4083829c1ce5acebd2fd5670e316f17b4625a0edd9 + md5: 84a5c31b9b99f06caf9b71fd5048a4bf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, flowWorkspaceData, knitr, rmarkdown, flowStats, openCyto, flowViz, ggridges, vdiffr requirements: host: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - r-base - r-data.table - 'r-ggplot2 >=2.2.1.9000' @@ -30,9 +32,9 @@ requirements: - r-rlang - r-scales run: - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - r-base - r-data.table - 'r-ggplot2 >=2.2.1.9000' @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'With the dedicated fortify method implemented for flowSet, ncdfFlowSet and GatingSet classes, both raw and gated flow cytometry data can be plotted directly with ggplot. ggcyto wrapper and some customed layers also make it easy to add gates and population statistics to the plot.' extra: identifiers: - biotools:ggcyto - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ggcyto + path: recipes/bioconductor-ggcyto + version: 1.8.2 + diff --git a/recipes/bioconductor-ggdata/meta.yaml b/recipes/bioconductor-ggdata/meta.yaml new file mode 100644 index 0000000000000..34a135232c979 --- /dev/null +++ b/recipes/bioconductor-ggdata/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "GGdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dffb9127f0d21be6e27478b178bf9d13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-illuminahumanv1.db >=1.26.0,<1.27.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-illuminahumanv1.db >=1.26.0,<1.27.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'data exemplars dealing with hapmap SNP reports, GWAS, etc.' + diff --git a/recipes/bioconductor-ggdata/post-link.sh b/recipes/bioconductor-ggdata/post-link.sh new file mode 100644 index 0000000000000..c57b7dfc0e72d --- /dev/null +++ b/recipes/bioconductor-ggdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GGdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GGdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/GGdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ggdata/bioconductor-ggdata_1.20.0_src_all.tar.gz" +) +MD5="dffb9127f0d21be6e27478b178bf9d13" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ggdata/pre-unlink.sh b/recipes/bioconductor-ggdata/pre-unlink.sh new file mode 100644 index 0000000000000..ecfb2903f8b7b --- /dev/null +++ b/recipes/bioconductor-ggdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GGdata diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml new file mode 100644 index 0000000000000..56c52d0b42921 --- /dev/null +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.4.1" %} +{% set name = "GGHumanMethCancerPanelv1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e8f4a37182b175fb33dd54f8093e6f52 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Golden Gate Human Methylation Cancer Panel Version 1 annotation data (chip GGHumanMethCancerPanelv1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh b/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh new file mode 100644 index 0000000000000..c57236256cec9 --- /dev/null +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" + "https://bioarchive.galaxyproject.org/GGHumanMethCancerPanelv1.db_1.4.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gghumanmethcancerpanelv1.db/bioconductor-gghumanmethcancerpanelv1.db_1.4.1_src_all.tar.gz" +) +MD5="e8f4a37182b175fb33dd54f8093e6f52" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gghumanmethcancerpanelv1.db/pre-unlink.sh b/recipes/bioconductor-gghumanmethcancerpanelv1.db/pre-unlink.sh new file mode 100644 index 0000000000000..3fd6be849813a --- /dev/null +++ b/recipes/bioconductor-gghumanmethcancerpanelv1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GGHumanMethCancerPanelv1.db diff --git a/recipes/bioconductor-ggtools/build.sh b/recipes/bioconductor-ggtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ggtools/build.sh +++ b/recipes/bioconductor-ggtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggtools/meta.yaml b/recipes/bioconductor-ggtools/meta.yaml index 81989860e2995..c85288cb634e8 100644 --- a/recipes/bioconductor-ggtools/meta.yaml +++ b/recipes/bioconductor-ggtools/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "5.16.0" %} +{% set version = "5.18.0" %} {% set name = "GGtools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e86780b6d4583bf5f31f2b6063120f4c75b461b2807063293b161397a0d25a3c + md5: 7c5237419693c7989d912bd329dd982b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GGdata, illuminaHumanv1.db, SNPlocs.Hsapiens.dbSNP144.GRCh37, multtest, aod, rmeta requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbase >=3.42.0,<3.44.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-snpstats >=1.30.0,<1.32.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-biglm - r-bit @@ -44,21 +46,21 @@ requirements: - r-reshape2 - r-rocr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbase >=3.42.0,<3.44.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-snpstats >=1.30.0,<1.32.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-biglm - r-bit @@ -73,9 +75,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'software and data for analyses in genetics of gene expression and/or DNA methylation' extra: identifiers: - biotools:ggtools + parent_recipe: + name: bioconductor-ggtools + path: recipes/bioconductor-ggtools + version: 5.16.0 + diff --git a/recipes/bioconductor-ggtree/build.sh b/recipes/bioconductor-ggtree/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ggtree/build.sh +++ b/recipes/bioconductor-ggtree/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ggtree/meta.yaml b/recipes/bioconductor-ggtree/meta.yaml index 3bd216026ac5d..b179a3cf8c9ed 100644 --- a/recipes/bioconductor-ggtree/meta.yaml +++ b/recipes/bioconductor-ggtree/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.12.7" %} +{% set version = "1.14.4" %} {% set name = "ggtree" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 901344970ebb84e50b43d41c167fbdf1045ed92e52378fa60a4a11fc4ab0c685 + md5: a3b646ef7d33440ededc0239f77f4e7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: colorspace, cowplot, emojifont, ggimage, knitr, prettydoc, rmarkdown, testthat requirements: host: - - 'bioconductor-treeio >=1.4.3,<1.6.0' + - 'bioconductor-treeio >=1.6.0,<1.7.0' - r-ape - r-base - r-dplyr - - 'r-ggplot2 >=2.2.1.9000' + - 'r-ggplot2 >=3.0.0' - r-magrittr - r-purrr - r-rlang @@ -30,13 +32,13 @@ requirements: - r-scales - r-tibble - r-tidyr - - 'r-tidytree >=0.1.5' + - 'r-tidytree >=0.1.9' run: - - 'bioconductor-treeio >=1.4.3,<1.6.0' + - 'bioconductor-treeio >=1.6.0,<1.7.0' - r-ape - r-base - r-dplyr - - 'r-ggplot2 >=2.2.1.9000' + - 'r-ggplot2 >=3.0.0' - r-magrittr - r-purrr - r-rlang @@ -44,15 +46,20 @@ requirements: - r-scales - r-tibble - r-tidyr - - 'r-tidytree >=0.1.5' + - 'r-tidytree >=0.1.9' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: '''ggtree'' extends the ''ggplot2'' plotting system which implemented the grammar of graphics. ''ggtree'' is designed for visualization and annotation of phylogenetic trees with their covariates and other associated data.' extra: identifiers: - biotools:ggtree - doi:10.1111/2041-210X.12628 + parent_recipe: + name: bioconductor-ggtree + path: recipes/bioconductor-ggtree + version: 1.12.7 + diff --git a/recipes/bioconductor-gigsea/build.sh b/recipes/bioconductor-gigsea/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gigsea/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gigsea/meta.yaml b/recipes/bioconductor-gigsea/meta.yaml new file mode 100644 index 0000000000000..288341a1bd4f8 --- /dev/null +++ b/recipes/bioconductor-gigsea/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "GIGSEA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b2a1158dd46f573307badd416a2c2206 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - r-locfdr + - r-mass + - r-matrix + run: + - r-base + - r-locfdr + - r-mass + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'We presented the Genotype-imputed Gene Set Enrichment Analysis (GIGSEA), a novel method that uses GWAS-and-eQTL-imputed trait-associated differential gene expression to interrogate gene set enrichment for the trait-associated SNPs. By incorporating eQTL from large gene expression studies, e.g. GTEx, GIGSEA appropriately addresses such challenges for SNP enrichment as gene size, gene boundary, SNP distal regulation, and multiple-marker regulation. The weighted linear regression model, taking as weights both imputation accuracy and model completeness, was used to perform the enrichment test, properly adjusting the bias due to redundancy in different gene sets. The permutation test, furthermore, is used to evaluate the significance of enrichment, whose efficiency can be largely elevated by expressing the computational intensive part in terms of large matrix operation. We have shown the appropriate type I error rates for GIGSEA (<5%), and the preliminary results also demonstrate its good performance to uncover the real signal.' + diff --git a/recipes/bioconductor-gigseadata/meta.yaml b/recipes/bioconductor-gigseadata/meta.yaml new file mode 100644 index 0000000000000..388658b12b881 --- /dev/null +++ b/recipes/bioconductor-gigseadata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "GIGSEAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9036142a6d2c9eecdfec8023c032aa7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GIGSEA, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-3 + summary: 'The gene set collection used for the GIGSEA package.' + diff --git a/recipes/bioconductor-gigseadata/post-link.sh b/recipes/bioconductor-gigseadata/post-link.sh new file mode 100644 index 0000000000000..b389d98e38e3e --- /dev/null +++ b/recipes/bioconductor-gigseadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GIGSEAdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GIGSEAdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/GIGSEAdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gigseadata/bioconductor-gigseadata_1.0.0_src_all.tar.gz" +) +MD5="9036142a6d2c9eecdfec8023c032aa7f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gigseadata/pre-unlink.sh b/recipes/bioconductor-gigseadata/pre-unlink.sh new file mode 100644 index 0000000000000..395615403cb58 --- /dev/null +++ b/recipes/bioconductor-gigseadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GIGSEAdata diff --git a/recipes/bioconductor-girafe/build.sh b/recipes/bioconductor-girafe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-girafe/build.sh +++ b/recipes/bioconductor-girafe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-girafe/meta.yaml b/recipes/bioconductor-girafe/meta.yaml index 16b845f951eb4..e74813b3dc35d 100644 --- a/recipes/bioconductor-girafe/meta.yaml +++ b/recipes/bioconductor-girafe/meta.yaml @@ -1,42 +1,43 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "girafe" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 18090a1f196e19f69fdb4ec9404a8e54bc5c8613ed6bb5d5047413ebe330d4b2 + md5: 18a9eabd7dba531cefb42bbd99372c25 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: MASS, org.Mm.eg.db, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - 'r-intervals >=0.13.1' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeintervals >=1.36.0,<1.38.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeintervals >=1.38.0,<1.39.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - 'r-intervals >=0.13.1' build: @@ -47,9 +48,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package ''girafe'' deals with the genome-level representation of aligned reads from next-generation sequencing data. It contains an object class for enabling a detailed description of genome intervals with aligned reads and functions for comparing, visualising, exporting and working with such intervals and the aligned reads. As such, the package interacts with and provides a link between the packages ShortRead, IRanges and genomeIntervals.' extra: identifiers: - biotools:girafe + parent_recipe: + name: bioconductor-girafe + path: recipes/bioconductor-girafe + version: 1.32.0 + diff --git a/recipes/bioconductor-gispa/build.sh b/recipes/bioconductor-gispa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gispa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gispa/meta.yaml b/recipes/bioconductor-gispa/meta.yaml new file mode 100644 index 0000000000000..64a8063d4875a --- /dev/null +++ b/recipes/bioconductor-gispa/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "GISPA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f8b3bfbd6ddbb19055508854568fa4b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-changepoint + - r-data.table + - r-hh + - r-lattice + - r-latticeextra + - r-plyr + - r-scatterplot3d + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-changepoint + - r-data.table + - r-hh + - r-lattice + - r-latticeextra + - r-plyr + - r-scatterplot3d +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'GISPA is a method intended for the researchers who are interested in defining gene sets with similar, a priori specified molecular profile. GISPA method has been previously published in Nucleic Acid Research (Kowalski et al., 2016; PMID: 26826710).' + diff --git a/recipes/bioconductor-glad/build.sh b/recipes/bioconductor-glad/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-glad/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-glad/meta.yaml b/recipes/bioconductor-glad/meta.yaml new file mode 100644 index 0000000000000..f4587ee2d6be1 --- /dev/null +++ b/recipes/bioconductor-glad/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.46.0" %} +{% set name = "GLAD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a27d757cf431fe1ca45706b90060d032 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# SystemRequirements: gsl. Note: users should have GSL installed. Windows users: 'consult the README file available in the inst directory of the source distribution for necessary configuration instructions'. +requirements: + host: + - r-aws + - r-base + run: + - r-aws + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Analysis of array CGH data : detection of breakpoints in genomic profiles and assignment of a status (gain, normal or loss) to each chromosomal regions identified.' + diff --git a/recipes/bioconductor-glimma/build.sh b/recipes/bioconductor-glimma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-glimma/build.sh +++ b/recipes/bioconductor-glimma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-glimma/meta.yaml b/recipes/bioconductor-glimma/meta.yaml index 316a8488e7643..0a79e7598e076 100644 --- a/recipes/bioconductor-glimma/meta.yaml +++ b/recipes/bioconductor-glimma/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.8.2" %} +{% set version = "1.10.0" %} {% set name = "Glimma" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ba88b72acce876fd192c164b67cff27c2e1e03e8b141d6aa32dad3bc8151d14d + md5: ab4dc8722c5bdb3c062b1b932bfd6715 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, IRanges, GenomicRanges, SummarizedExperiment, DESeq2, limma, testthat, knitr, rmarkdown, pryr requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-jsonlite run: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-jsonlite test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'This package generates interactive visualisations for analysis of RNA-sequencing data using output from limma, edgeR or DESeq2 packages in an HTML page. The interactions are built on top of the popular static representations of analysis results in order to provide additional information.' extra: identifiers: - biotools:glimma - doi:10.1101/096107 + parent_recipe: + name: bioconductor-glimma + path: recipes/bioconductor-glimma + version: 1.8.2 + diff --git a/recipes/bioconductor-glmsparsenet/build.sh b/recipes/bioconductor-glmsparsenet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-glmsparsenet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-glmsparsenet/meta.yaml b/recipes/bioconductor-glmsparsenet/meta.yaml new file mode 100644 index 0000000000000..1b3f933cbe790 --- /dev/null +++ b/recipes/bioconductor-glmsparsenet/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "glmSparseNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ed879fd69f8bd537dcefa694c561bce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, survival, survcomp, pROC, VennDiagram, BiocStyle, curatedTCGAData, TCGAutils +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-forcats + - r-futile.logger + - r-ggplot2 + - r-glmnet + - r-loose.rock + - r-matrix + - r-readr + - r-reshape2 + - r-rlang + - r-sparsebn + - r-sparsebnutils + - r-stringr + - r-survminer + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-forcats + - r-futile.logger + - r-ggplot2 + - r-glmnet + - r-loose.rock + - r-matrix + - r-readr + - r-reshape2 + - r-rlang + - r-sparsebn + - r-sparsebnutils + - r-stringr + - r-survminer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'glmSparseNet is an R-package that generalizes sparse regression models when the features (e.g. genes) have a graph structure (e.g. protein-protein interactions), by including network-based regularizers. glmSparseNet uses the glmnet R-package, by including centrality measures of the network as penalty weights in the regularization. The current version implements regularization based on node degree, i.e. the strength and/or number of its associated edges, either by promoting hubs in the solution or orphan genes in the solution. All the glmnet distribution families are supported, namely "gaussian", "poisson", "binomial", "multinomial", "cox", and "mgaussian".' + diff --git a/recipes/bioconductor-globalancova/build.sh b/recipes/bioconductor-globalancova/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-globalancova/build.sh +++ b/recipes/bioconductor-globalancova/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-globalancova/meta.yaml b/recipes/bioconductor-globalancova/meta.yaml index 952cf0df0eeef..ec91b7a2509a0 100644 --- a/recipes/bioconductor-globalancova/meta.yaml +++ b/recipes/bioconductor-globalancova/meta.yaml @@ -1,34 +1,43 @@ -{% set version = "3.48.0" %} +{% set version = "4.0.0" %} {% set name = "GlobalAncova" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ee0cec93d5a5bd6ebe1a23a531ad6b447ac852586586d5f82fa0adcec018eee + md5: 9f9fd66217449c73f94bf8bd70ba82bb build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: GO.db, KEGG.db, golubEsets, hu6800.db, vsn, Rgraphviz requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-corpcor + - r-dendextend + - r-vgam run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-globaltest >=5.34.1,<5.36.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-corpcor + - r-dendextend + - r-vgam build: - {{ compiler('c') }} - make @@ -36,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany.' + summary: 'The association between a variable of interest (e.g. two groups) and the global pattern of a group of variables (e.g. a gene set) is tested via a global F-test. We give the following arguments in support of the GlobalAncova approach: After appropriate normalisation, gene-expression-data appear rather symmetrical and outliers are no real problem, so least squares should be rather robust. ANCOVA with interaction yields saturated data modelling e.g. different means per group and gene. Covariate adjustment can help to correct for possible selection bias. Variance homogeneity and uncorrelated residuals cannot be expected. Application of ordinary least squares gives unbiased, but no longer optimal estimates (Gauss-Markov-Aitken). Therefore, using the classical F-test is inappropriate, due to correlation. The test statistic however mirrors deviations from the null hypothesis. In combination with a permutation approach, empirical significance levels can be approximated. Alternatively, an approximation yields asymptotic p-values. The framework is generalized to groups of categorical variables or even mixed data by a likelihood ratio approach. Closed and hierarchical testing procedures are supported. This work was supported by the NGFN grant 01 GR 0459, BMBF, Germany and BMBF grant 01ZX1309B, Germany.' extra: identifiers: - biotools:globalancova - doi:10.1093/bioinformatics/btm531 + parent_recipe: + name: bioconductor-globalancova + path: recipes/bioconductor-globalancova + version: 3.48.0 + diff --git a/recipes/bioconductor-globalseq/build.sh b/recipes/bioconductor-globalseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-globalseq/build.sh +++ b/recipes/bioconductor-globalseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-globalseq/meta.yaml b/recipes/bioconductor-globalseq/meta.yaml index 498bb6e4f23df..fb8dbd0204a4e 100644 --- a/recipes/bioconductor-globalseq/meta.yaml +++ b/recipes/bioconductor-globalseq/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "globalSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d1e0e01cbeef11aaf9ca37ea633e764d7d1d26eb84743e8d67629d190d90bc4b + md5: ca6270790a85180a55d30c1ac8ee9191 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat, SummarizedExperiment, S4Vectors requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size.' + summary: 'The method may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. Useful for testing for association between RNA-Seq and high-dimensional data.' extra: identifiers: - biotools:globalseq + parent_recipe: + name: bioconductor-globalseq + path: recipes/bioconductor-globalseq + version: 1.8.0 + diff --git a/recipes/bioconductor-globaltest/build.sh b/recipes/bioconductor-globaltest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-globaltest/build.sh +++ b/recipes/bioconductor-globaltest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-globaltest/meta.yaml b/recipes/bioconductor-globaltest/meta.yaml index f17524b12c940..4acf75c3d5f10 100644 --- a/recipes/bioconductor-globaltest/meta.yaml +++ b/recipes/bioconductor-globaltest/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "5.34.1" %} +{% set version = "5.36.0" %} {% set name = "globaltest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: aac458fc1d896b2c317cd23b038e8646eccb92d6073f65702cfdf42991317ad0 + md5: 0c2d22bf1ee33788c7ab870b595e78b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: vsn, golubEsets, KEGG.db, hu6800.db, Rgraphviz, GO.db, lungExpression, org.Hs.eg.db, GSEABase, penalized, gss, MASS, boot, rpart requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-survival run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-survival test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The global test tests groups of covariates (or features) for association with a response variable. This package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms.' extra: identifiers: - biotools:globaltest + parent_recipe: + name: bioconductor-globaltest + path: recipes/bioconductor-globaltest + version: 5.34.1 + diff --git a/recipes/bioconductor-gmapr/build.sh b/recipes/bioconductor-gmapr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gmapr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gmapr/meta.yaml b/recipes/bioconductor-gmapr/meta.yaml new file mode 100644 index 0000000000000..505cd0849610c --- /dev/null +++ b/recipes/bioconductor-gmapr/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "1.24.1" %} +{% set name = "gmapR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de783ca018e6fd1ef451a819819bb1de +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BSgenome.Dmelanogaster.UCSC.dm3, BSgenome.Scerevisiae.UCSC.sacCer3, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, LungCancerLines +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + build: + - {{ compiler('c') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'GSNAP and GMAP are a pair of tools to align short-read data written by Tom Wu. This package provides convenience methods to work with GMAP and GSNAP from within R. In addition, it provides methods to tally alignment results on a per-nucleotide basis using the bam_tally tool.' + diff --git a/recipes/bioconductor-gmrp/build.sh b/recipes/bioconductor-gmrp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gmrp/build.sh +++ b/recipes/bioconductor-gmrp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gmrp/meta.yaml b/recipes/bioconductor-gmrp/meta.yaml index 237db368a834b..9a21469d09bc2 100644 --- a/recipes/bioconductor-gmrp/meta.yaml +++ b/recipes/bioconductor-gmrp/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.1" %} {% set name = "GMRP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6cdeebee72275c1200c303f14482a1f1f44175df29960985374d0ff30ad822a0 + md5: 4103cc393e2719f8324e96f4fcc67c9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-diagram - r-plotrix run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-diagram - r-plotrix @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Perform Mendelian randomization analysis of multiple SNPs to determine risk factors causing disease of study and to exclude confounding variabels and perform path analysis to construct path of risk factors to the disease.' extra: identifiers: - biotools:gmrp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gmrp + path: recipes/bioconductor-gmrp + version: 1.8.1 + diff --git a/recipes/bioconductor-go.db/meta.yaml b/recipes/bioconductor-go.db/meta.yaml index 4de79974e8eff..0f0ba213374b8 100644 --- a/recipes/bioconductor-go.db/meta.yaml +++ b/recipes/bioconductor-go.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "GO.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 120d1485f17a118b4d3145f40e5b26dbe6b70cc6093bec382defaa94b9c7223a + md5: bc452e3dd445711b27de93c15abd414c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Gene Ontology assembled using data from GO' - +extra: + parent_recipe: + name: bioconductor-go.db + path: recipes/bioconductor-go.db + version: 3.6.0 diff --git a/recipes/bioconductor-go.db/post-link.sh b/recipes/bioconductor-go.db/post-link.sh index 8b3e6288ac725..2f94f23fedf5f 100644 --- a/recipes/bioconductor-go.db/post-link.sh +++ b/recipes/bioconductor-go.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="GO.db_3.6.0.tar.gz" +FN="GO.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/GO.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/GO.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/GO.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/GO.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-go.db/bioconductor-go.db_3.7.0_src_all.tar.gz" ) -MD5="5ae3316dcda13d46c8cdfd18cf29dfcc" +MD5="bc452e3dd445711b27de93c15abd414c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-goexpress/build.sh b/recipes/bioconductor-goexpress/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-goexpress/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-goexpress/meta.yaml b/recipes/bioconductor-goexpress/meta.yaml new file mode 100644 index 0000000000000..df617bae71834 --- /dev/null +++ b/recipes/bioconductor-goexpress/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.16.0" %} +{% set name = "GOexpress" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7444623130b12f9cb3659718b52d190b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - 'r-ggplot2 >=0.9.0' + - 'r-gplots >=2.13.0' + - 'r-randomforest >=4.6' + - 'r-rcolorbrewer >=1.0' + - 'r-rcurl >=1.95' + - 'r-stringr >=0.6.2' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - 'r-ggplot2 >=0.9.0' + - 'r-gplots >=2.13.0' + - 'r-randomforest >=4.6' + - 'r-rcolorbrewer >=1.0' + - 'r-rcurl >=1.95' + - 'r-stringr >=0.6.2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'The package contains methods to visualise the expression profile of genes from a microarray or RNA-seq experiment, and offers a supervised clustering approach to identify GO terms containing genes with expression levels that best classify two or more predefined groups of samples. Annotations for the genes present in the expression dataset may be obtained from Ensembl through the biomaRt package, if not provided by the user. The default random forest framework is used to evaluate the capacity of each gene to cluster samples according to the factor of interest. Finally, GO terms are scored by averaging the rank (alternatively, score) of their respective gene sets to cluster the samples. P-values may be computed to assess the significance of GO term ranking. Visualisation function include gene expression profile, gene ontology-based heatmaps, and hierarchical clustering of experimental samples using gene expression data.' + diff --git a/recipes/bioconductor-gofuncr/build.sh b/recipes/bioconductor-gofuncr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gofuncr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gofuncr/meta.yaml b/recipes/bioconductor-gofuncr/meta.yaml new file mode 100644 index 0000000000000..bdc8bea6fa54e --- /dev/null +++ b/recipes/bioconductor-gofuncr/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.2.0" %} +{% set name = "GOfuncR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 751400dc73371df5c86c87511fecdede +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: Homo.sapiens, BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-gtools >=3.5.0' + - 'r-mapplots >=1.5' + - 'r-rcpp >=0.11.5' + - 'r-vioplot >=0.2' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-gtools >=3.5.0' + - 'r-mapplots >=1.5' + - 'r-rcpp >=0.11.5' + - 'r-vioplot >=0.2' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'GOfuncR performs a gene ontology enrichment analysis based on the ontology enrichment software FUNC. GO-annotations are obtained from OrganismDb or OrgDb packages (''Homo.sapiens'' by default); the GO-graph is included in the package and updated regularly (11-Oct-2018). GOfuncR provides the standard candidate vs. background enrichment analysis using the hypergeometric test, as well as three additional tests: (i) the Wilcoxon rank-sum test that is used when genes are ranked, (ii) a binomial test that is used when genes are associated with two counts and (iii) a Chi-square or Fisher''s exact test that is used in cases when genes are associated with four counts. To correct for multiple testing and interdependency of the tests, family-wise error rates are computed based on random permutations of the gene-associated variables. GOfuncR also provides tools for exploring the ontology graph and the annotations, and options to take gene-length or spatial clustering of genes into account. It is also possible to provide custom gene coordinates, annotations and ontologies.' + diff --git a/recipes/bioconductor-gofunction/build.sh b/recipes/bioconductor-gofunction/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gofunction/build.sh +++ b/recipes/bioconductor-gofunction/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gofunction/meta.yaml b/recipes/bioconductor-gofunction/meta.yaml index 7dc23884b2a26..6337f7fae6e01 100644 --- a/recipes/bioconductor-gofunction/meta.yaml +++ b/recipes/bioconductor-gofunction/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GOFunction" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 578464fffe8f97854ac3d3f6a61a4d77ed2591c75e791ab6a9eaf546634e3b2f + md5: 72307dd4950cad125f42856c1153729b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-dbi - 'r-sparsem >=0.85' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-dbi - 'r-sparsem >=0.85' @@ -39,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The GO-function package provides a tool to address the redundancy that result from the GO structure or multiple annotation genes and derive biologically relevant functions from the statistically significant functions based on some intuitive assumption and statistical testing.' extra: identifiers: - biotools:gofunction - doi:10.1093/bib/bbr041 + parent_recipe: + name: bioconductor-gofunction + path: recipes/bioconductor-gofunction + version: 1.28.0 + diff --git a/recipes/bioconductor-golubesets/meta.yaml b/recipes/bioconductor-golubesets/meta.yaml index d0e7e6dc04e18..9dddd76337257 100644 --- a/recipes/bioconductor-golubesets/meta.yaml +++ b/recipes/bioconductor-golubesets/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "golubEsets" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b0fc7482331f9d890133cb367bd25442c75a7b9266e336d810d3b2e9121c677d + md5: 0fe60bd861eca25969193aeadcd0bc59 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: LGPL summary: 'representation of public golub data with some covariate data of provenance unknown to the maintainer at present; now employs ExpressionSet format' - +extra: + parent_recipe: + name: bioconductor-golubesets + path: recipes/bioconductor-golubesets + version: 1.22.0 diff --git a/recipes/bioconductor-golubesets/post-link.sh b/recipes/bioconductor-golubesets/post-link.sh index af62f26d5c339..15372b4c016ed 100644 --- a/recipes/bioconductor-golubesets/post-link.sh +++ b/recipes/bioconductor-golubesets/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="golubEsets_1.22.0.tar.gz" +FN="golubEsets_1.24.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/golubEsets_1.22.0.tar.gz" - "https://bioarchive.galaxyproject.org/golubEsets_1.22.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.22.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/golubEsets_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/golubEsets_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-golubesets/bioconductor-golubesets_1.24.0_src_all.tar.gz" ) -MD5="fbc8881356c1f9aa83c081c32093dda0" +MD5="0fe60bd861eca25969193aeadcd0bc59" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-googlegenomics/build.sh b/recipes/bioconductor-googlegenomics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-googlegenomics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-googlegenomics/meta.yaml b/recipes/bioconductor-googlegenomics/meta.yaml new file mode 100644 index 0000000000000..ece952c4ebe0c --- /dev/null +++ b/recipes/bioconductor-googlegenomics/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "2.4.0" %} +{% set name = "GoogleGenomics" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8617e932deeb38b5cb428ef2707b247e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, RProtoBuf, httpuv, knitr, rmarkdown, testthat, ggbio, ggplot2, BSgenome.Hsapiens.UCSC.hg19, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-httr + - r-rjson + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-httr + - r-rjson + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (== 2.0) | file LICENSE' + summary: 'Provides an R package to interact with the Google Genomics API.' + diff --git a/recipes/bioconductor-gopro/build.sh b/recipes/bioconductor-gopro/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gopro/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gopro/meta.yaml b/recipes/bioconductor-gopro/meta.yaml new file mode 100644 index 0000000000000..e11bd548c3aee --- /dev/null +++ b/recipes/bioconductor-gopro/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.8.0" %} +{% set name = "GOpro" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5d1245837ea8262a04366bef11ae4cf7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, RTCGA.PANCAN12, BiocStyle, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-bh + - r-dendextend + - r-doparallel + - r-foreach + - r-rcpp + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-bh + - r-dendextend + - r-doparallel + - r-foreach + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Find the most characteristic gene ontology terms for groups of human genes. This package was created as a part of the thesis which was developed under the auspices of MI^2 Group (http://mi2.mini.pw.edu.pl/, https://github.com/geneticsMiNIng).' + diff --git a/recipes/bioconductor-goprofiles/build.sh b/recipes/bioconductor-goprofiles/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-goprofiles/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-goprofiles/meta.yaml b/recipes/bioconductor-goprofiles/meta.yaml new file mode 100644 index 0000000000000..f0e74f2f28e65 --- /dev/null +++ b/recipes/bioconductor-goprofiles/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.44.0" %} +{% set name = "goProfiles" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cee2739892a0f493ca62346297a00d42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Hs.eg.db +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - r-base + - r-compquadform + - r-stringr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - r-base + - r-compquadform + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package implements methods to compare lists of genes based on comparing the corresponding ''functional profiles''.' + diff --git a/recipes/bioconductor-gosemsim/build.sh b/recipes/bioconductor-gosemsim/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gosemsim/build.sh +++ b/recipes/bioconductor-gosemsim/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gosemsim/meta.yaml b/recipes/bioconductor-gosemsim/meta.yaml index 0191380606cd5..13d1293059fef 100644 --- a/recipes/bioconductor-gosemsim/meta.yaml +++ b/recipes/bioconductor-gosemsim/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "2.6.2" %} +{% set version = "2.8.0" %} {% set name = "GOSemSim" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3a606ece278c4658186f022488e7cedcebe5345166c753782f0b83f3c51d04fb + md5: 8f4ba171e35070a482be6ea54d0cc814 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: AnnotationHub, BiocManager, clusterProfiler, DOSE, knitr, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base - r-rcpp run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base - r-rcpp build: @@ -35,9 +36,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The semantic comparisons of Gene Ontology (GO) annotations provide quantitative ways to compute similarities between genes and gene groups, and have became important basis for many bioinformatics analysis approaches. GOSemSim is an R package for semantic similarity computation among GO terms, sets of GO terms, gene products and gene clusters. GOSemSim implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively.' extra: identifiers: - biotools:gosemsim + parent_recipe: + name: bioconductor-gosemsim + path: recipes/bioconductor-gosemsim + version: 2.6.2 + diff --git a/recipes/bioconductor-goseq/build.sh b/recipes/bioconductor-goseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-goseq/build.sh +++ b/recipes/bioconductor-goseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-goseq/meta.yaml b/recipes/bioconductor-goseq/meta.yaml index 82bf30a0dde48..f942a8d3441e8 100644 --- a/recipes/bioconductor-goseq/meta.yaml +++ b/recipes/bioconductor-goseq/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "goseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 54f464d3cb096722138bd3771cb123f8eaf9c8f00265109077998aa12a5aab76 + md5: f43ed2099b8c8d58a4fc15b080042bde build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: edgeR, org.Hs.eg.db, rtracklayer requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base - r-biasedurn - r-mgcv run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base - r-biasedurn - r-mgcv @@ -37,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Detects Gene Ontology and/or other user defined categories which are over/under represented in RNA-seq data' extra: identifiers: - biotools:goseq + parent_recipe: + name: bioconductor-goseq + path: recipes/bioconductor-goseq + version: 1.32.0 + diff --git a/recipes/bioconductor-gosim/build.sh b/recipes/bioconductor-gosim/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gosim/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gosim/meta.yaml b/recipes/bioconductor-gosim/meta.yaml new file mode 100644 index 0000000000000..5399625b89872 --- /dev/null +++ b/recipes/bioconductor-gosim/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.20.0" %} +{% set name = "GOSim" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87d1eb1841be4fa7d9c2e145051806c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-cluster + - r-corpcor + - r-flexmix + - r-matrix + - r-rcpp + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-cluster + - r-corpcor + - r-flexmix + - r-matrix + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package implements several functions useful for computing similarities between GO terms and gene products based on their GO annotation. Moreover it allows for computing a GO enrichment analysis' + diff --git a/recipes/bioconductor-gostag/build.sh b/recipes/bioconductor-gostag/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gostag/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gostag/meta.yaml b/recipes/bioconductor-gostag/meta.yaml new file mode 100644 index 0000000000000..d73d0b0bf15db --- /dev/null +++ b/recipes/bioconductor-gostag/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.1" %} +{% set name = "goSTAG" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7e6c56c3730f5b5601d6ca456d4a8922 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - r-base + - r-memoise + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - r-base + - r-memoise +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Gene lists derived from the results of genomic analyses are rich in biological information. For instance, differentially expressed genes (DEGs) from a microarray or RNA-Seq analysis are related functionally in terms of their response to a treatment or condition. Gene lists can vary in size, up to several thousand genes, depending on the robustness of the perturbations or how widely different the conditions are biologically. Having a way to associate biological relatedness between hundreds and thousands of genes systematically is impractical by manually curating the annotation and function of each gene. Over-representation analysis (ORA) of genes was developed to identify biological themes. Given a Gene Ontology (GO) and an annotation of genes that indicate the categories each one fits into, significance of the over-representation of the genes within the ontological categories is determined by a Fisher''s exact test or modeling according to a hypergeometric distribution. Comparing a small number of enriched biological categories for a few samples is manageable using Venn diagrams or other means for assessing overlaps. However, with hundreds of enriched categories and many samples, the comparisons are laborious. Furthermore, if there are enriched categories that are shared between samples, trying to represent a common theme across them is highly subjective. goSTAG uses GO subtrees to tag and annotate genes within a set. goSTAG visualizes the similarities between the over-representation of DEGs by clustering the p-values from the enrichment statistical tests and labels clusters with the GO term that has the most paths to the root within the subtree generated from all the GO terms in the cluster.' + diff --git a/recipes/bioconductor-gostats/build.sh b/recipes/bioconductor-gostats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gostats/build.sh +++ b/recipes/bioconductor-gostats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gostats/meta.yaml b/recipes/bioconductor-gostats/meta.yaml index aed5b6401a37e..6f3c31537494c 100644 --- a/recipes/bioconductor-gostats/meta.yaml +++ b/recipes/bioconductor-gostats/meta.yaml @@ -1,51 +1,58 @@ -{% set version = "2.46.0" %} +{% set version = "2.48.0" %} {% set name = "GOstats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 00b769e3bee17a76d9962461594a8b82da55610032658cc414bca4567ef3b5c4 + md5: 5f5df1dbb7717f909a32a5ed83159006 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db (>= 1.13.0), ALL, multtest, genefilter, RColorBrewer, xtable, SparseM, GSEABase, geneplotter, org.Hs.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationforge >=1.22.2,<1.24.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationforge >=1.22.2,<1.24.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationforge >=1.24.0,<1.25.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of tools for interacting with GO and microarray data. A variety of basic manipulation tools for graphs, hypothesis testing and other simple calculations.' extra: identifiers: - biotools:gostats + parent_recipe: + name: bioconductor-gostats + path: recipes/bioconductor-gostats + version: 2.46.0 + diff --git a/recipes/bioconductor-gosummaries/build.sh b/recipes/bioconductor-gosummaries/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gosummaries/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gosummaries/meta.yaml b/recipes/bioconductor-gosummaries/meta.yaml new file mode 100644 index 0000000000000..e18bdbff12f2c --- /dev/null +++ b/recipes/bioconductor-gosummaries/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "2.18.0" %} +{% set name = "GOsummaries" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ea44c2e32bb5f0d12f0aad1b5ffdcdce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: vegan +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-ggplot2 + - r-gprofiler + - r-gtable + - r-plyr + - r-rcpp + - r-reshape2 + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-ggplot2 + - r-gprofiler + - r-gtable + - r-plyr + - r-rcpp + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A package to visualise Gene Ontology (GO) enrichment analysis results on gene lists arising from different analyses such clustering or PCA. The significant GO categories are visualised as word clouds that can be combined with different plots summarising the underlying data.' + diff --git a/recipes/bioconductor-gothic/build.sh b/recipes/bioconductor-gothic/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gothic/build.sh +++ b/recipes/bioconductor-gothic/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gothic/meta.yaml b/recipes/bioconductor-gothic/meta.yaml index de7454473a17a..54aa3f85c5a7a 100644 --- a/recipes/bioconductor-gothic/meta.yaml +++ b/recipes/bioconductor-gothic/meta.yaml @@ -1,45 +1,47 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "GOTHiC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dfeeed7502bc4339e3da803968eb00a37e917945a283ec39935dedbcb20d36be + md5: b9d8f7ee06dab41f8d1bf9dc03cc13dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: HiCDataLymphoblast requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-data.table - r-ggplot2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-data.table - r-ggplot2 @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This is a Hi-C analysis package using a cumulative binomial test to detect interactions between distal genomic loci that have significantly more reads than expected by chance in Hi-C experiments. It takes mapped paired NGS reads as input and gives back the list of significant interactions for a given bin size in the genome.' extra: identifiers: - biotools:gothic - doi:10.1101/gr.185272.114 + parent_recipe: + name: bioconductor-gothic + path: recipes/bioconductor-gothic + version: 1.16.0 + diff --git a/recipes/bioconductor-gotools/build.sh b/recipes/bioconductor-gotools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gotools/build.sh +++ b/recipes/bioconductor-gotools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gotools/meta.yaml b/recipes/bioconductor-gotools/meta.yaml index 2b9f807b4b2c2..9cc43c3be4986 100644 --- a/recipes/bioconductor-gotools/meta.yaml +++ b/recipes/bioconductor-gotools/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "goTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5d490d2c7f7e7eeef7565e40e005287b12e59aabeb83ae544053165e534c450 + md5: 61fbb92f3f3abdcb58dfdf024fe10d84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Wraper functions for description/comparison of oligo ID list using Gene Ontology database' extra: identifiers: - biotools:gotools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gotools + path: recipes/bioconductor-gotools + version: 1.54.0 + diff --git a/recipes/bioconductor-gp53cdf/meta.yaml b/recipes/bioconductor-gp53cdf/meta.yaml new file mode 100644 index 0000000000000..a2839c0ae5d8b --- /dev/null +++ b/recipes/bioconductor-gp53cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "gp53cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2887dd15d3fa29b5c13b068c8d641f61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the GP53.CDF file.' + diff --git a/recipes/bioconductor-gp53cdf/post-link.sh b/recipes/bioconductor-gp53cdf/post-link.sh new file mode 100644 index 0000000000000..9333e907245eb --- /dev/null +++ b/recipes/bioconductor-gp53cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="gp53cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/gp53cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/gp53cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gp53cdf/bioconductor-gp53cdf_2.18.0_src_all.tar.gz" +) +MD5="2887dd15d3fa29b5c13b068c8d641f61" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gp53cdf/pre-unlink.sh b/recipes/bioconductor-gp53cdf/pre-unlink.sh new file mode 100644 index 0000000000000..e1841b94d3fd0 --- /dev/null +++ b/recipes/bioconductor-gp53cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gp53cdf diff --git a/recipes/bioconductor-gpart/build.sh b/recipes/bioconductor-gpart/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gpart/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gpart/meta.yaml b/recipes/bioconductor-gpart/meta.yaml new file mode 100644 index 0000000000000..c0b8cef97ec6f --- /dev/null +++ b/recipes/bioconductor-gpart/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set name = "gpart" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 823ed883bf941ecae5644533d1ba464a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocStyle, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - r-base + - r-data.table + - r-igraph + - r-rcpp + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - r-base + - r-data.table + - r-igraph + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'we provide a new SNP sequence partitioning method which partitions the whole SNP sequence based on not only LD block structures but also gene location information. The LD block construction for GPART is performed using Big-LD algorithm, with additional improvement from previous version reported in Kim et al.(2017). We also add a visualization tool to show the LD heatmap with the information of LD block boundaries and gene locations in the package.' + diff --git a/recipes/bioconductor-gpls/build.sh b/recipes/bioconductor-gpls/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gpls/build.sh +++ b/recipes/bioconductor-gpls/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gpls/meta.yaml b/recipes/bioconductor-gpls/meta.yaml index 9fc6bedded97d..a4c2d247f8a36 100644 --- a/recipes/bioconductor-gpls/meta.yaml +++ b/recipes/bioconductor-gpls/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "gpls" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e1ddd66e585cc2d18d26127c068e31b2c906c5cfabe3a8e547cb0846be0ecaf4 + md5: 0ff76e002a0dcaa8da6bfb4435129896 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MASS requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Classification using generalized partial least squares for two-group and multi-group (more than 2 group) classification.' extra: identifiers: - biotools:gpls - doi:10.1198/106186005X47697 + parent_recipe: + name: bioconductor-gpls + path: recipes/bioconductor-gpls + version: 1.52.0 + diff --git a/recipes/bioconductor-gprege/build.sh b/recipes/bioconductor-gprege/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gprege/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gprege/meta.yaml b/recipes/bioconductor-gprege/meta.yaml new file mode 100644 index 0000000000000..b5d526a2bbcf9 --- /dev/null +++ b/recipes/bioconductor-gprege/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.26.0" %} +{% set name = "gprege" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8c3464efa7978c37ba0203de3ae063ae +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: spam +requirements: + host: + - r-base + - r-gptk + run: + - r-base + - r-gptk +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'The gprege package implements the methodology described in Kalaitzis & Lawrence (2011) "A simple approach to ranking differentially expressed gene expression time-courses through Gaussian process regression". The software fits two GPs with the an RBF (+ noise diagonal) kernel on each profile. One GP kernel is initialised wih a short lengthscale hyperparameter, signal variance as the observed variance and a zero noise variance. It is optimised via scaled conjugate gradients (netlab). A second GP has fixed hyperparameters: zero inverse-width, zero signal variance and noise variance as the observed variance. The log-ratio of marginal likelihoods of the two hypotheses acts as a score of differential expression for the profile. Comparison via ROC curves is performed against BATS (Angelini et.al, 2007). A detailed discussion of the ranking approach and dataset used can be found in the paper (http://www.biomedcentral.com/1471-2105/12/180).' + diff --git a/recipes/bioconductor-gqtlbase/build.sh b/recipes/bioconductor-gqtlbase/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gqtlbase/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gqtlbase/meta.yaml b/recipes/bioconductor-gqtlbase/meta.yaml new file mode 100644 index 0000000000000..b126b4bcd55b9 --- /dev/null +++ b/recipes/bioconductor-gqtlbase/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.14.0" %} +{% set name = "gQTLBase" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0b4b30b4c1152b7f98e2c7a8f2f130d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: geuvStore2, knitr, rmarkdown, BiocStyle, RUnit, GGtools, Homo.sapiens, IRanges, erma, GenomeInfoDb, gwascat, geuvPack +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-batchjobs + - r-bbmisc + - r-bit + - r-doparallel + - r-ff + - r-ffbase + - r-foreach + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-batchjobs + - r-bbmisc + - r-bit + - r-doparallel + - r-ff + - r-ffbase + - r-foreach +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Infrastructure for eQTL, mQTL and similar studies.' + diff --git a/recipes/bioconductor-gqtlstats/build.sh b/recipes/bioconductor-gqtlstats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gqtlstats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gqtlstats/meta.yaml b/recipes/bioconductor-gqtlstats/meta.yaml new file mode 100644 index 0000000000000..755ddbbe5212a --- /dev/null +++ b/recipes/bioconductor-gqtlstats/meta.yaml @@ -0,0 +1,93 @@ +{% set version = "1.14.0" %} +{% set name = "gQTLstats" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: df3a3589b6080c6b24d7364536fe302f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: geuvPack, geuvStore2, Rsamtools, knitr, rmarkdown, ggbio, BiocStyle, RUnit, multtest, gwascat, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, ldblock +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-erma >=0.14.0,<0.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-batchjobs + - r-bbmisc + - r-beeswarm + - r-doparallel + - r-dplyr + - r-ffbase + - r-foreach + - r-ggbeeswarm + - r-ggplot2 + - r-hardyweinberg + - r-mgcv + - r-plotly + - r-reshape2 + - r-shiny + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-erma >=0.14.0,<0.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-batchjobs + - r-bbmisc + - r-beeswarm + - r-doparallel + - r-dplyr + - r-ffbase + - r-foreach + - r-ggbeeswarm + - r-ggplot2 + - r-hardyweinberg + - r-mgcv + - r-plotly + - r-reshape2 + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'computationally efficient analysis of eQTL, mQTL, dsQTL, etc.' + diff --git a/recipes/bioconductor-graph/build.sh b/recipes/bioconductor-graph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-graph/build.sh +++ b/recipes/bioconductor-graph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graph/meta.yaml b/recipes/bioconductor-graph/meta.yaml index 355a795610134..3576f3d497acc 100644 --- a/recipes/bioconductor-graph/meta.yaml +++ b/recipes/bioconductor-graph/meta.yaml @@ -1,39 +1,45 @@ -{% set version = "1.58.2" %} +{% set version = "1.60.0" %} {% set name = "graph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ea81f17367f1e15616bfdd60d14d974567f0740f28bc22482ef982c1c65a551f + md5: ee2a677386e14496f7efcdb18b033bff build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: SparseM (>= 0.36), XML, RBGL, RUnit, cluster requirements: - build: - - {{ compiler('c') }} - - make host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base + build: + - {{ compiler('c') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that implements some simple graph handling capabilities.' extra: identifiers: - biotools:graph - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-graph + path: recipes/bioconductor-graph + version: 1.58.2 + diff --git a/recipes/bioconductor-graphalignment/build.sh b/recipes/bioconductor-graphalignment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-graphalignment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphalignment/meta.yaml b/recipes/bioconductor-graphalignment/meta.yaml new file mode 100644 index 0000000000000..fb5b2cf76ffb2 --- /dev/null +++ b/recipes/bioconductor-graphalignment/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.46.0" %} +{% set name = "GraphAlignment" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bdea26bff023e6e73179fc7d34097a1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Graph alignment is an extension package for the R programming environment which provides functions for finding an alignment between two networks based on link and node similarity scores. (J. Berg and M. Laessig, "Cross-species analysis of biological networks by Bayesian alignment", PNAS 103 (29), 10967-10972 (2006))' + diff --git a/recipes/bioconductor-graphat/build.sh b/recipes/bioconductor-graphat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-graphat/build.sh +++ b/recipes/bioconductor-graphat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphat/meta.yaml b/recipes/bioconductor-graphat/meta.yaml index 3f7d5dca394a9..1e14500876201 100644 --- a/recipes/bioconductor-graphat/meta.yaml +++ b/recipes/bioconductor-graphat/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "GraphAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2feaff6c04b3c3941b94dab2834c013fa7bc3390746c024fd08de9ab195cecf + md5: 01fbc5e58324e882d6885a62e4c037c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-mcmcpack run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-mcmcpack test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions and data used in Balasubramanian, et al. (2004)' extra: identifiers: - biotools:graphat - doi:10.1093/bioinformatics/bth405 + parent_recipe: + name: bioconductor-graphat + path: recipes/bioconductor-graphat + version: 1.52.0 + diff --git a/recipes/bioconductor-graphite/build.sh b/recipes/bioconductor-graphite/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-graphite/build.sh +++ b/recipes/bioconductor-graphite/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphite/meta.yaml b/recipes/bioconductor-graphite/meta.yaml index a5aa5cf05f400..d2d8218d3c574 100644 --- a/recipes/bioconductor-graphite/meta.yaml +++ b/recipes/bioconductor-graphite/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.26.3" %} +{% set version = "1.28.1" %} {% set name = "graphite" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a6a62e225b31c37082624f90e15d1da30323fba35e6bef5b8c7e4f0ce342f2a0 + md5: 84177d6adbe04cdfeceb712e7f58cf6f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: a4Preproc, ALL, BiocStyle, clipper, codetools, hgu133plus2.db, hgu95av2.db, impute, knitr, org.Hs.eg.db, parallel, R.rsp, RCy3, rmarkdown, SPIA (>= 2.2), testthat, topologyGSA (>= 1.4.0) requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-checkmate - r-httr - r-rappdirs run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-checkmate - r-httr @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 - summary: 'Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, Reactome and SPIKE databases.' + summary: 'Graph objects from pathway topology derived from Biocarta, HumanCyc, KEGG, NCI, Panther, PathBank, PharmGKB, Reactome and SMPDB databases.' extra: identifiers: - biotools:graphite + parent_recipe: + name: bioconductor-graphite + path: recipes/bioconductor-graphite + version: 1.26.3 + diff --git a/recipes/bioconductor-graphpac/build.sh b/recipes/bioconductor-graphpac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-graphpac/build.sh +++ b/recipes/bioconductor-graphpac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-graphpac/meta.yaml b/recipes/bioconductor-graphpac/meta.yaml index 8ab3d16db68da..2b901d093c167 100644 --- a/recipes/bioconductor-graphpac/meta.yaml +++ b/recipes/bioconductor-graphpac/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.22.1" %} +{% set version = "1.24.0" %} {% set name = "GraphPAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fd75feff6524bfd48fa5cca73ecd317ccca661f28b6df510c06c5696cb028239 + md5: a4ca5bc3f6a808a8fbdadf2da251e745 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' - r-base - r-igraph - r-rmallow - r-tsp run: - - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' - r-base - r-igraph - r-rmallow @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies mutational clusters of amino acids in a protein while utilizing the proteins tertiary structure via a graph theoretical model.' extra: identifiers: - biotools:graphpac - doi:10.1186/1471-2105-15-86 + parent_recipe: + name: bioconductor-graphpac + path: recipes/bioconductor-graphpac + version: 1.22.1 + diff --git a/recipes/bioconductor-grasp2db/meta.yaml b/recipes/bioconductor-grasp2db/meta.yaml new file mode 100644 index 0000000000000..5bfa047ea3fb1 --- /dev/null +++ b/recipes/bioconductor-grasp2db/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.1.0" %} +{% set name = "grasp2db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3fc90fc7c99e7da51dcbb687fd2d5515 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gwascat, knitr +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - r-base + - r-dbplyr + - r-digest + - r-dplyr + - r-rsqlite + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - r-base + - r-dbplyr + - r-digest + - r-dplyr + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'Artistic-2.0 + file LICENSE' + summary: 'grasp2db, sqlite wrap of NHLBI GRASP 2.0, an extended GWAS catalog.' + diff --git a/recipes/bioconductor-grasp2db/post-link.sh b/recipes/bioconductor-grasp2db/post-link.sh new file mode 100644 index 0000000000000..514eaf8383bc0 --- /dev/null +++ b/recipes/bioconductor-grasp2db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="grasp2db_1.1.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/grasp2db_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/grasp2db_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-grasp2db/bioconductor-grasp2db_1.1.0_src_all.tar.gz" +) +MD5="3fc90fc7c99e7da51dcbb687fd2d5515" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-grasp2db/pre-unlink.sh b/recipes/bioconductor-grasp2db/pre-unlink.sh new file mode 100644 index 0000000000000..7aeafbfc94b4e --- /dev/null +++ b/recipes/bioconductor-grasp2db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ grasp2db diff --git a/recipes/bioconductor-greengenes13.5mgdb/meta.yaml b/recipes/bioconductor-greengenes13.5mgdb/meta.yaml new file mode 100644 index 0000000000000..b5dac48de249a --- /dev/null +++ b/recipes/bioconductor-greengenes13.5mgdb/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.0.0" %} +{% set name = "greengenes13.5MgDb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c06d8d5b702636bb5fb3e6229869578c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + run: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Metagenome annotation package with for the Greengenes 16S rRNA Database version 13.5. Contains a MgDb-class object, defined in the metagenomeFeatures package.' + diff --git a/recipes/bioconductor-greengenes13.5mgdb/post-link.sh b/recipes/bioconductor-greengenes13.5mgdb/post-link.sh new file mode 100644 index 0000000000000..05b2b5934d983 --- /dev/null +++ b/recipes/bioconductor-greengenes13.5mgdb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="greengenes13.5MgDb_2.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/greengenes13.5MgDb_2.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/greengenes13.5MgDb_2.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-greengenes13.5mgdb/bioconductor-greengenes13.5mgdb_2.0.0_src_all.tar.gz" +) +MD5="c06d8d5b702636bb5fb3e6229869578c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-greengenes13.5mgdb/pre-unlink.sh b/recipes/bioconductor-greengenes13.5mgdb/pre-unlink.sh new file mode 100644 index 0000000000000..c8ac4b197135a --- /dev/null +++ b/recipes/bioconductor-greengenes13.5mgdb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ greengenes13.5MgDb diff --git a/recipes/bioconductor-grenits/build.sh b/recipes/bioconductor-grenits/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-grenits/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-grenits/meta.yaml b/recipes/bioconductor-grenits/meta.yaml new file mode 100644 index 0000000000000..7ebe519a31e36 --- /dev/null +++ b/recipes/bioconductor-grenits/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.34.0" %} +{% set name = "GRENITS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 70f49c97897e351c99d0b6c2394f520b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: network +requirements: + host: + - r-base + - 'r-ggplot2 >=0.9.0' + - 'r-rcpp >=0.8.6' + - 'r-rcpparmadillo >=0.2.8' + - r-reshape2 + run: + - r-base + - 'r-ggplot2 >=0.9.0' + - 'r-rcpp >=0.8.6' + - 'r-rcpparmadillo >=0.2.8' + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package offers four network inference statistical models using Dynamic Bayesian Networks and Gibbs Variable Selection: a linear interaction model, two linear interaction models with added experimental noise (Gaussian and Student distributed) for the case where replicates are available and a non-linear interaction model.' + diff --git a/recipes/bioconductor-greylistchip/build.sh b/recipes/bioconductor-greylistchip/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-greylistchip/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-greylistchip/meta.yaml b/recipes/bioconductor-greylistchip/meta.yaml new file mode 100644 index 0000000000000..c02085d032bce --- /dev/null +++ b/recipes/bioconductor-greylistchip/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.14.0" %} +{% set name = "GreyListChIP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff01f53cc4c0b6c6a42e908cc436bdb4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics, RUnit +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mass + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Identify regions of ChIP experiments with high signal in the input, that lead to spurious peaks during peak calling. Remove reads aligning to these regions prior to peak calling, for cleaner ChIP analysis.' + diff --git a/recipes/bioconductor-grmetrics/build.sh b/recipes/bioconductor-grmetrics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-grmetrics/build.sh +++ b/recipes/bioconductor-grmetrics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-grmetrics/meta.yaml b/recipes/bioconductor-grmetrics/meta.yaml index 6ed27aeda54a9..58ad092f3dfd5 100644 --- a/recipes/bioconductor-grmetrics/meta.yaml +++ b/recipes/bioconductor-grmetrics/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "GRmetrics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 778a0930864c40b88337d9188bf20e4c3bc20d519fc3d9e38ebf5369d79955f9 + md5: 459794f88af3289de54626a1953589fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle requirements: host: - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-drc - r-ggplot2 - r-plotly run: - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-drc - r-ggplot2 @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Functions for calculating and visualizing growth-rate inhibition (GR) metrics.' extra: identifiers: - biotools:grmetrics - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-grmetrics + path: recipes/bioconductor-grmetrics + version: 1.6.1 + diff --git a/recipes/bioconductor-grndata/meta.yaml b/recipes/bioconductor-grndata/meta.yaml new file mode 100644 index 0000000000000..89cac523febe2 --- /dev/null +++ b/recipes/bioconductor-grndata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "grndata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: aacdf027236c99022b11fdabb983bbe4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Simulated expression data for five large Gene Regulatory Networks from different simulators' + diff --git a/recipes/bioconductor-grndata/post-link.sh b/recipes/bioconductor-grndata/post-link.sh new file mode 100644 index 0000000000000..91d12a31080d4 --- /dev/null +++ b/recipes/bioconductor-grndata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="grndata_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/grndata_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/grndata_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-grndata/bioconductor-grndata_1.14.0_src_all.tar.gz" +) +MD5="aacdf027236c99022b11fdabb983bbe4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-grndata/pre-unlink.sh b/recipes/bioconductor-grndata/pre-unlink.sh new file mode 100644 index 0000000000000..5c57ce318705b --- /dev/null +++ b/recipes/bioconductor-grndata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ grndata diff --git a/recipes/bioconductor-grohmm/build.sh b/recipes/bioconductor-grohmm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-grohmm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-grohmm/meta.yaml b/recipes/bioconductor-grohmm/meta.yaml new file mode 100644 index 0000000000000..73d6684271a83 --- /dev/null +++ b/recipes/bioconductor-grohmm/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.16.0" %} +{% set name = "groHMM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3d1cc353a06a4bc8d282f3712167ade0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, GenomicFeatures, edgeR, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-mass + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-mass + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A pipeline for the analysis of GRO-seq data.' + diff --git a/recipes/bioconductor-grridge/build.sh b/recipes/bioconductor-grridge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-grridge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-grridge/meta.yaml b/recipes/bioconductor-grridge/meta.yaml new file mode 100644 index 0000000000000..5df7a9c2f7ffc --- /dev/null +++ b/recipes/bioconductor-grridge/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "GRridge" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d5da4e835e460089ca8be2f16538e44c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-glmnet + - r-iso + - r-mvtnorm + - r-penalized + - r-survival + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-glmnet + - r-iso + - r-mvtnorm + - r-penalized + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package allows the use of multiple sources of co-data (e.g. external p-values, gene lists, annotation) to improve prediction of binary, continuous and survival response using (logistic, linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction diagnostics by cross-validation using ROC curves and AUC.' + diff --git a/recipes/bioconductor-gsalightning/build.sh b/recipes/bioconductor-gsalightning/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsalightning/build.sh +++ b/recipes/bioconductor-gsalightning/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsalightning/meta.yaml b/recipes/bioconductor-gsalightning/meta.yaml index a90fc3f946be0..f944353572a0a 100644 --- a/recipes/bioconductor-gsalightning/meta.yaml +++ b/recipes/bioconductor-gsalightning/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "GSALightning" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9ff71cd1c042d01e0faffb7927c43d5a9072bc052a246ffd4bd5e31f070c5c75 + md5: 28383657aa63e5f8fe8140563135c3d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'GSALightning provides a fast implementation of permutation-based gene set analysis for two-sample problem. This package is particularly useful when testing simultaneously a large number of gene sets, or when a large number of permutations is necessary for more accurate p-values estimation.' extra: identifiers: - biotools:gsalightning - doi:10.1093/bioinformatics/btw349 + parent_recipe: + name: bioconductor-gsalightning + path: recipes/bioconductor-gsalightning + version: 1.8.0 + diff --git a/recipes/bioconductor-gsar/build.sh b/recipes/bioconductor-gsar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gsar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsar/meta.yaml b/recipes/bioconductor-gsar/meta.yaml new file mode 100644 index 0000000000000..aa60c48887d09 --- /dev/null +++ b/recipes/bioconductor-gsar/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.16.0" %} +{% set name = "GSAR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dfc4fe251c7b1129b68af45dfb7a3d4d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MASS, GSVAdata, ALL, tweeDEseqCountData, GSEABase, annotate, org.Hs.eg.db, Biobase, genefilter, hgu95av2.db, edgeR, BiocStyle +requirements: + host: + - r-base + - 'r-igraph >=0.7.1' + run: + - r-base + - 'r-igraph >=0.7.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Gene set analysis using specific alternative hypotheses. Tests for differential expression, scale and net correlation structure.' + diff --git a/recipes/bioconductor-gsbenchmark/meta.yaml b/recipes/bioconductor-gsbenchmark/meta.yaml new file mode 100644 index 0000000000000..70e064bcf540a --- /dev/null +++ b/recipes/bioconductor-gsbenchmark/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "GSBenchMark" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5fa1f183443b3841de7e075441d47c5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Benchmarks for Machine Learning Analysis of the Gene Sets. The package contains a list of pathways and gene expression data sets used in "Identifying Tightly Regulated and Variably Expressed Networks by Differential Rank Conservation (DIRAC)" (2010) by Eddy et al.' + diff --git a/recipes/bioconductor-gsbenchmark/post-link.sh b/recipes/bioconductor-gsbenchmark/post-link.sh new file mode 100644 index 0000000000000..c196735a78565 --- /dev/null +++ b/recipes/bioconductor-gsbenchmark/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GSBenchMark_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSBenchMark_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSBenchMark_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gsbenchmark/bioconductor-gsbenchmark_1.2.0_src_all.tar.gz" +) +MD5="5fa1f183443b3841de7e075441d47c5d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gsbenchmark/pre-unlink.sh b/recipes/bioconductor-gsbenchmark/pre-unlink.sh new file mode 100644 index 0000000000000..7fb70db5c2687 --- /dev/null +++ b/recipes/bioconductor-gsbenchmark/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GSBenchMark diff --git a/recipes/bioconductor-gsca/build.sh b/recipes/bioconductor-gsca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsca/build.sh +++ b/recipes/bioconductor-gsca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsca/meta.yaml b/recipes/bioconductor-gsca/meta.yaml index 4967d25469ba8..c8b485e0a2962 100644 --- a/recipes/bioconductor-gsca/meta.yaml +++ b/recipes/bioconductor-gsca/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "GSCA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b90399fd68600c9f6ec632316e74b55f12a6e97f91e5a264fa4292d923e84390 + md5: 5c525cb073c7ab3b0d0d2db4e4dc2f9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Affyhgu133aExpr, Affymoe4302Expr, Affyhgu133A2Expr, Affyhgu133Plus2Expr requirements: host: - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - r-base - r-ggplot2 - r-gplots @@ -27,7 +29,7 @@ requirements: - r-shiny - r-sp run: - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' - r-base - r-ggplot2 - r-gplots @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'GSCA takes as input several lists of activated and repressed genes. GSCA then searches through a compendium of publicly available gene expression profiles for biological contexts that are enriched with a specified pattern of gene expression. GSCA provides both traditional R functions and interactive, user-friendly user interface.' extra: identifiers: - biotools:gsca + parent_recipe: + name: bioconductor-gsca + path: recipes/bioconductor-gsca + version: 2.10.0 + diff --git a/recipes/bioconductor-gse62944/meta.yaml b/recipes/bioconductor-gse62944/meta.yaml new file mode 100644 index 0000000000000..e9802af3acf3e --- /dev/null +++ b/recipes/bioconductor-gse62944/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.10.0" %} +{% set name = "GSE62944" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fecc45362eda757435ba7a0735c96b11 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ExperimentHub (>= 0.99.6), knitr, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'TCGA processed RNA-Seq data for 9264 tumor and 741 normal samples across 24 cancer types and made them available as GEO accession [GSE62944](http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE62944). GSE62944 data have been parsed into a SummarizedExperiment object available in ExperimentHub.' + diff --git a/recipes/bioconductor-gse62944/post-link.sh b/recipes/bioconductor-gse62944/post-link.sh new file mode 100644 index 0000000000000..dbb15005e76c1 --- /dev/null +++ b/recipes/bioconductor-gse62944/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GSE62944_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSE62944_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSE62944_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gse62944/bioconductor-gse62944_1.10.0_src_all.tar.gz" +) +MD5="fecc45362eda757435ba7a0735c96b11" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gse62944/pre-unlink.sh b/recipes/bioconductor-gse62944/pre-unlink.sh new file mode 100644 index 0000000000000..2b4244d94e7af --- /dev/null +++ b/recipes/bioconductor-gse62944/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GSE62944 diff --git a/recipes/bioconductor-gseabase/build.sh b/recipes/bioconductor-gseabase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gseabase/build.sh +++ b/recipes/bioconductor-gseabase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gseabase/meta.yaml b/recipes/bioconductor-gseabase/meta.yaml index 40283d7fc77c2..ba73d42e5672e 100644 --- a/recipes/bioconductor-gseabase/meta.yaml +++ b/recipes/bioconductor-gseabase/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "GSEABase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ead00709a662c67665f4c176df3b32789118ce3269cb730c4e69ccb8b5487b85 + md5: 5b59c4714c169230996c60cf235300bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db, GO.db, org.Hs.eg.db, Rgraphviz, ReportingTools, testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides classes and methods to support Gene Set Enrichment Analysis (GSEA).' extra: identifiers: - biotools:gseabase - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gseabase + path: recipes/bioconductor-gseabase + version: 1.42.0 + diff --git a/recipes/bioconductor-gseabenchmarker/build.sh b/recipes/bioconductor-gseabenchmarker/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gseabenchmarker/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gseabenchmarker/meta.yaml b/recipes/bioconductor-gseabenchmarker/meta.yaml new file mode 100644 index 0000000000000..4ec64a318faf9 --- /dev/null +++ b/recipes/bioconductor-gseabenchmarker/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.0" %} +{% set name = "GSEABenchmarkeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9955f0c7c9c12de28436f4d794eec517 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.2.0,<1.3.0' + - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rappdirs + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-keggandmetacoredzpathwaysgeo >=1.2.0,<1.3.0' + - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rappdirs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The GSEABenchmarkeR package implements an extendable framework for reproducible evaluation of set- and network-based methods for enrichment analysis of gene expression data. This includes support for the efficient execution of these methods on comprehensive real data compendia (microarray and RNA-seq) using parallel computation on standard workstations and institutional computer grids. Methods can then be assessed with respect to runtime, statistical significance, and relevance of the results for the phenotypes investigated.' + diff --git a/recipes/bioconductor-gsealm/build.sh b/recipes/bioconductor-gsealm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsealm/build.sh +++ b/recipes/bioconductor-gsealm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsealm/meta.yaml b/recipes/bioconductor-gsealm/meta.yaml index ebcea4bb2027e..a60e0c6e9ec4e 100644 --- a/recipes/bioconductor-gsealm/meta.yaml +++ b/recipes/bioconductor-gsealm/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "GSEAlm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aa23f37fcd8673044ba263c2daea9e4b775801be0c1d7800b196d9e749af762e + md5: 042abec16df906184e23c4677d4ab42d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GSEABase,Category, multtest, ALL, annotate, hgu95av2.db, genefilter, GOstats, RColorBrewer requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Models and methods for fitting linear models to gene expression data, together with tools for computing and using various regression diagnostics.' extra: identifiers: - biotools:gsealm - doi:10.1093/bioinformatics/btn465 + parent_recipe: + name: bioconductor-gsealm + path: recipes/bioconductor-gsealm + version: 1.40.0 + diff --git a/recipes/bioconductor-gsean/build.sh b/recipes/bioconductor-gsean/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gsean/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsean/meta.yaml b/recipes/bioconductor-gsean/meta.yaml new file mode 100644 index 0000000000000..63bb63ffb9d36 --- /dev/null +++ b/recipes/bioconductor-gsean/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "gsean" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 03265cedf007c831dba2d78d84309d67 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DESeq2, knitr, plotly, RANKS, WGCNA +requirements: + host: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-ppinfer >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-ppinfer >=1.8.0,<1.9.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Biological molecules in a living organism seldom work individually. They usually interact each other in a cooperative way. Biological process is too complicated to understand without considering such interactions. Thus, network-based procedures can be seen as powerful methods for studying complex process. However, many methods are devised for analyzing individual genes. It is said that techniques based on biological networks such as gene co-expression are more precise ways to represent information than those using lists of genes only. This package is aimed to integrate the gene expression and biological network. A biological network is constructed from gene expression data and it is used for Gene Set Enrichment Analysis.' + diff --git a/recipes/bioconductor-gskb/meta.yaml b/recipes/bioconductor-gskb/meta.yaml new file mode 100644 index 0000000000000..05f1d15bdee08 --- /dev/null +++ b/recipes/bioconductor-gskb/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "gskb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d2053bb9fd322f0c71360f6721761443 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: PGSEA +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene Set Knowledgebase (GSKB) is a comprehensive knowledgebase for pathway analysis in mouse. Interpretation of high-throughput genomics data based on biological pathways constitutes a constant challenge, partly because of the lack of supporting pathway database. We created a functional genomics knowledgebase in mouse, which includes 33,261 pathways and gene sets compiled from 40 sources such as Gene Ontology, KEGG, GeneSetDB, PANTHER, microRNA and transcription factor target genes, etc. In addition, we also manually collected and curated 8,747 lists of differentially expressed genes from 2,526 published gene expression studies to enable the detection of similarity to previously reported gene expression signatures. These two types of data constitute a comprehensive Gene Set Knowledgebase (GSKB), which can be readily used by various pathway analysis software such as gene set enrichment analysis (GSEA). As a first step, we gathered annotation information from 40 existing databases for mouse-related gene sets. These gene sets are divided into 7 categories, namely, Gene Ontology, Curated pathways, Metabolic Pathways, Transcription Factor (TF) and microRNA target genes, location (cytogenetics band), and others. We used information in GeneSetDB for some of the databases. Detailed information on these 40 sources and the citations is available http://ge-lab.org/gskb/Table%201-sources.pdf . The gene lists from literature were retrieved manually from individual gene expression studies through a process similar to the one used to create AraPath, a similar resource for Arabidopsis[12]. As most expression studies upload raw data to repositories like GEO and ArrayExpress, we used the meta-data in these databases to search for publications. We scanned all datasets we can found and retrieved 4,313 potentially useful papers reporting gene expression studies in mouse. These papers were individually read by curators to identify lists of differentially expressed genes in various conditions. We compiled a total of 8,747 lists of differently expressed genes from 2,518 of papers. Each gene list was annotated with a unique name, brief description, and publication information, similar to the protocol used in MSigDB and Arapath. These gene lists constitute a large collection of published gene expression signatures that form a foundation for interpret new gene lists and expression profiles. More information about this data is available here http://ge-lab.org/gskb/. There is also a paper describing these data are currently in revision by Database: The Journal of Biological Databases and Curation.' + diff --git a/recipes/bioconductor-gskb/post-link.sh b/recipes/bioconductor-gskb/post-link.sh new file mode 100644 index 0000000000000..a4a08a2beeb43 --- /dev/null +++ b/recipes/bioconductor-gskb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="gskb_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/gskb_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/gskb_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gskb/bioconductor-gskb_1.14.0_src_all.tar.gz" +) +MD5="d2053bb9fd322f0c71360f6721761443" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gskb/pre-unlink.sh b/recipes/bioconductor-gskb/pre-unlink.sh new file mode 100644 index 0000000000000..9802561f36945 --- /dev/null +++ b/recipes/bioconductor-gskb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ gskb diff --git a/recipes/bioconductor-gsreg/build.sh b/recipes/bioconductor-gsreg/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsreg/build.sh +++ b/recipes/bioconductor-gsreg/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsreg/meta.yaml b/recipes/bioconductor-gsreg/meta.yaml index f4e0586c4e318..1b1c8bb3c61f4 100644 --- a/recipes/bioconductor-gsreg/meta.yaml +++ b/recipes/bioconductor-gsreg/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "GSReg" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3a3bcbe759a31640819d1d914d425aa1e76202a29713a32ebbffbd6ca42e96f6 + md5: 723ed94d28d5f414bde41f093c8409b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: GenomicRanges, GSBenchMark requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-homo.sapiens >=1.3.1,<1.5.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base build: - {{ compiler('c') }} @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package for gene set analysis based on the variability of expressions as well as a method to detect Alternative Splicing Events . It implements DIfferential RAnk Conservation (DIRAC) and gene set Expression Variation Analysis (EVA) methods. For detecting Differentially Spliced genes, it provides an implementation of the Spliced-EVA (SEVA).' extra: identifiers: - biotools:gsreg - doi:10.4137/CIN.S14066 + parent_recipe: + name: bioconductor-gsreg + path: recipes/bioconductor-gsreg + version: 1.14.0 + diff --git a/recipes/bioconductor-gsri/build.sh b/recipes/bioconductor-gsri/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsri/build.sh +++ b/recipes/bioconductor-gsri/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsri/meta.yaml b/recipes/bioconductor-gsri/meta.yaml index 2b3df63deaeb0..f32bd472881bf 100644 --- a/recipes/bioconductor-gsri/meta.yaml +++ b/recipes/bioconductor-gsri/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "GSRI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 783e8a8d24ebe663da7e0a062ef4d6f6d01d1d7ef500223ea1a9d554dafe618b + md5: f57c37cdbe4fd009e96b330b0c6d4272 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma, hgu95av2.db requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-les >=1.30.0,<1.32.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-les >=1.32.0,<1.33.0' - r-base - r-fdrtool run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-les >=1.30.0,<1.32.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-les >=1.32.0,<1.33.0' - r-base - r-fdrtool test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The GSRI package estimates the number of differentially expressed genes in gene sets, utilizing the concept of the Gene Set Regulation Index (GSRI).' extra: identifiers: - biotools:gsri - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-gsri + path: recipes/bioconductor-gsri + version: 2.28.0 + diff --git a/recipes/bioconductor-gsva/build.sh b/recipes/bioconductor-gsva/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gsva/build.sh +++ b/recipes/bioconductor-gsva/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gsva/meta.yaml b/recipes/bioconductor-gsva/meta.yaml index dc3ae9129af4a..afb18b627f499 100644 --- a/recipes/bioconductor-gsva/meta.yaml +++ b/recipes/bioconductor-gsva/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "GSVA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 70bb8cab331f3257bf18ba3c3315fccdc7e711d2646e632636af9a19b445bd46 + md5: eab560c63cf486e47723ab7d6292bc76 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: limma, RColorBrewer, genefilter, mclust, edgeR, snow, parallel, GSVAdata requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-shiny - r-shinythemes run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base - r-shiny - r-shinythemes @@ -40,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Gene Set Variation Analysis (GSVA) is a non-parametric, unsupervised method for estimating variation of gene set enrichment through the samples of a expression data set. GSVA performs a change in coordinate systems, transforming the data from a gene by sample matrix to a gene-set by sample matrix, thereby allowing the evaluation of pathway enrichment for each sample. This new matrix of GSVA enrichment scores facilitates applying standard analytical methods like functional enrichment, survival analysis, clustering, CNV-pathway analysis or cross-tissue pathway analysis, in a pathway-centric manner.' extra: identifiers: - biotools:gsva + parent_recipe: + name: bioconductor-gsva + path: recipes/bioconductor-gsva + version: 1.28.0 + diff --git a/recipes/bioconductor-gsvadata/meta.yaml b/recipes/bioconductor-gsvadata/meta.yaml new file mode 100644 index 0000000000000..8ad4798171329 --- /dev/null +++ b/recipes/bioconductor-gsvadata/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.18.0" %} +{% set name = "GSVAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 10c95ec0b4214f43609e0bfdfc860bc8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-hgu95a.db >=3.2.0,<3.3.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-hgu95a.db >=3.2.0,<3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package stores the data employed in the vignette of the GSVA package. These data belong to the following publications: Armstrong et al. Nat Genet 30:41-47, 2002; Cahoy et al. J Neurosci 28:264-278, 2008; Carrel and Willard, Nature, 434:400-404, 2005; Huang et al. PNAS, 104:9758-9763, 2007; Pickrell et al. Nature, 464:768-722, 2010; Skaletsky et al. Nature, 423:825-837; Verhaak et al. Cancer Cell 17:98-110, 2010' + diff --git a/recipes/bioconductor-gsvadata/post-link.sh b/recipes/bioconductor-gsvadata/post-link.sh new file mode 100644 index 0000000000000..c228480ee0d3c --- /dev/null +++ b/recipes/bioconductor-gsvadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GSVAdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GSVAdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/GSVAdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gsvadata/bioconductor-gsvadata_1.18.0_src_all.tar.gz" +) +MD5="10c95ec0b4214f43609e0bfdfc860bc8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gsvadata/pre-unlink.sh b/recipes/bioconductor-gsvadata/pre-unlink.sh new file mode 100644 index 0000000000000..6696ee47e8335 --- /dev/null +++ b/recipes/bioconductor-gsvadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GSVAdata diff --git a/recipes/bioconductor-gtrellis/build.sh b/recipes/bioconductor-gtrellis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gtrellis/build.sh +++ b/recipes/bioconductor-gtrellis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gtrellis/meta.yaml b/recipes/bioconductor-gtrellis/meta.yaml index 26a1abffb7bf4..3c06ddff1b61f 100644 --- a/recipes/bioconductor-gtrellis/meta.yaml +++ b/recipes/bioconductor-gtrellis/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "gtrellis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 46f271ed43225e5c264c4bcc4c52bc65f7f5ba40c8e0e121273f426ff770abbd + md5: 8fc5688a3249a05d5088b29ea8885535 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat (>= 1.0.0), knitr, RColorBrewer, markdown, ComplexHeatmap (>= 1.9.7), Cairo, png, jpeg, tiff requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-circlize >=0.3.3' - r-getoptlong run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-circlize >=0.3.3' - r-getoptlong @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Genome level Trellis graph visualizes genomic data conditioned by genomic categories (e.g. chromosomes). For each genomic category, multiple dimensional data which are represented as tracks describe different features from different aspects. This package provides high flexibility to arrange genomic categories and to add self-defined graphics in the plot.' extra: identifiers: - biotools:gtrellis + parent_recipe: + name: bioconductor-gtrellis + path: recipes/bioconductor-gtrellis + version: 1.12.1 + diff --git a/recipes/bioconductor-guideseq/build.sh b/recipes/bioconductor-guideseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-guideseq/build.sh +++ b/recipes/bioconductor-guideseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-guideseq/conda_build_config.yaml b/recipes/bioconductor-guideseq/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-guideseq/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-guideseq/meta.yaml b/recipes/bioconductor-guideseq/meta.yaml index d6f014722aed7..ee86b59cfb1f5 100644 --- a/recipes/bioconductor-guideseq/meta.yaml +++ b/recipes/bioconductor-guideseq/meta.yaml @@ -1,54 +1,56 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "GUIDEseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 02b1c2a033ee3baf3caf97fc9db1457d7ae883e855a793781d8df2e6d9e4ec2d + md5: eeef16c619ade79a8efac593cde02193 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-crisprseek >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-crisprseek >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-hash - r-matrixstats run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chippeakanno >=3.14.2,<3.16.0' - - 'bioconductor-crisprseek >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-crisprseek >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-hash @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package implements GUIDE-seq analysis workflow including functions for obtaining unique insertion sites (proxy of cleavage sites), estimating the locations of the insertion sites, aka, peaks, merging estimated insertion sites from plus and minus strand, and performing off target search of the extended regions around insertion sites.' extra: identifiers: - biotools:guideseq - doi:10.1186/s12864-017-3746-y + parent_recipe: + name: bioconductor-guideseq + path: recipes/bioconductor-guideseq + version: 1.10.0 + diff --git a/recipes/bioconductor-guitar/build.sh b/recipes/bioconductor-guitar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-guitar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-guitar/meta.yaml b/recipes/bioconductor-guitar/meta.yaml new file mode 100644 index 0000000000000..1cb0955016f9d --- /dev/null +++ b/recipes/bioconductor-guitar/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.20.0" %} +{% set name = "Guitar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8f2fe8190f13fc6908fbd347bbf9f347 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package is designed for visualization of RNA-related genomic features with respect to the landmarks of RNA transcripts, i.e., transcription starting site, start codon, stop codon and transcription ending site.' + diff --git a/recipes/bioconductor-gviz/build.sh b/recipes/bioconductor-gviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-gviz/build.sh +++ b/recipes/bioconductor-gviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gviz/meta.yaml b/recipes/bioconductor-gviz/meta.yaml index 075aa976b853d..995a3c781d08c 100644 --- a/recipes/bioconductor-gviz/meta.yaml +++ b/recipes/bioconductor-gviz/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.3" %} {% set name = "Gviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a45f8ea3d11f7d66078866bcecb1914db91ac88a093108e420b9d009d58914ba + md5: 23720099d9531a42dcc30d8f3d84828b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: xtable, BSgenome.Hsapiens.UCSC.hg19, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-digest >=0.6.8' - r-lattice @@ -41,22 +43,22 @@ requirements: - 'r-matrixstats >=0.8.14' - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-digest >=0.6.8' - r-lattice @@ -67,9 +69,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genomic data analyses requires integrated visualization of known genomic information and new experimental data. Gviz uses the biomaRt and the rtracklayer packages to perform live annotation queries to Ensembl and UCSC and translates this to e.g. gene/transcript structures in viewports of the grid graphics package. This results in genomic information plotted together with your data.' extra: identifiers: - biotools:gviz + parent_recipe: + name: bioconductor-gviz + path: recipes/bioconductor-gviz + version: 1.24.0 + diff --git a/recipes/bioconductor-gwascat/build.sh b/recipes/bioconductor-gwascat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gwascat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gwascat/meta.yaml b/recipes/bioconductor-gwascat/meta.yaml new file mode 100644 index 0000000000000..c5d5492b6fdff --- /dev/null +++ b/recipes/bioconductor-gwascat/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "2.14.0" %} +{% set name = "gwascat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4a30aafb9ce69767d6b21553fbba9607 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DO.db, DT, utils, knitr, RBGL, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gqtlstats >=1.14.0,<1.15.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gqtlstats >=1.14.0,<1.15.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Represent and model data in the EMBL-EBI GWAS catalog.' + diff --git a/recipes/bioconductor-gwasdata/meta.yaml b/recipes/bioconductor-gwasdata/meta.yaml new file mode 100644 index 0000000000000..09b34f7ec74b1 --- /dev/null +++ b/recipes/bioconductor-gwasdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "GWASdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6b7ab74910c712639fa896f6b19e2934 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Selected Affymetrix and Illlumina SNP data for HapMap subjects. Data provided by the Center for Inherited Disease Research at Johns Hopkins University and the Broad Institute of MIT and Harvard University.' + diff --git a/recipes/bioconductor-gwasdata/post-link.sh b/recipes/bioconductor-gwasdata/post-link.sh new file mode 100644 index 0000000000000..d395df474b575 --- /dev/null +++ b/recipes/bioconductor-gwasdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="GWASdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/GWASdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/GWASdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-gwasdata/bioconductor-gwasdata_1.20.0_src_all.tar.gz" +) +MD5="6b7ab74910c712639fa896f6b19e2934" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-gwasdata/pre-unlink.sh b/recipes/bioconductor-gwasdata/pre-unlink.sh new file mode 100644 index 0000000000000..36352774ac615 --- /dev/null +++ b/recipes/bioconductor-gwasdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ GWASdata diff --git a/recipes/bioconductor-gwastools/build.sh b/recipes/bioconductor-gwastools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gwastools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gwastools/meta.yaml b/recipes/bioconductor-gwastools/meta.yaml new file mode 100644 index 0000000000000..056210cb85df8 --- /dev/null +++ b/recipes/bioconductor-gwastools/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.28.0" %} +{% set name = "GWASTools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e37216b340d24ffb378566279397852a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ncdf4, GWASdata, BiocGenerics, RUnit, Biostrings, GenomicRanges, IRanges, SNPRelate, snpStats, S4Vectors, VariantAnnotation +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - r-base + - r-dbi + - r-gwasexacthw + - r-lmtest + - r-logistf + - r-rsqlite + - r-sandwich + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' + - r-base + - r-dbi + - r-gwasexacthw + - r-lmtest + - r-logistf + - r-rsqlite + - r-sandwich + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis.' + diff --git a/recipes/bioconductor-gwasurvivr/build.sh b/recipes/bioconductor-gwasurvivr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-gwasurvivr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-gwasurvivr/meta.yaml b/recipes/bioconductor-gwasurvivr/meta.yaml new file mode 100644 index 0000000000000..5ca82baee00aa --- /dev/null +++ b/recipes/bioconductor-gwasurvivr/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "gwasurvivr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0ac5d680b32b6c05cd5774b9691580bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-matrixstats + - r-survival + run: + - 'bioconductor-gwastools >=1.28.0,<1.29.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-matrixstats + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'gwasurvivr is a package to perform survival analysis using Cox proportional hazard models on imputed genetic data.' + diff --git a/recipes/bioconductor-h10kcod.db/meta.yaml b/recipes/bioconductor-h10kcod.db/meta.yaml new file mode 100644 index 0000000000000..6b8a19a1dcb53 --- /dev/null +++ b/recipes/bioconductor-h10kcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "h10kcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a555739cea229f286953c3297c145e9c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink UniSet Human I Bioarray (~10 000 human genes) annotation data (chip h10kcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-h10kcod.db/post-link.sh b/recipes/bioconductor-h10kcod.db/post-link.sh new file mode 100644 index 0000000000000..ba6e431eb3155 --- /dev/null +++ b/recipes/bioconductor-h10kcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="h10kcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/h10kcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/h10kcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h10kcod.db/bioconductor-h10kcod.db_3.4.0_src_all.tar.gz" +) +MD5="a555739cea229f286953c3297c145e9c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-h10kcod.db/pre-unlink.sh b/recipes/bioconductor-h10kcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..74fee30e4572c --- /dev/null +++ b/recipes/bioconductor-h10kcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ h10kcod.db diff --git a/recipes/bioconductor-h20kcod.db/meta.yaml b/recipes/bioconductor-h20kcod.db/meta.yaml new file mode 100644 index 0000000000000..311c2bd019deb --- /dev/null +++ b/recipes/bioconductor-h20kcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "h20kcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3647facb272f58424f4c94ef92e8ee45 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink UniSet Human 20k I Bioarray annotation data (chip h20kcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-h20kcod.db/post-link.sh b/recipes/bioconductor-h20kcod.db/post-link.sh new file mode 100644 index 0000000000000..1abaa82214930 --- /dev/null +++ b/recipes/bioconductor-h20kcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="h20kcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/h20kcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/h20kcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h20kcod.db/bioconductor-h20kcod.db_3.4.0_src_all.tar.gz" +) +MD5="3647facb272f58424f4c94ef92e8ee45" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-h20kcod.db/pre-unlink.sh b/recipes/bioconductor-h20kcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..e4dc13b3aa623 --- /dev/null +++ b/recipes/bioconductor-h20kcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ h20kcod.db diff --git a/recipes/bioconductor-h5vc/build.sh b/recipes/bioconductor-h5vc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-h5vc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-h5vc/meta.yaml b/recipes/bioconductor-h5vc/meta.yaml new file mode 100644 index 0000000000000..ac47fe485d691 --- /dev/null +++ b/recipes/bioconductor-h5vc/meta.yaml @@ -0,0 +1,64 @@ +{% set version = "2.16.0" %} +{% set name = "h5vc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eb32bc8bba6b5a375da0738e0b28c392 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, locfit, BSgenome.Hsapiens.UCSC.hg19, biomaRt, BSgenome.Hsapiens.NCBI.GRCh38, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-h5vcdata >=2.2.0,<2.3.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-abind + - r-base + - r-batchjobs + - r-ggplot2 + - r-gridextra + - r-reshape + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-h5vcdata >=2.2.0,<2.3.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-abind + - r-base + - r-batchjobs + - r-ggplot2 + - r-gridextra + - r-reshape + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package contains functions to interact with tally data from NGS experiments that is stored in HDF5 files.' + diff --git a/recipes/bioconductor-h5vcdata/meta.yaml b/recipes/bioconductor-h5vcdata/meta.yaml new file mode 100644 index 0000000000000..955d5c0a49126 --- /dev/null +++ b/recipes/bioconductor-h5vcdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.2.0" %} +{% set name = "h5vcData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dafde62ac2fd221e41398ba6b3d6ccc2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: h5vc +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package contains the data used in the vignettes and examples of the ''h5vc'' package' + diff --git a/recipes/bioconductor-h5vcdata/post-link.sh b/recipes/bioconductor-h5vcdata/post-link.sh new file mode 100644 index 0000000000000..a40bf2bc1dc41 --- /dev/null +++ b/recipes/bioconductor-h5vcdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="h5vcData_2.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/h5vcData_2.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/h5vcData_2.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-h5vcdata/bioconductor-h5vcdata_2.2.0_src_all.tar.gz" +) +MD5="dafde62ac2fd221e41398ba6b3d6ccc2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-h5vcdata/pre-unlink.sh b/recipes/bioconductor-h5vcdata/pre-unlink.sh new file mode 100644 index 0000000000000..5290ac80b5d0a --- /dev/null +++ b/recipes/bioconductor-h5vcdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ h5vcData diff --git a/recipes/bioconductor-hapfabia/build.sh b/recipes/bioconductor-hapfabia/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hapfabia/build.sh +++ b/recipes/bioconductor-hapfabia/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hapfabia/meta.yaml b/recipes/bioconductor-hapfabia/meta.yaml index 11dc930e04a21..0a3e311f7565c 100644 --- a/recipes/bioconductor-hapfabia/meta.yaml +++ b/recipes/bioconductor-hapfabia/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "hapFabia" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cd048ee9d404032bfc7a7d926589e7973a064ee07500423581674dbbbb457606 + md5: acb38ecfda83a4ce592621b4fa13583c build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-fabia >=2.26.0,<2.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fabia >=2.28.0,<2.29.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-fabia >=2.26.0,<2.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fabia >=2.28.0,<2.29.0' - r-base build: - {{ compiler('c') }} @@ -32,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.1)' summary: 'A package to identify very short IBD segments in large sequencing data by FABIA biclustering. Two haplotypes are identical by descent (IBD) if they share a segment that both inherited from a common ancestor. Current IBD methods reliably detect long IBD segments because many minor alleles in the segment are concordant between the two haplotypes. However, many cohort studies contain unrelated individuals which share only short IBD segments. This package provides software to identify short IBD segments in sequencing data. Knowledge of short IBD segments are relevant for phasing of genotyping data, association studies, and for population genetics, where they shed light on the evolutionary history of humans. The package supports VCF formats, is based on sparse matrix operations, and provides visualization of haplotype clusters in different formats.' extra: identifiers: - biotools:hapfabia + parent_recipe: + name: bioconductor-hapfabia + path: recipes/bioconductor-hapfabia + version: 1.22.0 + diff --git a/recipes/bioconductor-hapmap100khind/meta.yaml b/recipes/bioconductor-hapmap100khind/meta.yaml new file mode 100644 index 0000000000000..d5c168ea556f9 --- /dev/null +++ b/recipes/bioconductor-hapmap100khind/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmap100khind" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 41f5b3455328c928df5b6ae2d81e7c8b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmap100khind/post-link.sh b/recipes/bioconductor-hapmap100khind/post-link.sh new file mode 100644 index 0000000000000..619467b249cd0 --- /dev/null +++ b/recipes/bioconductor-hapmap100khind/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmap100khind_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap100khind_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap100khind_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap100khind/bioconductor-hapmap100khind_1.24.0_src_all.tar.gz" +) +MD5="41f5b3455328c928df5b6ae2d81e7c8b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmap100khind/pre-unlink.sh b/recipes/bioconductor-hapmap100khind/pre-unlink.sh new file mode 100644 index 0000000000000..7c46cc14fe26f --- /dev/null +++ b/recipes/bioconductor-hapmap100khind/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmap100khind diff --git a/recipes/bioconductor-hapmap100kxba/meta.yaml b/recipes/bioconductor-hapmap100kxba/meta.yaml new file mode 100644 index 0000000000000..9a276dae13bcb --- /dev/null +++ b/recipes/bioconductor-hapmap100kxba/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmap100kxba" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a1d77e1d940c42e5b253d8517a29f414 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmap100kxba/post-link.sh b/recipes/bioconductor-hapmap100kxba/post-link.sh new file mode 100644 index 0000000000000..f364bdf1da0b2 --- /dev/null +++ b/recipes/bioconductor-hapmap100kxba/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmap100kxba_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap100kxba_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap100kxba_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap100kxba/bioconductor-hapmap100kxba_1.24.0_src_all.tar.gz" +) +MD5="a1d77e1d940c42e5b253d8517a29f414" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmap100kxba/pre-unlink.sh b/recipes/bioconductor-hapmap100kxba/pre-unlink.sh new file mode 100644 index 0000000000000..c20e95b9de8a2 --- /dev/null +++ b/recipes/bioconductor-hapmap100kxba/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmap100kxba diff --git a/recipes/bioconductor-hapmap370k/meta.yaml b/recipes/bioconductor-hapmap370k/meta.yaml new file mode 100644 index 0000000000000..7519e144a5a8e --- /dev/null +++ b/recipes/bioconductor-hapmap370k/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.1" %} +{% set name = "hapmap370k" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 569556341a45da799372aaf1012be72e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: crlmm +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL + summary: 'Example HapMap data from Illumina 370k BeadChips' + diff --git a/recipes/bioconductor-hapmap370k/post-link.sh b/recipes/bioconductor-hapmap370k/post-link.sh new file mode 100644 index 0000000000000..80834d45d096f --- /dev/null +++ b/recipes/bioconductor-hapmap370k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmap370k_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hapmap370k_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap370k_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap370k/bioconductor-hapmap370k_1.0.1_src_all.tar.gz" +) +MD5="569556341a45da799372aaf1012be72e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmap370k/pre-unlink.sh b/recipes/bioconductor-hapmap370k/pre-unlink.sh new file mode 100644 index 0000000000000..bf3f166b5ccf6 --- /dev/null +++ b/recipes/bioconductor-hapmap370k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmap370k diff --git a/recipes/bioconductor-hapmap500knsp/meta.yaml b/recipes/bioconductor-hapmap500knsp/meta.yaml new file mode 100644 index 0000000000000..3a5d299eba8f3 --- /dev/null +++ b/recipes/bioconductor-hapmap500knsp/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmap500knsp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6a1ab68e668feec8e7388dbbd4308252 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmap500knsp/post-link.sh b/recipes/bioconductor-hapmap500knsp/post-link.sh new file mode 100644 index 0000000000000..4d5b1128e8e69 --- /dev/null +++ b/recipes/bioconductor-hapmap500knsp/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmap500knsp_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap500knsp_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap500knsp_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap500knsp/bioconductor-hapmap500knsp_1.24.0_src_all.tar.gz" +) +MD5="6a1ab68e668feec8e7388dbbd4308252" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmap500knsp/pre-unlink.sh b/recipes/bioconductor-hapmap500knsp/pre-unlink.sh new file mode 100644 index 0000000000000..5a10a63915b0d --- /dev/null +++ b/recipes/bioconductor-hapmap500knsp/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmap500knsp diff --git a/recipes/bioconductor-hapmap500ksty/meta.yaml b/recipes/bioconductor-hapmap500ksty/meta.yaml new file mode 100644 index 0000000000000..3840fe07119ca --- /dev/null +++ b/recipes/bioconductor-hapmap500ksty/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmap500ksty" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b33d5168b902765a63c25a6f2dae66af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmap500ksty/post-link.sh b/recipes/bioconductor-hapmap500ksty/post-link.sh new file mode 100644 index 0000000000000..703ea68535d61 --- /dev/null +++ b/recipes/bioconductor-hapmap500ksty/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmap500ksty_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmap500ksty_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmap500ksty_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmap500ksty/bioconductor-hapmap500ksty_1.24.0_src_all.tar.gz" +) +MD5="b33d5168b902765a63c25a6f2dae66af" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmap500ksty/pre-unlink.sh b/recipes/bioconductor-hapmap500ksty/pre-unlink.sh new file mode 100644 index 0000000000000..1966b5cd476a4 --- /dev/null +++ b/recipes/bioconductor-hapmap500ksty/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmap500ksty diff --git a/recipes/bioconductor-hapmapsnp5/meta.yaml b/recipes/bioconductor-hapmapsnp5/meta.yaml new file mode 100644 index 0000000000000..b0e88eb647892 --- /dev/null +++ b/recipes/bioconductor-hapmapsnp5/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmapsnp5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 518ce21d478eb25e29ed81256154e6fe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmapsnp5/post-link.sh b/recipes/bioconductor-hapmapsnp5/post-link.sh new file mode 100644 index 0000000000000..57e9d1c90e23f --- /dev/null +++ b/recipes/bioconductor-hapmapsnp5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmapsnp5_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmapsnp5_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmapsnp5_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp5/bioconductor-hapmapsnp5_1.24.0_src_all.tar.gz" +) +MD5="518ce21d478eb25e29ed81256154e6fe" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmapsnp5/pre-unlink.sh b/recipes/bioconductor-hapmapsnp5/pre-unlink.sh new file mode 100644 index 0000000000000..070c1fbcbda57 --- /dev/null +++ b/recipes/bioconductor-hapmapsnp5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmapsnp5 diff --git a/recipes/bioconductor-hapmapsnp6/meta.yaml b/recipes/bioconductor-hapmapsnp6/meta.yaml new file mode 100644 index 0000000000000..3839692a18ed4 --- /dev/null +++ b/recipes/bioconductor-hapmapsnp6/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.24.0" %} +{% set name = "hapmapsnp6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2d6a0cd7f337c99834d143215d74e787 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo, oligoClasses +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Sample dataset obtained from http://www.hapmap.org' + diff --git a/recipes/bioconductor-hapmapsnp6/post-link.sh b/recipes/bioconductor-hapmapsnp6/post-link.sh new file mode 100644 index 0000000000000..b9b29e242e5a0 --- /dev/null +++ b/recipes/bioconductor-hapmapsnp6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hapmapsnp6_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hapmapsnp6_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/hapmapsnp6_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hapmapsnp6/bioconductor-hapmapsnp6_1.24.0_src_all.tar.gz" +) +MD5="2d6a0cd7f337c99834d143215d74e787" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hapmapsnp6/pre-unlink.sh b/recipes/bioconductor-hapmapsnp6/pre-unlink.sh new file mode 100644 index 0000000000000..bc187a1ff3d6f --- /dev/null +++ b/recipes/bioconductor-hapmapsnp6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hapmapsnp6 diff --git a/recipes/bioconductor-harbchip/meta.yaml b/recipes/bioconductor-harbchip/meta.yaml new file mode 100644 index 0000000000000..f543b485b637d --- /dev/null +++ b/recipes/bioconductor-harbchip/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.20.0" %} +{% set name = "harbChIP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2dedda8ec8b79f7cd73648090853a31a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'data from a yeast ChIP-chip experiment' + diff --git a/recipes/bioconductor-harbchip/post-link.sh b/recipes/bioconductor-harbchip/post-link.sh new file mode 100644 index 0000000000000..df3db69385dc5 --- /dev/null +++ b/recipes/bioconductor-harbchip/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="harbChIP_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/harbChIP_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/harbChIP_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harbchip/bioconductor-harbchip_1.20.0_src_all.tar.gz" +) +MD5="2dedda8ec8b79f7cd73648090853a31a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-harbchip/pre-unlink.sh b/recipes/bioconductor-harbchip/pre-unlink.sh new file mode 100644 index 0000000000000..54e4a9a5478ac --- /dev/null +++ b/recipes/bioconductor-harbchip/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ harbChIP diff --git a/recipes/bioconductor-harman/build.sh b/recipes/bioconductor-harman/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-harman/build.sh +++ b/recipes/bioconductor-harman/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harman/conda_build_config.yaml b/recipes/bioconductor-harman/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-harman/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-harman/meta.yaml b/recipes/bioconductor-harman/meta.yaml index 5603d87020996..4646a05819a16 100644 --- a/recipes/bioconductor-harman/meta.yaml +++ b/recipes/bioconductor-harman/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Harman" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dc1afe939d228f239690e1482caf807927dfccf7497fff4e5c44640a623023bc + md5: d93baf47bf61f0f0fb45d0a06e0e797a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: HarmanData, BiocGenerics, BiocStyle, knitr, rmarkdown, RUnit, RColorBrewer, bladderbatch, limma, minfi, lumi, msmsEDA, affydata, minfiData, sva requirements: host: - r-base @@ -31,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENCE' summary: 'Harman is a PCA and constrained optimisation based technique that maximises the removal of batch effects from datasets, with the constraint that the probability of overcorrection (i.e. removing genuine biological signal along with batch noise) is kept to a fraction which is set by the end-user.' extra: identifiers: - biotools:harman + parent_recipe: + name: bioconductor-harman + path: recipes/bioconductor-harman + version: 1.8.0 + diff --git a/recipes/bioconductor-harmandata/meta.yaml b/recipes/bioconductor-harmandata/meta.yaml new file mode 100644 index 0000000000000..8d0f532d842e8 --- /dev/null +++ b/recipes/bioconductor-harmandata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "HarmanData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 527bf6823b7a6135e7c04b0031c8c486 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Datasets of accompany Harman, a PCA and constrained optimisation based technique. Contains three datasets: IMR90, Human lung fibroblast cells exposed to nitric oxide; NPM, an experiment to test skin penetration of metal oxide nanoparticles following topical application of sunscreens in non-pregnant mice; OLF; an experiment to gauge the response of human olfactory neurosphere-derived (hONS) cells to ZnO nanoparticles.' + diff --git a/recipes/bioconductor-harmandata/post-link.sh b/recipes/bioconductor-harmandata/post-link.sh new file mode 100644 index 0000000000000..34b56f0f21f43 --- /dev/null +++ b/recipes/bioconductor-harmandata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HarmanData_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HarmanData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/HarmanData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harmandata/bioconductor-harmandata_1.10.0_src_all.tar.gz" +) +MD5="527bf6823b7a6135e7c04b0031c8c486" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-harmandata/pre-unlink.sh b/recipes/bioconductor-harmandata/pre-unlink.sh new file mode 100644 index 0000000000000..4a01707ff7b94 --- /dev/null +++ b/recipes/bioconductor-harmandata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HarmanData diff --git a/recipes/bioconductor-harmonizedtcgadata/meta.yaml b/recipes/bioconductor-harmonizedtcgadata/meta.yaml new file mode 100644 index 0000000000000..0dbfbe1131337 --- /dev/null +++ b/recipes/bioconductor-harmonizedtcgadata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "HarmonizedTCGAData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 064823184770359197455c835096eacb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationHub, knitr, rmarkdown, igraph, survival, ANF, stats, testthat +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This package contains the processed harmonized TCGA data of five cancer types used in "Tianle Ma and Aidong Zhang, Integrate Multi-omic Data Using Affinity Network Fusion (ANF) for Cancer Patient Clustering".' + diff --git a/recipes/bioconductor-harmonizedtcgadata/post-link.sh b/recipes/bioconductor-harmonizedtcgadata/post-link.sh new file mode 100644 index 0000000000000..699358eed7cc5 --- /dev/null +++ b/recipes/bioconductor-harmonizedtcgadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HarmonizedTCGAData_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HarmonizedTCGAData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/HarmonizedTCGAData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-harmonizedtcgadata/bioconductor-harmonizedtcgadata_1.4.0_src_all.tar.gz" +) +MD5="064823184770359197455c835096eacb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-harmonizedtcgadata/pre-unlink.sh b/recipes/bioconductor-harmonizedtcgadata/pre-unlink.sh new file mode 100644 index 0000000000000..de46288df35b1 --- /dev/null +++ b/recipes/bioconductor-harmonizedtcgadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HarmonizedTCGAData diff --git a/recipes/bioconductor-harshlight/build.sh b/recipes/bioconductor-harshlight/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-harshlight/build.sh +++ b/recipes/bioconductor-harshlight/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-harshlight/conda_build_config.yaml b/recipes/bioconductor-harshlight/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-harshlight/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-harshlight/meta.yaml b/recipes/bioconductor-harshlight/meta.yaml index 55aced634b1a6..76d45f5a4d222 100644 --- a/recipes/bioconductor-harshlight/meta.yaml +++ b/recipes/bioconductor-harshlight/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "Harshlight" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5286c8ed1071d19b5b2ee6275c3a18749a989809b76c592fa959b1aee7d1278 + md5: 001fce5a89c331b48513365b01adceb5 build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-altcdfenvs >=2.42.0,<2.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-altcdfenvs >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-altcdfenvs >=2.42.0,<2.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-altcdfenvs >=2.44.0,<2.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package is used to detect extended, diffuse and compact blemishes on microarray chips. Harshlight automatically marks the areas in a collection of chips (affybatch objects) and a corrected AffyBatch object is returned, in which the defected areas are substituted with NAs or the median of the values of the same probe in the other chips in the collection. The new version handle the substitute value as whole matrix to solve the memory problem.' extra: identifiers: - biotools:harshlight - doi:10.1186/1471-2105-6-294 + parent_recipe: + name: bioconductor-harshlight + path: recipes/bioconductor-harshlight + version: 1.52.0 + diff --git a/recipes/bioconductor-hcg110.db/meta.yaml b/recipes/bioconductor-hcg110.db/meta.yaml new file mode 100644 index 0000000000000..a942dcd5db612 --- /dev/null +++ b/recipes/bioconductor-hcg110.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hcg110.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eaba09d7e88bb913fd18f4e8fb72760b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Cancer G110 Array annotation data (chip hcg110) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hcg110.db/post-link.sh b/recipes/bioconductor-hcg110.db/post-link.sh new file mode 100644 index 0000000000000..a24675cd72d0f --- /dev/null +++ b/recipes/bioconductor-hcg110.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hcg110.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hcg110.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110.db/bioconductor-hcg110.db_3.2.3_src_all.tar.gz" +) +MD5="eaba09d7e88bb913fd18f4e8fb72760b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hcg110.db/pre-unlink.sh b/recipes/bioconductor-hcg110.db/pre-unlink.sh new file mode 100644 index 0000000000000..4957b2860b0b8 --- /dev/null +++ b/recipes/bioconductor-hcg110.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hcg110.db diff --git a/recipes/bioconductor-hcg110cdf/meta.yaml b/recipes/bioconductor-hcg110cdf/meta.yaml new file mode 100644 index 0000000000000..e6b5f49f6a236 --- /dev/null +++ b/recipes/bioconductor-hcg110cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hcg110cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b53167876217ddb301204719da23eafc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HC_G110.cdf file.' + diff --git a/recipes/bioconductor-hcg110cdf/post-link.sh b/recipes/bioconductor-hcg110cdf/post-link.sh new file mode 100644 index 0000000000000..bf76d5ea69451 --- /dev/null +++ b/recipes/bioconductor-hcg110cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hcg110cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hcg110cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110cdf/bioconductor-hcg110cdf_2.18.0_src_all.tar.gz" +) +MD5="b53167876217ddb301204719da23eafc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hcg110cdf/pre-unlink.sh b/recipes/bioconductor-hcg110cdf/pre-unlink.sh new file mode 100644 index 0000000000000..974b559e80ab1 --- /dev/null +++ b/recipes/bioconductor-hcg110cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hcg110cdf diff --git a/recipes/bioconductor-hcg110probe/meta.yaml b/recipes/bioconductor-hcg110probe/meta.yaml new file mode 100644 index 0000000000000..7926b07ad427b --- /dev/null +++ b/recipes/bioconductor-hcg110probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hcg110probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 51af8d6a7090ea7c5fe630dcea68bfb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HC-G110\_probe\_tab.' + diff --git a/recipes/bioconductor-hcg110probe/post-link.sh b/recipes/bioconductor-hcg110probe/post-link.sh new file mode 100644 index 0000000000000..ddc19382b9f5e --- /dev/null +++ b/recipes/bioconductor-hcg110probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hcg110probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hcg110probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hcg110probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hcg110probe/bioconductor-hcg110probe_2.18.0_src_all.tar.gz" +) +MD5="51af8d6a7090ea7c5fe630dcea68bfb3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hcg110probe/pre-unlink.sh b/recipes/bioconductor-hcg110probe/pre-unlink.sh new file mode 100644 index 0000000000000..2d2ef10815065 --- /dev/null +++ b/recipes/bioconductor-hcg110probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hcg110probe diff --git a/recipes/bioconductor-hd2013sgi/meta.yaml b/recipes/bioconductor-hd2013sgi/meta.yaml new file mode 100644 index 0000000000000..f4406aa4489f0 --- /dev/null +++ b/recipes/bioconductor-hd2013sgi/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.22.0" %} +{% set name = "HD2013SGI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e67f8f961700314d6ba0326dfebb0e3b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - r-base + - r-gplots + - r-lsd + - r-rcolorbrewer + - r-vcd + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - r-base + - r-gplots + - r-lsd + - r-rcolorbrewer + - r-vcd + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains the experimental data and a complete executable transcript (vignette) of the analysis of the HCT116 genetic interaction matrix presented in the paper "Mapping genetic interactions in human cancer cells with RNAi and multiparametric phenotyping" by C. Laufer, B. Fischer, M. Billmann, W. Huber, M. Boutros; Nature Methods (2013) 10:427-31. doi: 10.1038/nmeth.2436.' + diff --git a/recipes/bioconductor-hd2013sgi/post-link.sh b/recipes/bioconductor-hd2013sgi/post-link.sh new file mode 100644 index 0000000000000..3d0380bb26f2a --- /dev/null +++ b/recipes/bioconductor-hd2013sgi/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HD2013SGI_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HD2013SGI_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/HD2013SGI_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hd2013sgi/bioconductor-hd2013sgi_1.22.0_src_all.tar.gz" +) +MD5="e67f8f961700314d6ba0326dfebb0e3b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hd2013sgi/pre-unlink.sh b/recipes/bioconductor-hd2013sgi/pre-unlink.sh new file mode 100644 index 0000000000000..2728764e37dc4 --- /dev/null +++ b/recipes/bioconductor-hd2013sgi/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HD2013SGI diff --git a/recipes/bioconductor-hdcytodata/meta.yaml b/recipes/bioconductor-hdcytodata/meta.yaml new file mode 100644 index 0000000000000..26505e6aee0c0 --- /dev/null +++ b/recipes/bioconductor-hdcytodata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.2.1" %} +{% set name = "HDCytoData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 052694707ec8c44941417dc44e112d5a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, FlowSOM, Rtsne, ggplot2 +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Data package containing a set of high-dimensional cytometry datasets saved in SummarizedExperiment and flowSet Bioconductor object formats, including row and column metadata describing samples, cell populations (clusters), and protein markers.' + diff --git a/recipes/bioconductor-hdcytodata/post-link.sh b/recipes/bioconductor-hdcytodata/post-link.sh new file mode 100644 index 0000000000000..bbed9f230a3d8 --- /dev/null +++ b/recipes/bioconductor-hdcytodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HDCytoData_1.2.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HDCytoData_1.2.1.tar.gz" + "https://bioarchive.galaxyproject.org/HDCytoData_1.2.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hdcytodata/bioconductor-hdcytodata_1.2.1_src_all.tar.gz" +) +MD5="052694707ec8c44941417dc44e112d5a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hdcytodata/pre-unlink.sh b/recipes/bioconductor-hdcytodata/pre-unlink.sh new file mode 100644 index 0000000000000..411e51fd845e2 --- /dev/null +++ b/recipes/bioconductor-hdcytodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HDCytoData diff --git a/recipes/bioconductor-hdf5array/build.sh b/recipes/bioconductor-hdf5array/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hdf5array/build.sh +++ b/recipes/bioconductor-hdf5array/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hdf5array/meta.yaml b/recipes/bioconductor-hdf5array/meta.yaml index 10719b3660979..32033eb1aca37 100644 --- a/recipes/bioconductor-hdf5array/meta.yaml +++ b/recipes/bioconductor-hdf5array/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.1" %} {% set name = "HDF5Array" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5effb43e2b657130ad2f98dea2864bed7c3fb816d4cb4c85c023d99eafb84e8 + md5: 8364b79376541c14faea8f90d97be4a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: h5vcData, SummarizedExperiment (>= 1.9.6), GenomicRanges, ExperimentHub, BiocParallel, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'An array-like container for convenient access and manipulation of HDF5 datasets. Supports delayed operations and block processing.' + summary: 'Implements the HDF5Array and TENxMatrix classes, 2 convenient and memory-efficient array-like containers for on-disk representation of HDF5 datasets. HDF5Array is for datasets that use the conventional (i.e. dense) HDF5 representation. TENxMatrix is for datasets that use the HDF5-based sparse matrix representation from 10x Genomics (e.g. the 1.3 Million Brain Cell Dataset). Both containers being DelayedArray extensions, they support all operations supported by DelayedArray objects. These operations can be either delayed or block-processed.' extra: identifiers: - biotools:hdf5array - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hdf5array + path: recipes/bioconductor-hdf5array + version: 1.8.1 + diff --git a/recipes/bioconductor-hdtd/build.sh b/recipes/bioconductor-hdtd/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hdtd/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hdtd/meta.yaml b/recipes/bioconductor-hdtd/meta.yaml new file mode 100644 index 0000000000000..7b0be57e00ff0 --- /dev/null +++ b/recipes/bioconductor-hdtd/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.16.0" %} +{% set name = "HDTD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e4763c7b65d7e166c2f1d04aece51437 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, markdown +requirements: + host: + - r-base + - 'r-rcpp >=0.12.13' + - r-rcpparmadillo + run: + - r-base + - 'r-rcpp >=0.12.13' + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Characterization of intra-individual variability using physiologically relevant measurements provides important insights into fundamental biological questions ranging from cell type identity to tumor development. For each individual, the data measurements can be written as a matrix with the different subsamples of the individual recorded in the columns and the different phenotypic units recorded in the rows. Datasets of this type are called high-dimensional transposable data. The HDTD package provides functions for conducting statistical inference for the mean relationship between the row and column variables and for the covariance structure within and between the row and column variables.' + diff --git a/recipes/bioconductor-healthyflowdata/meta.yaml b/recipes/bioconductor-healthyflowdata/meta.yaml new file mode 100644 index 0000000000000..f53e7f9f09826 --- /dev/null +++ b/recipes/bioconductor-healthyflowdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "healthyFlowData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b8581160bd5bfcc2d539dd7c15b6015b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A healthy dataset with 20 flow cytometry samples used by the flowMatch package.' + diff --git a/recipes/bioconductor-healthyflowdata/post-link.sh b/recipes/bioconductor-healthyflowdata/post-link.sh new file mode 100644 index 0000000000000..f85ad89c65493 --- /dev/null +++ b/recipes/bioconductor-healthyflowdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="healthyFlowData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/healthyFlowData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/healthyFlowData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-healthyflowdata/bioconductor-healthyflowdata_1.20.0_src_all.tar.gz" +) +MD5="b8581160bd5bfcc2d539dd7c15b6015b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-healthyflowdata/pre-unlink.sh b/recipes/bioconductor-healthyflowdata/pre-unlink.sh new file mode 100644 index 0000000000000..f04265f290e6d --- /dev/null +++ b/recipes/bioconductor-healthyflowdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ healthyFlowData diff --git a/recipes/bioconductor-heatmaps/build.sh b/recipes/bioconductor-heatmaps/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-heatmaps/build.sh +++ b/recipes/bioconductor-heatmaps/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-heatmaps/meta.yaml b/recipes/bioconductor-heatmaps/meta.yaml index 3c120a8bab863..14bc650fb4ea6 100644 --- a/recipes/bioconductor-heatmaps/meta.yaml +++ b/recipes/bioconductor-heatmaps/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "heatmaps" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9cec782a3346ffe0ac7f7c2d53262735e2ddcc408cf27aa4da07b9fe88eccb01 + md5: fc9f322f10602a84bcea0fe147003763 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Drerio.UCSC.danRer7, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-kernsmooth - r-matrix - r-plotrix - r-rcolorbrewer run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-kernsmooth - r-matrix @@ -45,8 +47,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides functions for plotting heatmaps of genome-wide data across genomic intervals, such as ChIP-seq signals at peaks or across promoters. Many functions are also provided for investigating sequence features.' - +extra: + parent_recipe: + name: bioconductor-heatmaps + path: recipes/bioconductor-heatmaps + version: 1.4.0 diff --git a/recipes/bioconductor-heatplus/build.sh b/recipes/bioconductor-heatplus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-heatplus/build.sh +++ b/recipes/bioconductor-heatplus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-heatplus/meta.yaml b/recipes/bioconductor-heatplus/meta.yaml index f3610e42c30fb..7d5d5d8af3a5e 100644 --- a/recipes/bioconductor-heatplus/meta.yaml +++ b/recipes/bioconductor-heatplus/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "Heatplus" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d3af59cbfcff1f48b5f49eee84c33ea76cde2145d92caca50fe4fb568fceb54c + md5: 20b3fb9d045f7ca40aa14fd4c9cef45c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, hgu95av2.db, limma requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Display a rectangular heatmap (intensity plot) of a data matrix. By default, both samples (columns) and features (row) of the matrix are sorted according to a hierarchical clustering, and the corresponding dendrogram is plotted. Optionally, panels with additional information about samples and features can be added to the plot.' extra: identifiers: - biotools:heatplus - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-heatplus + path: recipes/bioconductor-heatplus + version: 2.26.0 + diff --git a/recipes/bioconductor-heebodata/meta.yaml b/recipes/bioconductor-heebodata/meta.yaml new file mode 100644 index 0000000000000..8262d888237f8 --- /dev/null +++ b/recipes/bioconductor-heebodata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "HEEBOdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 637405f7b381653f36c87414a2902907 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'R objects describing the HEEBO oligo set.' + diff --git a/recipes/bioconductor-heebodata/post-link.sh b/recipes/bioconductor-heebodata/post-link.sh new file mode 100644 index 0000000000000..72c71d6a37ad5 --- /dev/null +++ b/recipes/bioconductor-heebodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HEEBOdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HEEBOdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/HEEBOdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-heebodata/bioconductor-heebodata_1.20.0_src_all.tar.gz" +) +MD5="637405f7b381653f36c87414a2902907" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-heebodata/pre-unlink.sh b/recipes/bioconductor-heebodata/pre-unlink.sh new file mode 100644 index 0000000000000..cf336f04f40dd --- /dev/null +++ b/recipes/bioconductor-heebodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HEEBOdata diff --git a/recipes/bioconductor-helloranges/build.sh b/recipes/bioconductor-helloranges/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-helloranges/build.sh +++ b/recipes/bioconductor-helloranges/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-helloranges/meta.yaml b/recipes/bioconductor-helloranges/meta.yaml index cb0cefd686536..23ad765b56bec 100644 --- a/recipes/bioconductor-helloranges/meta.yaml +++ b/recipes/bioconductor-helloranges/meta.yaml @@ -1,62 +1,69 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "HelloRanges" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e4fca3d307adf5e91c8f7b34ee7f1c4830136bb86c90e078f2bf302314bf5372 + md5: ff03ab06cd4a7cf29704657f16a06fd8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: HelloRangesData, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-docopt run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-docopt test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Translates bedtools command-line invocations to R code calling functions from the Bioconductor *Ranges infrastructure. This is intended to educate novice Bioconductor users and to compare the syntax and semantics of the two frameworks.' extra: identifiers: - biotools:helloranges - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-helloranges + path: recipes/bioconductor-helloranges + version: 1.6.0 + diff --git a/recipes/bioconductor-hellorangesdata/meta.yaml b/recipes/bioconductor-hellorangesdata/meta.yaml new file mode 100644 index 0000000000000..cfbb96c9b6b67 --- /dev/null +++ b/recipes/bioconductor-hellorangesdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.8.0" %} +{% set name = "HelloRangesData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 544429f8fe98d0ec98dd22061944d673 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Provides the data that were used in the bedtools tutorial by Aaron Quinlan (http://quinlanlab.org/tutorials/bedtools/bedtools.html). Includes a subset of the DnaseI hypersensitivity data from "Maurano et al. Systematic Localization of Common Disease-Associated Variation in Regulatory DNA. Science. 2012. Vol. 337 no. 6099 pp. 1190-1195." The rest of the tracks were originally downloaded from the UCSC table browser. See the HelloRanges vignette for a port of the bedtools tutorial to R.' + diff --git a/recipes/bioconductor-hellorangesdata/post-link.sh b/recipes/bioconductor-hellorangesdata/post-link.sh new file mode 100644 index 0000000000000..afe0244d385e6 --- /dev/null +++ b/recipes/bioconductor-hellorangesdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HelloRangesData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HelloRangesData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/HelloRangesData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hellorangesdata/bioconductor-hellorangesdata_1.8.0_src_all.tar.gz" +) +MD5="544429f8fe98d0ec98dd22061944d673" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hellorangesdata/pre-unlink.sh b/recipes/bioconductor-hellorangesdata/pre-unlink.sh new file mode 100644 index 0000000000000..145a385fc0557 --- /dev/null +++ b/recipes/bioconductor-hellorangesdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HelloRangesData diff --git a/recipes/bioconductor-help/build.sh b/recipes/bioconductor-help/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-help/build.sh +++ b/recipes/bioconductor-help/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-help/meta.yaml b/recipes/bioconductor-help/meta.yaml index 0d4fff59aa706..e4f8965aff838 100644 --- a/recipes/bioconductor-help/meta.yaml +++ b/recipes/bioconductor-help/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "HELP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 44d9ed27cf2e684659b52a6a3889dca8476f014256853e730b31b6ff663104f4 + md5: e91bbeed8854a990d4c6ae520eed86df build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains a modular pipeline for analysis of HELP microarray data, and includes graphical and mathematical tools with more general applications.' extra: identifiers: - biotools:help - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-help + path: recipes/bioconductor-help + version: 1.38.0 + diff --git a/recipes/bioconductor-hem/build.sh b/recipes/bioconductor-hem/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hem/build.sh +++ b/recipes/bioconductor-hem/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hem/meta.yaml b/recipes/bioconductor-hem/meta.yaml index 2a1b81196a9d1..f196729144b43 100644 --- a/recipes/bioconductor-hem/meta.yaml +++ b/recipes/bioconductor-hem/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "HEM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5acc5cbb29bdb1cd13e9be960d569f542941205ad177391db2b714e7124181c + md5: d2d002ac97b8d515dc6b5676329209fa build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package fits heterogeneous error models for analysis of microarray data' extra: identifiers: - biotools:hem - doi:10.1093/bioinformatics/bth192 + parent_recipe: + name: bioconductor-hem + path: recipes/bioconductor-hem + version: 1.52.0 + diff --git a/recipes/bioconductor-hgfocus.db/meta.yaml b/recipes/bioconductor-hgfocus.db/meta.yaml new file mode 100644 index 0000000000000..68d95b6208729 --- /dev/null +++ b/recipes/bioconductor-hgfocus.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgfocus.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7fb2bb82975ff21d075d3c8ce6f8162a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome Focus Array annotation data (chip hgfocus) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgfocus.db/post-link.sh b/recipes/bioconductor-hgfocus.db/post-link.sh new file mode 100644 index 0000000000000..68f3797476b12 --- /dev/null +++ b/recipes/bioconductor-hgfocus.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgfocus.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocus.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgfocus.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocus.db/bioconductor-hgfocus.db_3.2.3_src_all.tar.gz" +) +MD5="7fb2bb82975ff21d075d3c8ce6f8162a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgfocus.db/pre-unlink.sh b/recipes/bioconductor-hgfocus.db/pre-unlink.sh new file mode 100644 index 0000000000000..af9b896005dd5 --- /dev/null +++ b/recipes/bioconductor-hgfocus.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgfocus.db diff --git a/recipes/bioconductor-hgfocuscdf/meta.yaml b/recipes/bioconductor-hgfocuscdf/meta.yaml new file mode 100644 index 0000000000000..73676002c4710 --- /dev/null +++ b/recipes/bioconductor-hgfocuscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgfocuscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9883e53bfd9ddb9ad5f3a9c2e47bbd2c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-Focus.CDF file.' + diff --git a/recipes/bioconductor-hgfocuscdf/post-link.sh b/recipes/bioconductor-hgfocuscdf/post-link.sh new file mode 100644 index 0000000000000..cb0e564fa6f93 --- /dev/null +++ b/recipes/bioconductor-hgfocuscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgfocuscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocuscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgfocuscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocuscdf/bioconductor-hgfocuscdf_2.18.0_src_all.tar.gz" +) +MD5="9883e53bfd9ddb9ad5f3a9c2e47bbd2c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgfocuscdf/pre-unlink.sh b/recipes/bioconductor-hgfocuscdf/pre-unlink.sh new file mode 100644 index 0000000000000..5d53b0f13057e --- /dev/null +++ b/recipes/bioconductor-hgfocuscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgfocuscdf diff --git a/recipes/bioconductor-hgfocusprobe/meta.yaml b/recipes/bioconductor-hgfocusprobe/meta.yaml new file mode 100644 index 0000000000000..d1aed4a8eed82 --- /dev/null +++ b/recipes/bioconductor-hgfocusprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgfocusprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0a399ed276b89e3d80946b6cbbf167b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-Focus\_probe\_tab.' + diff --git a/recipes/bioconductor-hgfocusprobe/post-link.sh b/recipes/bioconductor-hgfocusprobe/post-link.sh new file mode 100644 index 0000000000000..45c46d333d084 --- /dev/null +++ b/recipes/bioconductor-hgfocusprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgfocusprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgfocusprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgfocusprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgfocusprobe/bioconductor-hgfocusprobe_2.18.0_src_all.tar.gz" +) +MD5="0a399ed276b89e3d80946b6cbbf167b4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgfocusprobe/pre-unlink.sh b/recipes/bioconductor-hgfocusprobe/pre-unlink.sh new file mode 100644 index 0000000000000..84cd58bfe2a02 --- /dev/null +++ b/recipes/bioconductor-hgfocusprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgfocusprobe diff --git a/recipes/bioconductor-hgu133a.db/meta.yaml b/recipes/bioconductor-hgu133a.db/meta.yaml index 8306bc4d6dc3b..23f16b2732959 100644 --- a/recipes/bioconductor-hgu133a.db/meta.yaml +++ b/recipes/bioconductor-hgu133a.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "3.2.3" %} {% set name = "hgu133a.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 75eaffa2bd09a694958b816fd575bb4cbdd35d3bbe60139ff0808516c931149a + md5: ce0397160fe78a92671e492a22542a79 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133 Set annotation data (chip hgu133a) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-hgu133a.db + path: recipes/bioconductor-hgu133a.db + version: 3.2.3 diff --git a/recipes/bioconductor-hgu133a.db/post-link.sh b/recipes/bioconductor-hgu133a.db/post-link.sh index eb12635cc0ae1..b4cdf6e2fdcfe 100644 --- a/recipes/bioconductor-hgu133a.db/post-link.sh +++ b/recipes/bioconductor-hgu133a.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133a.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a.db/bioconductor-hgu133a.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-hgu133a2.db/meta.yaml b/recipes/bioconductor-hgu133a2.db/meta.yaml index 1b4b7ca97b219..198a611bbf4de 100644 --- a/recipes/bioconductor-hgu133a2.db/meta.yaml +++ b/recipes/bioconductor-hgu133a2.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "3.2.3" %} {% set name = "hgu133a2.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 687e3bcc499440778a7482599d1f0dad48ff8222737b0a22dcb32757921490eb + md5: 15cad9bc3f5ef6fca5300638a9c8bb86 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133A 2.0 Array annotation data (chip hgu133a2) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-hgu133a2.db + path: recipes/bioconductor-hgu133a2.db + version: 3.2.3 diff --git a/recipes/bioconductor-hgu133a2.db/post-link.sh b/recipes/bioconductor-hgu133a2.db/post-link.sh index d7e23461451ca..9eb31dbf8fc5a 100644 --- a/recipes/bioconductor-hgu133a2.db/post-link.sh +++ b/recipes/bioconductor-hgu133a2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133a2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133a2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133a2.db/bioconductor-hgu133a2.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-hgu133a2cdf/meta.yaml b/recipes/bioconductor-hgu133a2cdf/meta.yaml new file mode 100644 index 0000000000000..81a9ea5307505 --- /dev/null +++ b/recipes/bioconductor-hgu133a2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133a2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 566bc70f0bb94a376bf88f191a2f067e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U133A_2.cdf file.' + diff --git a/recipes/bioconductor-hgu133a2cdf/post-link.sh b/recipes/bioconductor-hgu133a2cdf/post-link.sh new file mode 100644 index 0000000000000..85381f3207e38 --- /dev/null +++ b/recipes/bioconductor-hgu133a2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133a2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133a2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2cdf/bioconductor-hgu133a2cdf_2.18.0_src_all.tar.gz" +) +MD5="566bc70f0bb94a376bf88f191a2f067e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133a2cdf/pre-unlink.sh b/recipes/bioconductor-hgu133a2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..f284536dfde46 --- /dev/null +++ b/recipes/bioconductor-hgu133a2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133a2cdf diff --git a/recipes/bioconductor-hgu133a2frmavecs/meta.yaml b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml new file mode 100644 index 0000000000000..7d438aa8ade78 --- /dev/null +++ b/recipes/bioconductor-hgu133a2frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "hgu133a2frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4bf8cf5cbaf288ce0a9618d764c87044 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-hgu133a2frmavecs/post-link.sh b/recipes/bioconductor-hgu133a2frmavecs/post-link.sh new file mode 100644 index 0000000000000..d70f4b6cfadef --- /dev/null +++ b/recipes/bioconductor-hgu133a2frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133a2frmavecs_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2frmavecs_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133a2frmavecs_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2frmavecs/bioconductor-hgu133a2frmavecs_1.2.0_src_all.tar.gz" +) +MD5="4bf8cf5cbaf288ce0a9618d764c87044" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133a2frmavecs/pre-unlink.sh b/recipes/bioconductor-hgu133a2frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..7ecd4bcae2cca --- /dev/null +++ b/recipes/bioconductor-hgu133a2frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133a2frmavecs diff --git a/recipes/bioconductor-hgu133a2probe/meta.yaml b/recipes/bioconductor-hgu133a2probe/meta.yaml new file mode 100644 index 0000000000000..b3c63a687f726 --- /dev/null +++ b/recipes/bioconductor-hgu133a2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133a2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 736b43cfc37a297ccc0d30cb75fcc95a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu133a2probe/post-link.sh b/recipes/bioconductor-hgu133a2probe/post-link.sh new file mode 100644 index 0000000000000..4e1c45878877e --- /dev/null +++ b/recipes/bioconductor-hgu133a2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133a2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133a2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133a2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133a2probe/bioconductor-hgu133a2probe_2.18.0_src_all.tar.gz" +) +MD5="736b43cfc37a297ccc0d30cb75fcc95a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133a2probe/pre-unlink.sh b/recipes/bioconductor-hgu133a2probe/pre-unlink.sh new file mode 100644 index 0000000000000..ae93bfd14f58a --- /dev/null +++ b/recipes/bioconductor-hgu133a2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133a2probe diff --git a/recipes/bioconductor-hgu133abarcodevecs/meta.yaml b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml new file mode 100644 index 0000000000000..8f5e886b3ae5a --- /dev/null +++ b/recipes/bioconductor-hgu133abarcodevecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "hgu133abarcodevecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b32e4538a860079a21da485ffc31fbb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data used by the barcode package for microarrays of type hgu133a.' + diff --git a/recipes/bioconductor-hgu133abarcodevecs/post-link.sh b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh new file mode 100644 index 0000000000000..c25774c005786 --- /dev/null +++ b/recipes/bioconductor-hgu133abarcodevecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133abarcodevecs_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133abarcodevecs_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133abarcodevecs_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133abarcodevecs/bioconductor-hgu133abarcodevecs_1.20.0_src_all.tar.gz" +) +MD5="b32e4538a860079a21da485ffc31fbb9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133abarcodevecs/pre-unlink.sh b/recipes/bioconductor-hgu133abarcodevecs/pre-unlink.sh new file mode 100644 index 0000000000000..37a270ef4ac33 --- /dev/null +++ b/recipes/bioconductor-hgu133abarcodevecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133abarcodevecs diff --git a/recipes/bioconductor-hgu133acdf/meta.yaml b/recipes/bioconductor-hgu133acdf/meta.yaml new file mode 100644 index 0000000000000..fedc14d9ecc6d --- /dev/null +++ b/recipes/bioconductor-hgu133acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d3e0e22b2d3943d26c94e7c01b91035c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U133A.cdf file.' + diff --git a/recipes/bioconductor-hgu133acdf/post-link.sh b/recipes/bioconductor-hgu133acdf/post-link.sh new file mode 100644 index 0000000000000..c78e1fafe2133 --- /dev/null +++ b/recipes/bioconductor-hgu133acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133acdf/bioconductor-hgu133acdf_2.18.0_src_all.tar.gz" +) +MD5="d3e0e22b2d3943d26c94e7c01b91035c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133acdf/pre-unlink.sh b/recipes/bioconductor-hgu133acdf/pre-unlink.sh new file mode 100644 index 0000000000000..7369f6aa18ed9 --- /dev/null +++ b/recipes/bioconductor-hgu133acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133acdf diff --git a/recipes/bioconductor-hgu133afrmavecs/meta.yaml b/recipes/bioconductor-hgu133afrmavecs/meta.yaml new file mode 100644 index 0000000000000..5c3975c11bb27 --- /dev/null +++ b/recipes/bioconductor-hgu133afrmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.5.0" %} +{% set name = "hgu133afrmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 85034ab02491f5b3699d210cef50812d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-hgu133afrmavecs/post-link.sh b/recipes/bioconductor-hgu133afrmavecs/post-link.sh new file mode 100644 index 0000000000000..b68622250e322 --- /dev/null +++ b/recipes/bioconductor-hgu133afrmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133afrmavecs_1.5.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133afrmavecs_1.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133afrmavecs_1.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133afrmavecs/bioconductor-hgu133afrmavecs_1.5.0_src_all.tar.gz" +) +MD5="85034ab02491f5b3699d210cef50812d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133afrmavecs/pre-unlink.sh b/recipes/bioconductor-hgu133afrmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..2488dfaa4e9c7 --- /dev/null +++ b/recipes/bioconductor-hgu133afrmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133afrmavecs diff --git a/recipes/bioconductor-hgu133aprobe/meta.yaml b/recipes/bioconductor-hgu133aprobe/meta.yaml new file mode 100644 index 0000000000000..e94723b576637 --- /dev/null +++ b/recipes/bioconductor-hgu133aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 76cd9c54b0a8a0240dbb0fc758959d62 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu133aprobe/post-link.sh b/recipes/bioconductor-hgu133aprobe/post-link.sh new file mode 100644 index 0000000000000..0c0d0621da8a1 --- /dev/null +++ b/recipes/bioconductor-hgu133aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133aprobe/bioconductor-hgu133aprobe_2.18.0_src_all.tar.gz" +) +MD5="76cd9c54b0a8a0240dbb0fc758959d62" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133aprobe/pre-unlink.sh b/recipes/bioconductor-hgu133aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..0a38a80652d2b --- /dev/null +++ b/recipes/bioconductor-hgu133aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133aprobe diff --git a/recipes/bioconductor-hgu133atagcdf/meta.yaml b/recipes/bioconductor-hgu133atagcdf/meta.yaml new file mode 100644 index 0000000000000..57b2395658fa7 --- /dev/null +++ b/recipes/bioconductor-hgu133atagcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133atagcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 01f8809e0deb5b83f3f0decec881a1d8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U133A_tag.CDF file.' + diff --git a/recipes/bioconductor-hgu133atagcdf/post-link.sh b/recipes/bioconductor-hgu133atagcdf/post-link.sh new file mode 100644 index 0000000000000..37321aa43bcd1 --- /dev/null +++ b/recipes/bioconductor-hgu133atagcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133atagcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133atagcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133atagcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133atagcdf/bioconductor-hgu133atagcdf_2.18.0_src_all.tar.gz" +) +MD5="01f8809e0deb5b83f3f0decec881a1d8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133atagcdf/pre-unlink.sh b/recipes/bioconductor-hgu133atagcdf/pre-unlink.sh new file mode 100644 index 0000000000000..db62872b52a8b --- /dev/null +++ b/recipes/bioconductor-hgu133atagcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133atagcdf diff --git a/recipes/bioconductor-hgu133atagprobe/meta.yaml b/recipes/bioconductor-hgu133atagprobe/meta.yaml new file mode 100644 index 0000000000000..1bb71ac0e3bf6 --- /dev/null +++ b/recipes/bioconductor-hgu133atagprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133atagprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 97aeaf9ac9450369cf030581b8ec5a53 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133A\_tag\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu133atagprobe/post-link.sh b/recipes/bioconductor-hgu133atagprobe/post-link.sh new file mode 100644 index 0000000000000..7c3ac7aa6e33d --- /dev/null +++ b/recipes/bioconductor-hgu133atagprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133atagprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133atagprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133atagprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133atagprobe/bioconductor-hgu133atagprobe_2.18.0_src_all.tar.gz" +) +MD5="97aeaf9ac9450369cf030581b8ec5a53" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133atagprobe/pre-unlink.sh b/recipes/bioconductor-hgu133atagprobe/pre-unlink.sh new file mode 100644 index 0000000000000..89fc9afc46e16 --- /dev/null +++ b/recipes/bioconductor-hgu133atagprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133atagprobe diff --git a/recipes/bioconductor-hgu133b.db/meta.yaml b/recipes/bioconductor-hgu133b.db/meta.yaml new file mode 100644 index 0000000000000..5f5c4e4147de5 --- /dev/null +++ b/recipes/bioconductor-hgu133b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu133b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3e7c3fa57703d21d4a7624a45d921b24 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U133 Set annotation data (chip hgu133b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu133b.db/post-link.sh b/recipes/bioconductor-hgu133b.db/post-link.sh new file mode 100644 index 0000000000000..ffea8dbfdcbe7 --- /dev/null +++ b/recipes/bioconductor-hgu133b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133b.db/bioconductor-hgu133b.db_3.2.3_src_all.tar.gz" +) +MD5="3e7c3fa57703d21d4a7624a45d921b24" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133b.db/pre-unlink.sh b/recipes/bioconductor-hgu133b.db/pre-unlink.sh new file mode 100644 index 0000000000000..75b0550e57424 --- /dev/null +++ b/recipes/bioconductor-hgu133b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133b.db diff --git a/recipes/bioconductor-hgu133bcdf/meta.yaml b/recipes/bioconductor-hgu133bcdf/meta.yaml new file mode 100644 index 0000000000000..efa521158302f --- /dev/null +++ b/recipes/bioconductor-hgu133bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 649aaa5e6275be6ee4d24d80ca390ea5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U133B.cdf file.' + diff --git a/recipes/bioconductor-hgu133bcdf/post-link.sh b/recipes/bioconductor-hgu133bcdf/post-link.sh new file mode 100644 index 0000000000000..6bc36da9e77e0 --- /dev/null +++ b/recipes/bioconductor-hgu133bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133bcdf/bioconductor-hgu133bcdf_2.18.0_src_all.tar.gz" +) +MD5="649aaa5e6275be6ee4d24d80ca390ea5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133bcdf/pre-unlink.sh b/recipes/bioconductor-hgu133bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..c32f1dbfe4a66 --- /dev/null +++ b/recipes/bioconductor-hgu133bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133bcdf diff --git a/recipes/bioconductor-hgu133bprobe/meta.yaml b/recipes/bioconductor-hgu133bprobe/meta.yaml new file mode 100644 index 0000000000000..ac3f8a25e9bdf --- /dev/null +++ b/recipes/bioconductor-hgu133bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 203750510e51450e1267e08c241151c4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133B\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu133bprobe/post-link.sh b/recipes/bioconductor-hgu133bprobe/post-link.sh new file mode 100644 index 0000000000000..6b99e2000f0af --- /dev/null +++ b/recipes/bioconductor-hgu133bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133bprobe/bioconductor-hgu133bprobe_2.18.0_src_all.tar.gz" +) +MD5="203750510e51450e1267e08c241151c4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133bprobe/pre-unlink.sh b/recipes/bioconductor-hgu133bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..c73d6b0486c50 --- /dev/null +++ b/recipes/bioconductor-hgu133bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133bprobe diff --git a/recipes/bioconductor-hgu133plus2.db/meta.yaml b/recipes/bioconductor-hgu133plus2.db/meta.yaml index a0a04505b0a0d..7e6a068a43ca0 100644 --- a/recipes/bioconductor-hgu133plus2.db/meta.yaml +++ b/recipes/bioconductor-hgu133plus2.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "3.2.3" %} {% set name = "hgu133plus2.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a56b247b69a6b8c81d23410e9def44f8d3e7c133aedf09fb1561798dca2c0549 + md5: 45a376b6092da75907b9e73bbd90e5bf build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U133 Plus 2.0 Array annotation data (chip hgu133plus2) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-hgu133plus2.db + path: recipes/bioconductor-hgu133plus2.db + version: 3.2.3 diff --git a/recipes/bioconductor-hgu133plus2.db/post-link.sh b/recipes/bioconductor-hgu133plus2.db/post-link.sh index d3494be33bab3..77d92f5877c73 100644 --- a/recipes/bioconductor-hgu133plus2.db/post-link.sh +++ b/recipes/bioconductor-hgu133plus2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu133plus2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu133plus2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2.db/bioconductor-hgu133plus2.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml new file mode 100644 index 0000000000000..f486c4221622f --- /dev/null +++ b/recipes/bioconductor-hgu133plus2barcodevecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "hgu133plus2barcodevecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 638f4fcd029bb5b3d07a2c3b79ffa3f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data used by the barcode package for microarrays of type hgu133plus2.' + diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh new file mode 100644 index 0000000000000..e505f350f501e --- /dev/null +++ b/recipes/bioconductor-hgu133plus2barcodevecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133plus2barcodevecs_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133plus2barcodevecs_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2barcodevecs_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2barcodevecs/bioconductor-hgu133plus2barcodevecs_1.20.0_src_all.tar.gz" +) +MD5="638f4fcd029bb5b3d07a2c3b79ffa3f9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2barcodevecs/pre-unlink.sh b/recipes/bioconductor-hgu133plus2barcodevecs/pre-unlink.sh new file mode 100644 index 0000000000000..6f5265ea11b73 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2barcodevecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2barcodevecs diff --git a/recipes/bioconductor-hgu133plus2cdf/meta.yaml b/recipes/bioconductor-hgu133plus2cdf/meta.yaml new file mode 100644 index 0000000000000..f3830dd41e20d --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133plus2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 284fef2f0b777d7b53451538ddd53de3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U133_Plus_2.cdf file.' + diff --git a/recipes/bioconductor-hgu133plus2cdf/post-link.sh b/recipes/bioconductor-hgu133plus2cdf/post-link.sh new file mode 100644 index 0000000000000..2ef6564bd2c0d --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133plus2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cdf/bioconductor-hgu133plus2cdf_2.18.0_src_all.tar.gz" +) +MD5="284fef2f0b777d7b53451538ddd53de3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2cdf/pre-unlink.sh b/recipes/bioconductor-hgu133plus2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..053986c8d29b5 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2cdf diff --git a/recipes/bioconductor-hgu133plus2cellscore/meta.yaml b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml new file mode 100644 index 0000000000000..b5cec8370fe00 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cellscore/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2.0" %} +{% set name = "hgu133plus2CellScore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 354194eddcc3f67ac375b08422007602 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The CellScore Standard Dataset contains expression data from a wide variety of human cells and tissues, which should be used as standard cell types in the calculation of the CellScore. All data was curated from public databases such as Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov/geo/) or ArrayExpress (https://www.ebi.ac.uk/arrayexpress/). This standard dataset only contains data from the Affymetrix GeneChip Human Genome U133 Plus 2.0 microarrays. Samples were manually annotated using the database information or consulting the publications in which the datasets originated. The sample annotations are stored in the phenoData slot of the expressionSet object. Raw data (CEL files) were processed with the affy package to generate present/absent calls (mas5calls) and background-subtracted values, which were then normalized by the R-package yugene to yield the final expression values for the standard expression matrix. The annotation table for the microarray was retrieved from the BioC annotation package hgu133plus2. All data are stored in an expressionSet object.' + diff --git a/recipes/bioconductor-hgu133plus2cellscore/post-link.sh b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh new file mode 100644 index 0000000000000..2e4683f16db8b --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cellscore/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133plus2CellScore_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu133plus2CellScore_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2CellScore_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2cellscore/bioconductor-hgu133plus2cellscore_1.2.0_src_all.tar.gz" +) +MD5="354194eddcc3f67ac375b08422007602" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2cellscore/pre-unlink.sh b/recipes/bioconductor-hgu133plus2cellscore/pre-unlink.sh new file mode 100644 index 0000000000000..d36335b6e6e52 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2cellscore/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2CellScore diff --git a/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml new file mode 100644 index 0000000000000..0e76aa1829eb4 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.5.0" %} +{% set name = "hgu133plus2frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a4781cbcccc1ee17dfd16259f1c7bebc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh b/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh new file mode 100644 index 0000000000000..42f0febf0fa10 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133plus2frmavecs_1.5.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2frmavecs_1.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2frmavecs_1.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2frmavecs/bioconductor-hgu133plus2frmavecs_1.5.0_src_all.tar.gz" +) +MD5="a4781cbcccc1ee17dfd16259f1c7bebc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2frmavecs/pre-unlink.sh b/recipes/bioconductor-hgu133plus2frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..e15681f8547f1 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2frmavecs diff --git a/recipes/bioconductor-hgu133plus2probe/meta.yaml b/recipes/bioconductor-hgu133plus2probe/meta.yaml new file mode 100644 index 0000000000000..3b782bac87614 --- /dev/null +++ b/recipes/bioconductor-hgu133plus2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu133plus2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7a244787a0269bc72732ac3d830f34dd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U133\_Plus\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu133plus2probe/post-link.sh b/recipes/bioconductor-hgu133plus2probe/post-link.sh new file mode 100644 index 0000000000000..8cfd65258b5ef --- /dev/null +++ b/recipes/bioconductor-hgu133plus2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu133plus2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu133plus2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu133plus2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu133plus2probe/bioconductor-hgu133plus2probe_2.18.0_src_all.tar.gz" +) +MD5="7a244787a0269bc72732ac3d830f34dd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu133plus2probe/pre-unlink.sh b/recipes/bioconductor-hgu133plus2probe/pre-unlink.sh new file mode 100644 index 0000000000000..7b6e5140cc07b --- /dev/null +++ b/recipes/bioconductor-hgu133plus2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu133plus2probe diff --git a/recipes/bioconductor-hgu219.db/meta.yaml b/recipes/bioconductor-hgu219.db/meta.yaml new file mode 100644 index 0000000000000..33c546ffc5c6b --- /dev/null +++ b/recipes/bioconductor-hgu219.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu219.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a4a0fd2ac170a75d8b17618615fcd7a0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome 219 Plate annotation data (chip hgu219) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu219.db/post-link.sh b/recipes/bioconductor-hgu219.db/post-link.sh new file mode 100644 index 0000000000000..6e0d3f12c17a1 --- /dev/null +++ b/recipes/bioconductor-hgu219.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu219.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu219.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219.db/bioconductor-hgu219.db_3.2.3_src_all.tar.gz" +) +MD5="a4a0fd2ac170a75d8b17618615fcd7a0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu219.db/pre-unlink.sh b/recipes/bioconductor-hgu219.db/pre-unlink.sh new file mode 100644 index 0000000000000..4158ea17f256e --- /dev/null +++ b/recipes/bioconductor-hgu219.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu219.db diff --git a/recipes/bioconductor-hgu219cdf/meta.yaml b/recipes/bioconductor-hgu219cdf/meta.yaml new file mode 100644 index 0000000000000..a04736e216f6d --- /dev/null +++ b/recipes/bioconductor-hgu219cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu219cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 157a4280a9de960902260ab18f678949 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG-U219.cdf file.' + diff --git a/recipes/bioconductor-hgu219cdf/post-link.sh b/recipes/bioconductor-hgu219cdf/post-link.sh new file mode 100644 index 0000000000000..7a7b1e893ce0e --- /dev/null +++ b/recipes/bioconductor-hgu219cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu219cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu219cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219cdf/bioconductor-hgu219cdf_2.18.0_src_all.tar.gz" +) +MD5="157a4280a9de960902260ab18f678949" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu219cdf/pre-unlink.sh b/recipes/bioconductor-hgu219cdf/pre-unlink.sh new file mode 100644 index 0000000000000..cc0398befacc2 --- /dev/null +++ b/recipes/bioconductor-hgu219cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu219cdf diff --git a/recipes/bioconductor-hgu219probe/meta.yaml b/recipes/bioconductor-hgu219probe/meta.yaml new file mode 100644 index 0000000000000..b42e348bc9519 --- /dev/null +++ b/recipes/bioconductor-hgu219probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu219probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c5bb2f7b2e0f8fa89e6a30befaee6497 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U219\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu219probe/post-link.sh b/recipes/bioconductor-hgu219probe/post-link.sh new file mode 100644 index 0000000000000..47745a1cf31cd --- /dev/null +++ b/recipes/bioconductor-hgu219probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu219probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu219probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu219probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu219probe/bioconductor-hgu219probe_2.18.0_src_all.tar.gz" +) +MD5="c5bb2f7b2e0f8fa89e6a30befaee6497" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu219probe/pre-unlink.sh b/recipes/bioconductor-hgu219probe/pre-unlink.sh new file mode 100644 index 0000000000000..a6272c0b76b92 --- /dev/null +++ b/recipes/bioconductor-hgu219probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu219probe diff --git a/recipes/bioconductor-hgu2beta7/meta.yaml b/recipes/bioconductor-hgu2beta7/meta.yaml new file mode 100644 index 0000000000000..ce65b5ba5caae --- /dev/null +++ b/recipes/bioconductor-hgu2beta7/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.22.0" %} +{% set name = "hgu2beta7" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 66fe43b6e1b602122964c9026dc9a660 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Annotation data file for hgu2beta7 assembled using data from public data repositories' + diff --git a/recipes/bioconductor-hgu2beta7/post-link.sh b/recipes/bioconductor-hgu2beta7/post-link.sh new file mode 100644 index 0000000000000..fbb30749e69d8 --- /dev/null +++ b/recipes/bioconductor-hgu2beta7/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu2beta7_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hgu2beta7_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu2beta7_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu2beta7/bioconductor-hgu2beta7_1.22.0_src_all.tar.gz" +) +MD5="66fe43b6e1b602122964c9026dc9a660" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu2beta7/pre-unlink.sh b/recipes/bioconductor-hgu2beta7/pre-unlink.sh new file mode 100644 index 0000000000000..463ca857c66d1 --- /dev/null +++ b/recipes/bioconductor-hgu2beta7/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu2beta7 diff --git a/recipes/bioconductor-hgu95a.db/meta.yaml b/recipes/bioconductor-hgu95a.db/meta.yaml new file mode 100644 index 0000000000000..fc79c9284690d --- /dev/null +++ b/recipes/bioconductor-hgu95a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e509dd32292601d81af8aa61ec782ca7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu95a.db/post-link.sh b/recipes/bioconductor-hgu95a.db/post-link.sh new file mode 100644 index 0000000000000..ffdee503dfde8 --- /dev/null +++ b/recipes/bioconductor-hgu95a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95a.db/bioconductor-hgu95a.db_3.2.3_src_all.tar.gz" +) +MD5="e509dd32292601d81af8aa61ec782ca7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95a.db/pre-unlink.sh b/recipes/bioconductor-hgu95a.db/pre-unlink.sh new file mode 100644 index 0000000000000..d3fa571584889 --- /dev/null +++ b/recipes/bioconductor-hgu95a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95a.db diff --git a/recipes/bioconductor-hgu95acdf/meta.yaml b/recipes/bioconductor-hgu95acdf/meta.yaml new file mode 100644 index 0000000000000..51ca4b15e7026 --- /dev/null +++ b/recipes/bioconductor-hgu95acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: afc999d77b1532154d45911ad15a5897 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95A.CDF file.' + diff --git a/recipes/bioconductor-hgu95acdf/post-link.sh b/recipes/bioconductor-hgu95acdf/post-link.sh new file mode 100644 index 0000000000000..f0ff2131b842b --- /dev/null +++ b/recipes/bioconductor-hgu95acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95acdf/bioconductor-hgu95acdf_2.18.0_src_all.tar.gz" +) +MD5="afc999d77b1532154d45911ad15a5897" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95acdf/pre-unlink.sh b/recipes/bioconductor-hgu95acdf/pre-unlink.sh new file mode 100644 index 0000000000000..c42efed54f154 --- /dev/null +++ b/recipes/bioconductor-hgu95acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95acdf diff --git a/recipes/bioconductor-hgu95aprobe/meta.yaml b/recipes/bioconductor-hgu95aprobe/meta.yaml new file mode 100644 index 0000000000000..0894785612641 --- /dev/null +++ b/recipes/bioconductor-hgu95aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 67d94ecdc1889acc19dafd19d26700a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95A\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95aprobe/post-link.sh b/recipes/bioconductor-hgu95aprobe/post-link.sh new file mode 100644 index 0000000000000..781cc5229197d --- /dev/null +++ b/recipes/bioconductor-hgu95aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95aprobe/bioconductor-hgu95aprobe_2.18.0_src_all.tar.gz" +) +MD5="67d94ecdc1889acc19dafd19d26700a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95aprobe/pre-unlink.sh b/recipes/bioconductor-hgu95aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..a05d212b121fb --- /dev/null +++ b/recipes/bioconductor-hgu95aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95aprobe diff --git a/recipes/bioconductor-hgu95av2.db/meta.yaml b/recipes/bioconductor-hgu95av2.db/meta.yaml index d3a84a02442ef..8d68fc38bf99b 100644 --- a/recipes/bioconductor-hgu95av2.db/meta.yaml +++ b/recipes/bioconductor-hgu95av2.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "3.2.3" %} {% set name = "hgu95av2.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c56a023573de68a82fba79952dd10774ea096a1eb3083b15ad3cb21bc2f35189 + md5: a0ee1ba7f115a1504ca89619a0bc56dd build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95av2) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-hgu95av2.db + path: recipes/bioconductor-hgu95av2.db + version: 3.2.3 diff --git a/recipes/bioconductor-hgu95av2.db/post-link.sh b/recipes/bioconductor-hgu95av2.db/post-link.sh index 682fa8336e6e6..f8e1f0de85dff 100644 --- a/recipes/bioconductor-hgu95av2.db/post-link.sh +++ b/recipes/bioconductor-hgu95av2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hgu95av2.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/hgu95av2.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hgu95av2.db/bioconductor-hgu95av2.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-hgu95av2/meta.yaml b/recipes/bioconductor-hgu95av2/meta.yaml new file mode 100644 index 0000000000000..df87105dfd118 --- /dev/null +++ b/recipes/bioconductor-hgu95av2/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.2.0" %} +{% set name = "hgu95av2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b92585c0f43e91bd1abd234b9465a6a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'Affymetrix Human Genome U95 Set annotation data (hgu95av2) assembled using data from public data repositories' + diff --git a/recipes/bioconductor-hgu95av2/post-link.sh b/recipes/bioconductor-hgu95av2/post-link.sh new file mode 100644 index 0000000000000..b027a27e7477b --- /dev/null +++ b/recipes/bioconductor-hgu95av2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95av2_2.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2_2.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95av2_2.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2/bioconductor-hgu95av2_2.2.0_src_all.tar.gz" +) +MD5="b92585c0f43e91bd1abd234b9465a6a7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95av2/pre-unlink.sh b/recipes/bioconductor-hgu95av2/pre-unlink.sh new file mode 100644 index 0000000000000..b1edda4d5ee37 --- /dev/null +++ b/recipes/bioconductor-hgu95av2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95av2 diff --git a/recipes/bioconductor-hgu95av2cdf/meta.yaml b/recipes/bioconductor-hgu95av2cdf/meta.yaml new file mode 100644 index 0000000000000..2dd366ea3584d --- /dev/null +++ b/recipes/bioconductor-hgu95av2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95av2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 026bae2f76433593f75ca6c79bc9a9d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95Av2.CDF file.' + diff --git a/recipes/bioconductor-hgu95av2cdf/post-link.sh b/recipes/bioconductor-hgu95av2cdf/post-link.sh new file mode 100644 index 0000000000000..0aa7f29b39e09 --- /dev/null +++ b/recipes/bioconductor-hgu95av2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95av2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95av2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2cdf/bioconductor-hgu95av2cdf_2.18.0_src_all.tar.gz" +) +MD5="026bae2f76433593f75ca6c79bc9a9d0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95av2cdf/pre-unlink.sh b/recipes/bioconductor-hgu95av2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..96c8c9479ea35 --- /dev/null +++ b/recipes/bioconductor-hgu95av2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95av2cdf diff --git a/recipes/bioconductor-hgu95av2probe/meta.yaml b/recipes/bioconductor-hgu95av2probe/meta.yaml new file mode 100644 index 0000000000000..357d23999dbda --- /dev/null +++ b/recipes/bioconductor-hgu95av2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95av2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d3efb56f7e7a264b633fac787a5a2b95 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG\_U95Av2\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95av2probe/post-link.sh b/recipes/bioconductor-hgu95av2probe/post-link.sh new file mode 100644 index 0000000000000..c2eb80031eb64 --- /dev/null +++ b/recipes/bioconductor-hgu95av2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95av2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95av2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95av2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95av2probe/bioconductor-hgu95av2probe_2.18.0_src_all.tar.gz" +) +MD5="d3efb56f7e7a264b633fac787a5a2b95" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95av2probe/pre-unlink.sh b/recipes/bioconductor-hgu95av2probe/pre-unlink.sh new file mode 100644 index 0000000000000..2e4cc42c6c96a --- /dev/null +++ b/recipes/bioconductor-hgu95av2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95av2probe diff --git a/recipes/bioconductor-hgu95b.db/meta.yaml b/recipes/bioconductor-hgu95b.db/meta.yaml new file mode 100644 index 0000000000000..2457ac4002295 --- /dev/null +++ b/recipes/bioconductor-hgu95b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c532e54fd7087f1b1cce0c1e61ae1c16 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu95b.db/post-link.sh b/recipes/bioconductor-hgu95b.db/post-link.sh new file mode 100644 index 0000000000000..23ea569b20c19 --- /dev/null +++ b/recipes/bioconductor-hgu95b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95b.db/bioconductor-hgu95b.db_3.2.3_src_all.tar.gz" +) +MD5="c532e54fd7087f1b1cce0c1e61ae1c16" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95b.db/pre-unlink.sh b/recipes/bioconductor-hgu95b.db/pre-unlink.sh new file mode 100644 index 0000000000000..2e064300e7305 --- /dev/null +++ b/recipes/bioconductor-hgu95b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95b.db diff --git a/recipes/bioconductor-hgu95bcdf/meta.yaml b/recipes/bioconductor-hgu95bcdf/meta.yaml new file mode 100644 index 0000000000000..134321e0a5665 --- /dev/null +++ b/recipes/bioconductor-hgu95bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e6e56b7a107bb2df25b3c25a8191385d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95B.CDF file.' + diff --git a/recipes/bioconductor-hgu95bcdf/post-link.sh b/recipes/bioconductor-hgu95bcdf/post-link.sh new file mode 100644 index 0000000000000..ac47f078abf73 --- /dev/null +++ b/recipes/bioconductor-hgu95bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95bcdf/bioconductor-hgu95bcdf_2.18.0_src_all.tar.gz" +) +MD5="e6e56b7a107bb2df25b3c25a8191385d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95bcdf/pre-unlink.sh b/recipes/bioconductor-hgu95bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..0431b5dda8b3d --- /dev/null +++ b/recipes/bioconductor-hgu95bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95bcdf diff --git a/recipes/bioconductor-hgu95bprobe/meta.yaml b/recipes/bioconductor-hgu95bprobe/meta.yaml new file mode 100644 index 0000000000000..a2cab30e0e15e --- /dev/null +++ b/recipes/bioconductor-hgu95bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 60dcb57fd402dc24d53ef9390c893cfc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95B\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95bprobe/post-link.sh b/recipes/bioconductor-hgu95bprobe/post-link.sh new file mode 100644 index 0000000000000..c11144c32d5c0 --- /dev/null +++ b/recipes/bioconductor-hgu95bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95bprobe/bioconductor-hgu95bprobe_2.18.0_src_all.tar.gz" +) +MD5="60dcb57fd402dc24d53ef9390c893cfc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95bprobe/pre-unlink.sh b/recipes/bioconductor-hgu95bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e3a51278c6515 --- /dev/null +++ b/recipes/bioconductor-hgu95bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95bprobe diff --git a/recipes/bioconductor-hgu95c.db/meta.yaml b/recipes/bioconductor-hgu95c.db/meta.yaml new file mode 100644 index 0000000000000..16ca6ee86075a --- /dev/null +++ b/recipes/bioconductor-hgu95c.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95c.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 273595199acfafe4c50182916c9893ca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95c) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu95c.db/post-link.sh b/recipes/bioconductor-hgu95c.db/post-link.sh new file mode 100644 index 0000000000000..36522464748ca --- /dev/null +++ b/recipes/bioconductor-hgu95c.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95c.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95c.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95c.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95c.db/bioconductor-hgu95c.db_3.2.3_src_all.tar.gz" +) +MD5="273595199acfafe4c50182916c9893ca" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95c.db/pre-unlink.sh b/recipes/bioconductor-hgu95c.db/pre-unlink.sh new file mode 100644 index 0000000000000..7fefb4409b9e6 --- /dev/null +++ b/recipes/bioconductor-hgu95c.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95c.db diff --git a/recipes/bioconductor-hgu95ccdf/meta.yaml b/recipes/bioconductor-hgu95ccdf/meta.yaml new file mode 100644 index 0000000000000..52683b8e05c7e --- /dev/null +++ b/recipes/bioconductor-hgu95ccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95ccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 976151eac05c320aec7a24397a6b5806 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95C.CDF file.' + diff --git a/recipes/bioconductor-hgu95ccdf/post-link.sh b/recipes/bioconductor-hgu95ccdf/post-link.sh new file mode 100644 index 0000000000000..acfe3b381336c --- /dev/null +++ b/recipes/bioconductor-hgu95ccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95ccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95ccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95ccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95ccdf/bioconductor-hgu95ccdf_2.18.0_src_all.tar.gz" +) +MD5="976151eac05c320aec7a24397a6b5806" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95ccdf/pre-unlink.sh b/recipes/bioconductor-hgu95ccdf/pre-unlink.sh new file mode 100644 index 0000000000000..abf3ebf5cb955 --- /dev/null +++ b/recipes/bioconductor-hgu95ccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95ccdf diff --git a/recipes/bioconductor-hgu95cprobe/meta.yaml b/recipes/bioconductor-hgu95cprobe/meta.yaml new file mode 100644 index 0000000000000..2cad6e52a8376 --- /dev/null +++ b/recipes/bioconductor-hgu95cprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95cprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3fe935a52c70105dc7a214174c946455 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95C\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95cprobe/post-link.sh b/recipes/bioconductor-hgu95cprobe/post-link.sh new file mode 100644 index 0000000000000..6c72c2cfe35b2 --- /dev/null +++ b/recipes/bioconductor-hgu95cprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95cprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95cprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95cprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95cprobe/bioconductor-hgu95cprobe_2.18.0_src_all.tar.gz" +) +MD5="3fe935a52c70105dc7a214174c946455" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95cprobe/pre-unlink.sh b/recipes/bioconductor-hgu95cprobe/pre-unlink.sh new file mode 100644 index 0000000000000..d895bd7b83fea --- /dev/null +++ b/recipes/bioconductor-hgu95cprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95cprobe diff --git a/recipes/bioconductor-hgu95d.db/meta.yaml b/recipes/bioconductor-hgu95d.db/meta.yaml new file mode 100644 index 0000000000000..4f90320f19780 --- /dev/null +++ b/recipes/bioconductor-hgu95d.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95d.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e56da8022bb88c1cd495ea516eae6613 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95d) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu95d.db/post-link.sh b/recipes/bioconductor-hgu95d.db/post-link.sh new file mode 100644 index 0000000000000..ce756fc368adb --- /dev/null +++ b/recipes/bioconductor-hgu95d.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95d.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95d.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95d.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95d.db/bioconductor-hgu95d.db_3.2.3_src_all.tar.gz" +) +MD5="e56da8022bb88c1cd495ea516eae6613" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95d.db/pre-unlink.sh b/recipes/bioconductor-hgu95d.db/pre-unlink.sh new file mode 100644 index 0000000000000..87c601a206dc6 --- /dev/null +++ b/recipes/bioconductor-hgu95d.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95d.db diff --git a/recipes/bioconductor-hgu95dcdf/meta.yaml b/recipes/bioconductor-hgu95dcdf/meta.yaml new file mode 100644 index 0000000000000..fcc0cfc6a3aa6 --- /dev/null +++ b/recipes/bioconductor-hgu95dcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95dcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 36e11ff001b1bec3f34ba7c93132ad6f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95D.CDF file.' + diff --git a/recipes/bioconductor-hgu95dcdf/post-link.sh b/recipes/bioconductor-hgu95dcdf/post-link.sh new file mode 100644 index 0000000000000..7abd799673d67 --- /dev/null +++ b/recipes/bioconductor-hgu95dcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95dcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95dcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95dcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95dcdf/bioconductor-hgu95dcdf_2.18.0_src_all.tar.gz" +) +MD5="36e11ff001b1bec3f34ba7c93132ad6f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95dcdf/pre-unlink.sh b/recipes/bioconductor-hgu95dcdf/pre-unlink.sh new file mode 100644 index 0000000000000..b65db1b2e3f18 --- /dev/null +++ b/recipes/bioconductor-hgu95dcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95dcdf diff --git a/recipes/bioconductor-hgu95dprobe/meta.yaml b/recipes/bioconductor-hgu95dprobe/meta.yaml new file mode 100644 index 0000000000000..a43e3a52173dc --- /dev/null +++ b/recipes/bioconductor-hgu95dprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95dprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 165ce5029f49fc515b9ee0e6a6a29cb5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95D\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95dprobe/post-link.sh b/recipes/bioconductor-hgu95dprobe/post-link.sh new file mode 100644 index 0000000000000..d2186f470e988 --- /dev/null +++ b/recipes/bioconductor-hgu95dprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95dprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95dprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95dprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95dprobe/bioconductor-hgu95dprobe_2.18.0_src_all.tar.gz" +) +MD5="165ce5029f49fc515b9ee0e6a6a29cb5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95dprobe/pre-unlink.sh b/recipes/bioconductor-hgu95dprobe/pre-unlink.sh new file mode 100644 index 0000000000000..ffd0b10eabc2f --- /dev/null +++ b/recipes/bioconductor-hgu95dprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95dprobe diff --git a/recipes/bioconductor-hgu95e.db/meta.yaml b/recipes/bioconductor-hgu95e.db/meta.yaml new file mode 100644 index 0000000000000..2ea4a0b5d664a --- /dev/null +++ b/recipes/bioconductor-hgu95e.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgu95e.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 18bbf38f91172616a7f78e63e85630e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome U95 Set annotation data (chip hgu95e) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgu95e.db/post-link.sh b/recipes/bioconductor-hgu95e.db/post-link.sh new file mode 100644 index 0000000000000..28952b0d58bf0 --- /dev/null +++ b/recipes/bioconductor-hgu95e.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95e.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95e.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95e.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95e.db/bioconductor-hgu95e.db_3.2.3_src_all.tar.gz" +) +MD5="18bbf38f91172616a7f78e63e85630e5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95e.db/pre-unlink.sh b/recipes/bioconductor-hgu95e.db/pre-unlink.sh new file mode 100644 index 0000000000000..e27f341167dc3 --- /dev/null +++ b/recipes/bioconductor-hgu95e.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95e.db diff --git a/recipes/bioconductor-hgu95ecdf/meta.yaml b/recipes/bioconductor-hgu95ecdf/meta.yaml new file mode 100644 index 0000000000000..d352448a2348b --- /dev/null +++ b/recipes/bioconductor-hgu95ecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95ecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fa27cfff62a38fc51640d797bd628105 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HG U95E.CDF file.' + diff --git a/recipes/bioconductor-hgu95ecdf/post-link.sh b/recipes/bioconductor-hgu95ecdf/post-link.sh new file mode 100644 index 0000000000000..8420b9812c883 --- /dev/null +++ b/recipes/bioconductor-hgu95ecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95ecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95ecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95ecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95ecdf/bioconductor-hgu95ecdf_2.18.0_src_all.tar.gz" +) +MD5="fa27cfff62a38fc51640d797bd628105" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95ecdf/pre-unlink.sh b/recipes/bioconductor-hgu95ecdf/pre-unlink.sh new file mode 100644 index 0000000000000..67a494c52c0c4 --- /dev/null +++ b/recipes/bioconductor-hgu95ecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95ecdf diff --git a/recipes/bioconductor-hgu95eprobe/meta.yaml b/recipes/bioconductor-hgu95eprobe/meta.yaml new file mode 100644 index 0000000000000..a4deb05bc5d40 --- /dev/null +++ b/recipes/bioconductor-hgu95eprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hgu95eprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9e5407ab80c5bbb4065484be0b9c6191 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HG-U95E\_probe\_tab.' + diff --git a/recipes/bioconductor-hgu95eprobe/post-link.sh b/recipes/bioconductor-hgu95eprobe/post-link.sh new file mode 100644 index 0000000000000..816a40afa83a7 --- /dev/null +++ b/recipes/bioconductor-hgu95eprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgu95eprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgu95eprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hgu95eprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgu95eprobe/bioconductor-hgu95eprobe_2.18.0_src_all.tar.gz" +) +MD5="9e5407ab80c5bbb4065484be0b9c6191" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgu95eprobe/pre-unlink.sh b/recipes/bioconductor-hgu95eprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e2694de2e2f55 --- /dev/null +++ b/recipes/bioconductor-hgu95eprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgu95eprobe diff --git a/recipes/bioconductor-hguatlas13k.db/meta.yaml b/recipes/bioconductor-hguatlas13k.db/meta.yaml new file mode 100644 index 0000000000000..25639ed7d3d33 --- /dev/null +++ b/recipes/bioconductor-hguatlas13k.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hguatlas13k.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ab9ffe1a1de44c0f938129f193e7fb63 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Clontech BD Atlas Long Oligos Human 13K annotation data (chip hguatlas13k) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hguatlas13k.db/post-link.sh b/recipes/bioconductor-hguatlas13k.db/post-link.sh new file mode 100644 index 0000000000000..6399329cff633 --- /dev/null +++ b/recipes/bioconductor-hguatlas13k.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hguatlas13k.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguatlas13k.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hguatlas13k.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hguatlas13k.db/bioconductor-hguatlas13k.db_3.2.3_src_all.tar.gz" +) +MD5="ab9ffe1a1de44c0f938129f193e7fb63" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hguatlas13k.db/pre-unlink.sh b/recipes/bioconductor-hguatlas13k.db/pre-unlink.sh new file mode 100644 index 0000000000000..dfa5954d4b3c7 --- /dev/null +++ b/recipes/bioconductor-hguatlas13k.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hguatlas13k.db diff --git a/recipes/bioconductor-hgubeta7.db/meta.yaml b/recipes/bioconductor-hgubeta7.db/meta.yaml new file mode 100644 index 0000000000000..6d285ad63348a --- /dev/null +++ b/recipes/bioconductor-hgubeta7.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgubeta7.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1b8b065f95d2089985f59f22dcabc824 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Unknown annotation data (chip hgubeta7) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgubeta7.db/post-link.sh b/recipes/bioconductor-hgubeta7.db/post-link.sh new file mode 100644 index 0000000000000..6c2a8aafa4528 --- /dev/null +++ b/recipes/bioconductor-hgubeta7.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgubeta7.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgubeta7.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgubeta7.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgubeta7.db/bioconductor-hgubeta7.db_3.2.3_src_all.tar.gz" +) +MD5="1b8b065f95d2089985f59f22dcabc824" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgubeta7.db/pre-unlink.sh b/recipes/bioconductor-hgubeta7.db/pre-unlink.sh new file mode 100644 index 0000000000000..83c1776dfc9fd --- /dev/null +++ b/recipes/bioconductor-hgubeta7.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgubeta7.db diff --git a/recipes/bioconductor-hgudkfz31.db/meta.yaml b/recipes/bioconductor-hgudkfz31.db/meta.yaml new file mode 100644 index 0000000000000..0b351a983c07a --- /dev/null +++ b/recipes/bioconductor-hgudkfz31.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hguDKFZ31.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fa3ba493cebdac4253dea8fe5d58452b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Unknown annotation data (chip hguDKFZ31) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgudkfz31.db/post-link.sh b/recipes/bioconductor-hgudkfz31.db/post-link.sh new file mode 100644 index 0000000000000..43950bde2d58b --- /dev/null +++ b/recipes/bioconductor-hgudkfz31.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hguDKFZ31.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguDKFZ31.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hguDKFZ31.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgudkfz31.db/bioconductor-hgudkfz31.db_3.2.3_src_all.tar.gz" +) +MD5="fa3ba493cebdac4253dea8fe5d58452b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgudkfz31.db/pre-unlink.sh b/recipes/bioconductor-hgudkfz31.db/pre-unlink.sh new file mode 100644 index 0000000000000..14ac650125cf5 --- /dev/null +++ b/recipes/bioconductor-hgudkfz31.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hguDKFZ31.db diff --git a/recipes/bioconductor-hgug4100a.db/meta.yaml b/recipes/bioconductor-hgug4100a.db/meta.yaml new file mode 100644 index 0000000000000..cdd8890449ed8 --- /dev/null +++ b/recipes/bioconductor-hgug4100a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgug4100a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b7856928278a77d71f963410ea4f2376 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Human 1 cDNA Microarray Kit annotation data (chip hgug4100a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4100a.db/post-link.sh b/recipes/bioconductor-hgug4100a.db/post-link.sh new file mode 100644 index 0000000000000..6b11ae1fb769e --- /dev/null +++ b/recipes/bioconductor-hgug4100a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4100a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4100a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4100a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4100a.db/bioconductor-hgug4100a.db_3.2.3_src_all.tar.gz" +) +MD5="b7856928278a77d71f963410ea4f2376" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4100a.db/pre-unlink.sh b/recipes/bioconductor-hgug4100a.db/pre-unlink.sh new file mode 100644 index 0000000000000..e13442f8cd455 --- /dev/null +++ b/recipes/bioconductor-hgug4100a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4100a.db diff --git a/recipes/bioconductor-hgug4101a.db/meta.yaml b/recipes/bioconductor-hgug4101a.db/meta.yaml new file mode 100644 index 0000000000000..c9dfcaea266d2 --- /dev/null +++ b/recipes/bioconductor-hgug4101a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgug4101a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e4731217efbffd05d3ee7eec68ce0aa0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Human 2 cDNA Microarry Kit annotation data (chip hgug4101a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4101a.db/post-link.sh b/recipes/bioconductor-hgug4101a.db/post-link.sh new file mode 100644 index 0000000000000..0310926412d00 --- /dev/null +++ b/recipes/bioconductor-hgug4101a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4101a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4101a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4101a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4101a.db/bioconductor-hgug4101a.db_3.2.3_src_all.tar.gz" +) +MD5="e4731217efbffd05d3ee7eec68ce0aa0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4101a.db/pre-unlink.sh b/recipes/bioconductor-hgug4101a.db/pre-unlink.sh new file mode 100644 index 0000000000000..531e4ce39ade4 --- /dev/null +++ b/recipes/bioconductor-hgug4101a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4101a.db diff --git a/recipes/bioconductor-hgug4110b.db/meta.yaml b/recipes/bioconductor-hgug4110b.db/meta.yaml new file mode 100644 index 0000000000000..13abbaaf20551 --- /dev/null +++ b/recipes/bioconductor-hgug4110b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgug4110b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a9edcdbc121f22d4dec335a64598ff0e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Human 1A (V2) annotation data (chip hgug4110b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4110b.db/post-link.sh b/recipes/bioconductor-hgug4110b.db/post-link.sh new file mode 100644 index 0000000000000..e7badc58fbadc --- /dev/null +++ b/recipes/bioconductor-hgug4110b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4110b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4110b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4110b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4110b.db/bioconductor-hgug4110b.db_3.2.3_src_all.tar.gz" +) +MD5="a9edcdbc121f22d4dec335a64598ff0e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4110b.db/pre-unlink.sh b/recipes/bioconductor-hgug4110b.db/pre-unlink.sh new file mode 100644 index 0000000000000..d3c885a4ec509 --- /dev/null +++ b/recipes/bioconductor-hgug4110b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4110b.db diff --git a/recipes/bioconductor-hgug4111a.db/meta.yaml b/recipes/bioconductor-hgug4111a.db/meta.yaml new file mode 100644 index 0000000000000..eb01bf8f85b54 --- /dev/null +++ b/recipes/bioconductor-hgug4111a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgug4111a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a5f2c3b463915fa1ab0ca21e6b0f5840 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Human 1B annotation data (chip hgug4111a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4111a.db/post-link.sh b/recipes/bioconductor-hgug4111a.db/post-link.sh new file mode 100644 index 0000000000000..abaa4960b043b --- /dev/null +++ b/recipes/bioconductor-hgug4111a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4111a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4111a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4111a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4111a.db/bioconductor-hgug4111a.db_3.2.3_src_all.tar.gz" +) +MD5="a5f2c3b463915fa1ab0ca21e6b0f5840" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4111a.db/pre-unlink.sh b/recipes/bioconductor-hgug4111a.db/pre-unlink.sh new file mode 100644 index 0000000000000..12dd282bae2c4 --- /dev/null +++ b/recipes/bioconductor-hgug4111a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4111a.db diff --git a/recipes/bioconductor-hgug4112a.db/meta.yaml b/recipes/bioconductor-hgug4112a.db/meta.yaml new file mode 100644 index 0000000000000..52216aaef8948 --- /dev/null +++ b/recipes/bioconductor-hgug4112a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hgug4112a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 67ecf8c887e2ebe1941cc51d0f5fb468 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent "Human Genome, Whole" annotation data (chip hgug4112a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4112a.db/post-link.sh b/recipes/bioconductor-hgug4112a.db/post-link.sh new file mode 100644 index 0000000000000..c17bc4f92c38a --- /dev/null +++ b/recipes/bioconductor-hgug4112a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4112a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4112a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4112a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4112a.db/bioconductor-hgug4112a.db_3.2.3_src_all.tar.gz" +) +MD5="67ecf8c887e2ebe1941cc51d0f5fb468" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4112a.db/pre-unlink.sh b/recipes/bioconductor-hgug4112a.db/pre-unlink.sh new file mode 100644 index 0000000000000..63f55e3c3b548 --- /dev/null +++ b/recipes/bioconductor-hgug4112a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4112a.db diff --git a/recipes/bioconductor-hgug4845a.db/meta.yaml b/recipes/bioconductor-hgug4845a.db/meta.yaml new file mode 100644 index 0000000000000..d1a16438a16cf --- /dev/null +++ b/recipes/bioconductor-hgug4845a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.0.3" %} +{% set name = "hgug4845a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 46133d7bcb6d8c24c026304e8ddd150d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'agilent AMADID 026652 annotation data (chip hgug4845a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hgug4845a.db/post-link.sh b/recipes/bioconductor-hgug4845a.db/post-link.sh new file mode 100644 index 0000000000000..0f3460429d6ad --- /dev/null +++ b/recipes/bioconductor-hgug4845a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hgug4845a.db_0.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hgug4845a.db_0.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/hgug4845a.db_0.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hgug4845a.db/bioconductor-hgug4845a.db_0.0.3_src_all.tar.gz" +) +MD5="46133d7bcb6d8c24c026304e8ddd150d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hgug4845a.db/pre-unlink.sh b/recipes/bioconductor-hgug4845a.db/pre-unlink.sh new file mode 100644 index 0000000000000..1b524629fa1ff --- /dev/null +++ b/recipes/bioconductor-hgug4845a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hgug4845a.db diff --git a/recipes/bioconductor-hguqiagenv3.db/meta.yaml b/recipes/bioconductor-hguqiagenv3.db/meta.yaml new file mode 100644 index 0000000000000..15501e5faf010 --- /dev/null +++ b/recipes/bioconductor-hguqiagenv3.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hguqiagenv3.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 91ebb82e773ff799befdb8921b38e90e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Qiagen Qiagen V3.0 oligo set annotation data (chip hguqiagenv3) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hguqiagenv3.db/post-link.sh b/recipes/bioconductor-hguqiagenv3.db/post-link.sh new file mode 100644 index 0000000000000..1ed51e4385205 --- /dev/null +++ b/recipes/bioconductor-hguqiagenv3.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hguqiagenv3.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hguqiagenv3.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hguqiagenv3.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hguqiagenv3.db/bioconductor-hguqiagenv3.db_3.2.3_src_all.tar.gz" +) +MD5="91ebb82e773ff799befdb8921b38e90e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hguqiagenv3.db/pre-unlink.sh b/recipes/bioconductor-hguqiagenv3.db/pre-unlink.sh new file mode 100644 index 0000000000000..da5b9dd49ad7d --- /dev/null +++ b/recipes/bioconductor-hguqiagenv3.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hguqiagenv3.db diff --git a/recipes/bioconductor-hi16cod.db/meta.yaml b/recipes/bioconductor-hi16cod.db/meta.yaml new file mode 100644 index 0000000000000..accc37338f0f4 --- /dev/null +++ b/recipes/bioconductor-hi16cod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "hi16cod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: abdc77937e8d37fa5468691376ceb6a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Human Inflammation 16 Bioarray annotation data (chip hi16cod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hi16cod.db/post-link.sh b/recipes/bioconductor-hi16cod.db/post-link.sh new file mode 100644 index 0000000000000..9dc588fe66dd9 --- /dev/null +++ b/recipes/bioconductor-hi16cod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hi16cod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hi16cod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/hi16cod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hi16cod.db/bioconductor-hi16cod.db_3.4.0_src_all.tar.gz" +) +MD5="abdc77937e8d37fa5468691376ceb6a5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hi16cod.db/pre-unlink.sh b/recipes/bioconductor-hi16cod.db/pre-unlink.sh new file mode 100644 index 0000000000000..2ff6245342b14 --- /dev/null +++ b/recipes/bioconductor-hi16cod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hi16cod.db diff --git a/recipes/bioconductor-hiannotator/build.sh b/recipes/bioconductor-hiannotator/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hiannotator/build.sh +++ b/recipes/bioconductor-hiannotator/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hiannotator/meta.yaml b/recipes/bioconductor-hiannotator/meta.yaml index 11c56c44a050a..89c3d3975d068 100644 --- a/recipes/bioconductor-hiannotator/meta.yaml +++ b/recipes/bioconductor-hiannotator/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "hiAnnotator" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3ff1bf88402f050625733d2edc135247693f61419084d8b1db90e0567c8bf9a9 + md5: 708f87c006a43e2d4626012d67f9423b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, doParallel, testthat, BiocGenerics requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-dplyr - r-foreach @@ -28,9 +30,9 @@ requirements: - r-iterators - r-scales run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-dplyr - r-foreach @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'hiAnnotator contains set of functions which allow users to annotate a GRanges object with custom set of annotations. The basic philosophy of this package is to take two GRanges objects (query & subject) with common set of seqnames (i.e. chromosomes) and return associated annotation per seqnames and rows from the query matching seqnames and rows from the subject (i.e. genes or cpg islands). The package comes with three types of annotation functions which calculates if a position from query is: within a feature, near a feature, or count features in defined window sizes. Moreover, each function is equipped with parallel backend to utilize the foreach package. In addition, the package is equipped with wrapper functions, which finds appropriate columns needed to make a GRanges object from a common data frame.' extra: identifiers: - biotools:hiannotator - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hiannotator + path: recipes/bioconductor-hiannotator + version: 1.14.0 + diff --git a/recipes/bioconductor-hibag/build.sh b/recipes/bioconductor-hibag/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hibag/build.sh +++ b/recipes/bioconductor-hibag/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hibag/meta.yaml b/recipes/bioconductor-hibag/meta.yaml index 54f4ed53f2318..d15b8c49ab5c8 100644 --- a/recipes/bioconductor-hibag/meta.yaml +++ b/recipes/bioconductor-hibag/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.1" %} {% set name = "HIBAG" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8dae626b80ac14b9b420b3e8c7099809113d8f4f0ac5bf074e65faee9dd036e9 + md5: a1ba0ae738fdd4bac94f1e44b6710ce0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, knitr, gdsfmt (>= 1.2.2), SNPRelate (>= 1.1.6), ggplot2, reshape2 requirements: host: - r-base @@ -29,9 +30,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'It is a software package for imputing HLA types using SNP data, and relies on a training set of HLA and SNP genotypes. HIBAG can be used by researchers with published parameter estimates instead of requiring access to large training sample datasets. It combines the concepts of attribute bagging, an ensemble classifier method, with haplotype inference for SNPs and HLA types. Attribute bagging is a technique which improves the accuracy and stability of classifier ensembles using bootstrap aggregating and random variable selection.' extra: identifiers: - biotools:hibag + parent_recipe: + name: bioconductor-hibag + path: recipes/bioconductor-hibag + version: 1.16.0 + diff --git a/recipes/bioconductor-hicbricks/build.sh b/recipes/bioconductor-hicbricks/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hicbricks/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hicbricks/meta.yaml b/recipes/bioconductor-hicbricks/meta.yaml new file mode 100644 index 0000000000000..eef7227b0f66e --- /dev/null +++ b/recipes/bioconductor-hicbricks/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.0.0" %} +{% set name = "HiCBricks" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00c648457572e0c06e09e1abe2cc7c96 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-curl + - r-data.table + - r-digest + - r-ggplot2 + - r-r6 + - r-rappdirs + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-stringr + - r-viridis + run: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-curl + - r-data.table + - r-digest + - r-ggplot2 + - r-r6 + - r-rappdirs + - r-rcolorbrewer + - r-reshape2 + - r-scales + - r-stringr + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.' + diff --git a/recipes/bioconductor-hiccompare/build.sh b/recipes/bioconductor-hiccompare/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hiccompare/build.sh +++ b/recipes/bioconductor-hiccompare/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hiccompare/conda_build_config.yaml b/recipes/bioconductor-hiccompare/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-hiccompare/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-hiccompare/meta.yaml b/recipes/bioconductor-hiccompare/meta.yaml index 3626bdb8852a6..c88d5613388b1 100644 --- a/recipes/bioconductor-hiccompare/meta.yaml +++ b/recipes/bioconductor-hiccompare/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "HiCcompare" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c244a2fc060a7c858a42456e9b964aa6a6faf6a10d87b40c0c9aaeae603758ca + md5: 76d89712dadfae982a63327c74a4a2d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, multiHiCcompare requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-dplyr @@ -34,12 +36,12 @@ requirements: - r-mgcv - r-pheatmap run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-dplyr @@ -53,10 +55,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' - summary: 'HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust permutation method for detecting differences between Hi-C datasets.' + summary: 'HiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. HiCcompare operates on processed Hi-C data in the form of chromosome-specific chromatin interaction matrices. It accepts three-column tab-separated text files storing chromatin interaction matrices in a sparse matrix format which are available from several sources. HiCcompare is designed to give the user the ability to perform a comparative analysis on the 3-Dimensional structure of the genomes of cells in different biological states.`HiCcompare` differs from other packages that attempt to compare Hi-C data in that it works on processed data in chromatin interaction matrix format instead of pre-processed sequencing data. In addition, `HiCcompare` provides a non-parametric method for the joint normalization and removal of biases between two Hi-C datasets for the purpose of comparative analysis. `HiCcompare` also provides a simple yet robust method for detecting differences between Hi-C datasets.' extra: identifiers: - biotools:HiCcompare - doi:10.1186/s12859-018-2288-x + parent_recipe: + name: bioconductor-hiccompare + path: recipes/bioconductor-hiccompare + version: 1.2.0 + diff --git a/recipes/bioconductor-hicdatahumanimr90/meta.yaml b/recipes/bioconductor-hicdatahumanimr90/meta.yaml new file mode 100644 index 0000000000000..d088841be12b9 --- /dev/null +++ b/recipes/bioconductor-hicdatahumanimr90/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "HiCDataHumanIMR90" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cdf34ec2f78ce9a1482efbea622d81e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: HiTC +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The HiC data from Human Fibroblast IMR90 cell line (HindIII restriction) was retrieved from the GEO website, accession number GSE35156 (http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE35156). The raw reads were processed as explained in Dixon et al. (Nature 2012).' + diff --git a/recipes/bioconductor-hicdatahumanimr90/post-link.sh b/recipes/bioconductor-hicdatahumanimr90/post-link.sh new file mode 100644 index 0000000000000..2950ce18e7d6e --- /dev/null +++ b/recipes/bioconductor-hicdatahumanimr90/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HiCDataHumanIMR90_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HiCDataHumanIMR90_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/HiCDataHumanIMR90_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hicdatahumanimr90/bioconductor-hicdatahumanimr90_1.2.0_src_all.tar.gz" +) +MD5="cdf34ec2f78ce9a1482efbea622d81e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hicdatahumanimr90/pre-unlink.sh b/recipes/bioconductor-hicdatahumanimr90/pre-unlink.sh new file mode 100644 index 0000000000000..dcd33da34962f --- /dev/null +++ b/recipes/bioconductor-hicdatahumanimr90/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HiCDataHumanIMR90 diff --git a/recipes/bioconductor-hicdatalymphoblast/meta.yaml b/recipes/bioconductor-hicdatalymphoblast/meta.yaml new file mode 100644 index 0000000000000..d90da48d0a2ab --- /dev/null +++ b/recipes/bioconductor-hicdatalymphoblast/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "HiCDataLymphoblast" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 55d001daefcf400a6f3474a4a6859c6e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GOTHiC, ShortRead +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The HiC data from human lymphoblastoid cell line (HindIII restriction) was retrieved from the sequence read archive and two ends of the paired reads were aligned separately with bowtie.' + diff --git a/recipes/bioconductor-hicdatalymphoblast/post-link.sh b/recipes/bioconductor-hicdatalymphoblast/post-link.sh new file mode 100644 index 0000000000000..ee256d7faf5e3 --- /dev/null +++ b/recipes/bioconductor-hicdatalymphoblast/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HiCDataLymphoblast_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HiCDataLymphoblast_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/HiCDataLymphoblast_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hicdatalymphoblast/bioconductor-hicdatalymphoblast_1.18.0_src_all.tar.gz" +) +MD5="55d001daefcf400a6f3474a4a6859c6e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hicdatalymphoblast/pre-unlink.sh b/recipes/bioconductor-hicdatalymphoblast/pre-unlink.sh new file mode 100644 index 0000000000000..d98d53d9d192e --- /dev/null +++ b/recipes/bioconductor-hicdatalymphoblast/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HiCDataLymphoblast diff --git a/recipes/bioconductor-hicrep/build.sh b/recipes/bioconductor-hicrep/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hicrep/build.sh +++ b/recipes/bioconductor-hicrep/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hicrep/meta.yaml b/recipes/bioconductor-hicrep/meta.yaml index 8772b43dfd03f..5644dc92ec46c 100644 --- a/recipes/bioconductor-hicrep/meta.yaml +++ b/recipes/bioconductor-hicrep/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "hicrep" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9493bab6af88b05cbd02532a8a406f87c35613e471c5207cafb6f235cebd4fb5 + md5: 451cb0aae520cb05dca1b5766b9a8bd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat requirements: host: - r-base @@ -25,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.0)' summary: 'Hi-C is a powerful technology for studying genome-wide chromatin interactions. However, current methods for assessing Hi-C data reproducibility can produce misleading results because they ignore spatial features in Hi-C data, such as domain structure and distance-dependence. We present a novel reproducibility measure that systematically takes these features into consideration. This measure can assess pairwise differences between Hi-C matrices under a wide range of settings, and can be used to determine optimal sequencing depth. Compared to existing approaches, it consistently shows higher accuracy in distinguishing subtle differences in reproducibility and depicting interrelationships of cell lineages than existing approaches. This R package `hicrep` implements our approach.' - +extra: + parent_recipe: + name: bioconductor-hicrep + path: recipes/bioconductor-hicrep + version: 1.4.0 diff --git a/recipes/bioconductor-hiergwas/build.sh b/recipes/bioconductor-hiergwas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hiergwas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hiergwas/meta.yaml b/recipes/bioconductor-hiergwas/meta.yaml new file mode 100644 index 0000000000000..e4c8f43bdbcb4 --- /dev/null +++ b/recipes/bioconductor-hiergwas/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.12.0" %} +{% set name = "hierGWAS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 161b52663e1b82379b6d2a876d74d33a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit, MASS +requirements: + host: + - r-base + - r-fastcluster + - r-fmsb + - r-glmnet + run: + - r-base + - r-fastcluster + - r-fmsb + - r-glmnet +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Testing individual SNPs, as well as arbitrarily large groups of SNPs in GWA studies, using a joint model of all SNPs. The method controls the FWER, and provides an automatic, data-driven refinement of the SNP clusters to smaller groups or single markers.' + diff --git a/recipes/bioconductor-hierinf/build.sh b/recipes/bioconductor-hierinf/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hierinf/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hierinf/meta.yaml b/recipes/bioconductor-hierinf/meta.yaml new file mode 100644 index 0000000000000..782ac313ab810 --- /dev/null +++ b/recipes/bioconductor-hierinf/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "hierinf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f42529167e8ea2fd49e7290a6c4431d1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, MASS, testthat +requirements: + host: + - r-base + - r-fmsb + - r-glmnet + run: + - r-base + - r-fmsb + - r-glmnet +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'Tools to perform hierarchical inference for one or multiple studies / data sets based on high-dimensional multivariate (generalised) linear models. A possible application is to perform hierarchical inference for GWA studies to find significant groups or single SNPs (if the signal is strong) in a data-driven and automated procedure. The method is based on an efficient hierarchical multiple testing correction and controls the FWER. The functions can easily be run in parallel.' + diff --git a/recipes/bioconductor-hiiragi2013/meta.yaml b/recipes/bioconductor-hiiragi2013/meta.yaml new file mode 100644 index 0000000000000..eca3181ea23f6 --- /dev/null +++ b/recipes/bioconductor-hiiragi2013/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.18.0" %} +{% set name = "Hiiragi2013" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0e1fdc481e61f2612f88120f4d7cbdff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ArrayExpress, BiocStyle +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-mouse4302.db >=3.2.0,<3.3.0' + - r-base + - r-boot + - r-clue + - r-cluster + - r-gplots + - r-gtools + - r-lattice + - r-latticeextra + - r-mass + - r-rcolorbrewer + - r-xtable + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-mouse4302.db >=3.2.0,<3.3.0' + - r-base + - r-boot + - r-clue + - r-cluster + - r-gplots + - r-gtools + - r-lattice + - r-latticeextra + - r-mass + - r-rcolorbrewer + - r-xtable + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains the experimental data and a complete executable transcript (vignette) of the statistical analysis presented in the paper "Cell-to-cell expression variability followed by signal reinforcement progressively segregates early mouse lineages" by Y. Ohnishi, W. Huber, A. Tsumura, M. Kang, P. Xenopoulos, K. Kurimoto, A. K. Oles, M. J. Arauzo-Bravo, M. Saitou, A.-K. Hadjantonakis and T. Hiiragi; Nature Cell Biology (2014) 16(1): 27-37. doi: 10.1038/ncb2881."' + diff --git a/recipes/bioconductor-hiiragi2013/post-link.sh b/recipes/bioconductor-hiiragi2013/post-link.sh new file mode 100644 index 0000000000000..5b9f50f482abc --- /dev/null +++ b/recipes/bioconductor-hiiragi2013/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Hiiragi2013_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Hiiragi2013_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Hiiragi2013_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hiiragi2013/bioconductor-hiiragi2013_1.18.0_src_all.tar.gz" +) +MD5="0e1fdc481e61f2612f88120f4d7cbdff" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hiiragi2013/pre-unlink.sh b/recipes/bioconductor-hiiragi2013/pre-unlink.sh new file mode 100644 index 0000000000000..a94253a7f1bf5 --- /dev/null +++ b/recipes/bioconductor-hiiragi2013/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Hiiragi2013 diff --git a/recipes/bioconductor-hilbertcurve/build.sh b/recipes/bioconductor-hilbertcurve/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hilbertcurve/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hilbertcurve/meta.yaml b/recipes/bioconductor-hilbertcurve/meta.yaml new file mode 100644 index 0000000000000..1f53f802f572a --- /dev/null +++ b/recipes/bioconductor-hilbertcurve/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.12.0" %} +{% set name = "HilbertCurve" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ba470369553e2da65efa8ca89a886146 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat (>= 1.0.0), ComplexHeatmap (>= 1.13.2), markdown, RColorBrewer, RCurl, GetoptLong +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-circlize >=0.3.3' + - r-png + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - 'r-circlize >=0.3.3' + - r-png +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Hilbert curve is a type of space-filling curves that fold one dimensional axis into a two dimensional space, but with still preserves the locality. This package aims to provide an easy and flexible way to visualize data through Hilbert curve.' + diff --git a/recipes/bioconductor-hilbertvis/build.sh b/recipes/bioconductor-hilbertvis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hilbertvis/build.sh +++ b/recipes/bioconductor-hilbertvis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hilbertvis/meta.yaml b/recipes/bioconductor-hilbertvis/meta.yaml index fee62f2e700e8..aa2e72bd5d05d 100644 --- a/recipes/bioconductor-hilbertvis/meta.yaml +++ b/recipes/bioconductor-hilbertvis/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "HilbertVis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d54a7859f5addcfaedb252ba91be6b6f7d1a0c938a847adc36a230baaa71ff9f + md5: c7f99d6848ef995298d264b0e8996f1f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: IRanges, EBImage requirements: host: - r-base @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Functions to visualize long vectors of integer data by means of Hilbert curves' extra: identifiers: - biotools:hilbertvis - doi:10.1093/bioinformatics/btp152 + parent_recipe: + name: bioconductor-hilbertvis + path: recipes/bioconductor-hilbertvis + version: 1.38.0 + diff --git a/recipes/bioconductor-hilbertvisgui/build.sh b/recipes/bioconductor-hilbertvisgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hilbertvisgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hilbertvisgui/meta.yaml b/recipes/bioconductor-hilbertvisgui/meta.yaml new file mode 100644 index 0000000000000..1641a176d7a52 --- /dev/null +++ b/recipes/bioconductor-hilbertvisgui/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.40.0" %} +{% set name = "HilbertVisGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c57941da89777104f1818f25aefd8c5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: lattice, IRanges +# SystemRequirements: gtkmm-2.4, GNU make +requirements: + host: + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - r-base + run: + - 'bioconductor-hilbertvis >=1.40.0,<1.41.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'An interactive tool to visualize long vectors of integer data by means of Hilbert curves' + diff --git a/recipes/bioconductor-hipathia/build.sh b/recipes/bioconductor-hipathia/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hipathia/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hipathia/meta.yaml b/recipes/bioconductor-hipathia/meta.yaml new file mode 100644 index 0000000000000..fe5b94eb033ff --- /dev/null +++ b/recipes/bioconductor-hipathia/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "hipathia" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6ae5f72f8c6f9df994ff1962a6699498 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coin + - 'r-igraph >=1.0.1' + - r-matrixstats + - r-servr + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coin + - 'r-igraph >=1.0.1' + - r-matrixstats + - r-servr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Hipathia is a method for the computation of signal transduction along signaling pathways from transcriptomic data. The method is based on an iterative algorithm which is able to compute the signal intensity passing through the nodes of a network by taking into account the level of expression of each gene and the intensity of the signal arriving to it. It also provides a new approach to functional analysis allowing to compute the signal arriving to the functions annotated to each pathway.' + diff --git a/recipes/bioconductor-hireadsprocessor/build.sh b/recipes/bioconductor-hireadsprocessor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hireadsprocessor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hireadsprocessor/meta.yaml b/recipes/bioconductor-hireadsprocessor/meta.yaml new file mode 100644 index 0000000000000..8f7ebc997e77c --- /dev/null +++ b/recipes/bioconductor-hireadsprocessor/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.18.0" %} +{% set name = "hiReadsProcessor" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8dbd21ace9a68bf4f83bd337b8531f61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +# SystemRequirements: BLAT, UCSC hg18 in 2bit format for BLAT +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hiannotator >=1.16.0,<1.17.0' + - 'bioconductor-rsffreader >=0.30.0,<0.31.0' + - r-base + - r-dplyr + - r-readxl + - r-soniclength + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hiannotator >=1.16.0,<1.17.0' + - 'bioconductor-rsffreader >=0.30.0,<0.31.0' + - r-base + - r-dplyr + - r-readxl + - r-soniclength +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'hiReadsProcessor contains set of functions which allow users to process LM-PCR products sequenced using any platform. Given an excel/txt file containing parameters for demultiplexing and sample metadata, the functions automate trimming of adaptors and identification of the genomic product. Genomic products are further processed for QC and abundance quantification.' + diff --git a/recipes/bioconductor-hireewas/build.sh b/recipes/bioconductor-hireewas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hireewas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hireewas/meta.yaml b/recipes/bioconductor-hireewas/meta.yaml new file mode 100644 index 0000000000000..6c9c661f10b54 --- /dev/null +++ b/recipes/bioconductor-hireewas/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.2" %} +{% set name = "HIREewas" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: af011790e1dd234cbd7df579cb6f5fba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, BiocGenerics +requirements: + host: + - r-base + - r-gplots + - r-quadprog + run: + - r-base + - r-gplots + - r-quadprog + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'In epigenome-wide association studies, the measured signals for each sample are a mixture of methylation profiles from different cell types. The current approaches to the association detection only claim whether a cytosine-phosphate-guanine (CpG) site is associated with the phenotype or not, but they cannot determine the cell type in which the risk-CpG site is affected by the phenotype. We propose a solid statistical method, HIgh REsolution (HIRE), which not only substantially improves the power of association detection at the aggregated level as compared to the existing methods but also enables the detection of risk-CpG sites for individual cell types. The "HIREewas" R package is to implement HIRE model in R.' + diff --git a/recipes/bioconductor-hitc/build.sh b/recipes/bioconductor-hitc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hitc/build.sh +++ b/recipes/bioconductor-hitc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hitc/meta.yaml b/recipes/bioconductor-hitc/meta.yaml index 9b92d4e98070f..4af803a64c060 100644 --- a/recipes/bioconductor-hitc/meta.yaml +++ b/recipes/bioconductor-hitc/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "HiTC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5f54f9737ad49251158f16d61cf34da61548dd5cf6401f3ce734149746287362 + md5: eb493286bde0c875cc990d458b6b532d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, HiCDataHumanIMR90 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-matrix - r-rcolorbrewer @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The HiTC package was developed to explore high-throughput ''C'' data such as 5C or Hi-C. Dedicated R classes as well as standard methods for quality controls, normalization, visualization, and further analysis are also provided.' extra: identifiers: - biotools:hitc + parent_recipe: + name: bioconductor-hitc + path: recipes/bioconductor-hitc + version: 1.24.0 + diff --git a/recipes/bioconductor-hivcdnavantwout03/meta.yaml b/recipes/bioconductor-hivcdnavantwout03/meta.yaml new file mode 100644 index 0000000000000..13406acb38ea8 --- /dev/null +++ b/recipes/bioconductor-hivcdnavantwout03/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.22.0" %} +{% set name = "HIVcDNAvantWout03" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e6bf73521bce0a019338afdbb9bbef30 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The expression levels of approximately 4600 cellular RNA transcripts were assessed in CD4+ T cell lines at different times after infection with HIV-1BRU using DNA microarrays. This data corresponds to the first block of a 12 block array image (001030_08_1.GEL) in the first data set (2000095918 A) in the first experiment (CEM LAI vs HI-LAI 24hr). There are two data sets, which are part of a dye-swap experiment with replicates, representing the Cy3 (green) absorption intensities for channel 1 (hiv1raw) and the Cy5 (red) absorption intensities for channel 2 (hiv2raw).' + diff --git a/recipes/bioconductor-hivcdnavantwout03/post-link.sh b/recipes/bioconductor-hivcdnavantwout03/post-link.sh new file mode 100644 index 0000000000000..1da2b8e1acef1 --- /dev/null +++ b/recipes/bioconductor-hivcdnavantwout03/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HIVcDNAvantWout03_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HIVcDNAvantWout03_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/HIVcDNAvantWout03_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hivcdnavantwout03/bioconductor-hivcdnavantwout03_1.22.0_src_all.tar.gz" +) +MD5="e6bf73521bce0a019338afdbb9bbef30" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hivcdnavantwout03/pre-unlink.sh b/recipes/bioconductor-hivcdnavantwout03/pre-unlink.sh new file mode 100644 index 0000000000000..83d674cb4cf28 --- /dev/null +++ b/recipes/bioconductor-hivcdnavantwout03/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HIVcDNAvantWout03 diff --git a/recipes/bioconductor-hivprtplus2cdf/meta.yaml b/recipes/bioconductor-hivprtplus2cdf/meta.yaml new file mode 100644 index 0000000000000..5101d3b88c126 --- /dev/null +++ b/recipes/bioconductor-hivprtplus2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hivprtplus2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 143d9c2f5f328786bae7bb8dc4daf261 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HIV PRTPlus 2.CDF file.' + diff --git a/recipes/bioconductor-hivprtplus2cdf/post-link.sh b/recipes/bioconductor-hivprtplus2cdf/post-link.sh new file mode 100644 index 0000000000000..0b03c0276b47b --- /dev/null +++ b/recipes/bioconductor-hivprtplus2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hivprtplus2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hivprtplus2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hivprtplus2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hivprtplus2cdf/bioconductor-hivprtplus2cdf_2.18.0_src_all.tar.gz" +) +MD5="143d9c2f5f328786bae7bb8dc4daf261" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hivprtplus2cdf/pre-unlink.sh b/recipes/bioconductor-hivprtplus2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..95427b4b355d8 --- /dev/null +++ b/recipes/bioconductor-hivprtplus2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hivprtplus2cdf diff --git a/recipes/bioconductor-hmdbquery/build.sh b/recipes/bioconductor-hmdbquery/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hmdbquery/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hmdbquery/meta.yaml b/recipes/bioconductor-hmdbquery/meta.yaml new file mode 100644 index 0000000000000..c9542ac05b626 --- /dev/null +++ b/recipes/bioconductor-hmdbquery/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "hmdbQuery" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 146f2e50a7a23ec70e559d88066f3615 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, annotate, gwascat, testthat +requirements: + host: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-xml + run: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Define utilities for exploration of human metabolome database, including functions to retrieve specific metabolite entries and data snapshots with pairwise associations (metabolite-gene,-protein,-disease).' + diff --git a/recipes/bioconductor-hmmcopy/build.sh b/recipes/bioconductor-hmmcopy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hmmcopy/build.sh +++ b/recipes/bioconductor-hmmcopy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hmmcopy/meta.yaml b/recipes/bioconductor-hmmcopy/meta.yaml index 52775d556f2ef..c51f791cf816d 100644 --- a/recipes/bioconductor-hmmcopy/meta.yaml +++ b/recipes/bioconductor-hmmcopy/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "HMMcopy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 722eadf9a270ed3ad47a514f94dcca7101f777eb61c795014934c807b516a2f5 + md5: b9a3c1f7f7ac714bacc10a09afaa9664 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base build: - {{ compiler('c') }} @@ -32,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Corrects GC and mappability biases for readcounts (i.e. coverage) in non-overlapping windows of fixed length for single whole genome samples, yielding a rough estimate of copy number for furthur analysis. Designed for rapid correction of high coverage whole genome tumour and normal samples.' extra: identifiers: - biotools:hmmcopy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hmmcopy + path: recipes/bioconductor-hmmcopy + version: 1.22.0 + diff --git a/recipes/bioconductor-hmp16sdata/meta.yaml b/recipes/bioconductor-hmp16sdata/meta.yaml new file mode 100644 index 0000000000000..9b10893279370 --- /dev/null +++ b/recipes/bioconductor-hmp16sdata/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.2.0" %} +{% set name = "HMP16SData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d0369085597560d872684b5846833ee3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocCheck, BiocManager, BiocStyle, circlize, covr, cowplot, curatedMetagenomicData, dendextend, devtools, ggplot2, gridExtra, haven, phyloseq, rmarkdown, roxygen2, stats, testthat +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-assertthat + - r-base + - r-dplyr + - r-kableextra + - r-knitr + - r-magrittr + - r-readr + - r-tibble + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-assertthat + - r-base + - r-dplyr + - r-kableextra + - r-knitr + - r-magrittr + - r-readr + - r-tibble + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'HMP16SData is a Bioconductor ExperimentData package of the Human Microbiome Project (HMP) 16S rRNA sequencing data for variable regions 1–3 and 3–5. Raw data files are provided in the package as downloaded from the HMP Data Analysis and Coordination Center. Processed data is provided as SummarizedExperiment class objects via ExperimentHub.' + diff --git a/recipes/bioconductor-hmp16sdata/post-link.sh b/recipes/bioconductor-hmp16sdata/post-link.sh new file mode 100644 index 0000000000000..c2daa2c2cb56f --- /dev/null +++ b/recipes/bioconductor-hmp16sdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HMP16SData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HMP16SData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/HMP16SData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hmp16sdata/bioconductor-hmp16sdata_1.2.0_src_all.tar.gz" +) +MD5="d0369085597560d872684b5846833ee3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hmp16sdata/pre-unlink.sh b/recipes/bioconductor-hmp16sdata/pre-unlink.sh new file mode 100644 index 0000000000000..c8c97cb82f883 --- /dev/null +++ b/recipes/bioconductor-hmp16sdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HMP16SData diff --git a/recipes/bioconductor-hmyrib36/meta.yaml b/recipes/bioconductor-hmyrib36/meta.yaml new file mode 100644 index 0000000000000..cb7fdbac21188 --- /dev/null +++ b/recipes/bioconductor-hmyrib36/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.18.0" %} +{% set name = "hmyriB36" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b5674b509a47b85c82b4173b4a13e5f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GGtools, illuminaHumanv1.db +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'YRI hapmap + expression (GENEVAR), Build 36, r23a genotypes' + diff --git a/recipes/bioconductor-hmyrib36/post-link.sh b/recipes/bioconductor-hmyrib36/post-link.sh new file mode 100644 index 0000000000000..0b9dcb8e77e99 --- /dev/null +++ b/recipes/bioconductor-hmyrib36/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hmyriB36_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/hmyriB36_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hmyriB36_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hmyrib36/bioconductor-hmyrib36_1.18.0_src_all.tar.gz" +) +MD5="b5674b509a47b85c82b4173b4a13e5f1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hmyrib36/pre-unlink.sh b/recipes/bioconductor-hmyrib36/pre-unlink.sh new file mode 100644 index 0000000000000..cda9590de5bb5 --- /dev/null +++ b/recipes/bioconductor-hmyrib36/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hmyriB36 diff --git a/recipes/bioconductor-hom.at.inp.db/meta.yaml b/recipes/bioconductor-hom.at.inp.db/meta.yaml new file mode 100644 index 0000000000000..acad8a02df274 --- /dev/null +++ b/recipes/bioconductor-hom.at.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.At.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9d96d343202848e129b96e5e234bd269 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Arabidopsis thaliana from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.at.inp.db/post-link.sh b/recipes/bioconductor-hom.at.inp.db/post-link.sh new file mode 100644 index 0000000000000..93ae5b8811712 --- /dev/null +++ b/recipes/bioconductor-hom.at.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.At.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.At.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.At.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.at.inp.db/bioconductor-hom.at.inp.db_3.1.2_src_all.tar.gz" +) +MD5="9d96d343202848e129b96e5e234bd269" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.at.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.at.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..9cb5eccec83c7 --- /dev/null +++ b/recipes/bioconductor-hom.at.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.At.inp.db diff --git a/recipes/bioconductor-hom.ce.inp.db/meta.yaml b/recipes/bioconductor-hom.ce.inp.db/meta.yaml new file mode 100644 index 0000000000000..de889e0ccfedd --- /dev/null +++ b/recipes/bioconductor-hom.ce.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Ce.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 914b04390edfc06466fddd3bab1a5806 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Caenorhabditis elegans from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.ce.inp.db/post-link.sh b/recipes/bioconductor-hom.ce.inp.db/post-link.sh new file mode 100644 index 0000000000000..1c2ecb9e36ff8 --- /dev/null +++ b/recipes/bioconductor-hom.ce.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Ce.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Ce.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Ce.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.ce.inp.db/bioconductor-hom.ce.inp.db_3.1.2_src_all.tar.gz" +) +MD5="914b04390edfc06466fddd3bab1a5806" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.ce.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.ce.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..53ace06f2f036 --- /dev/null +++ b/recipes/bioconductor-hom.ce.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Ce.inp.db diff --git a/recipes/bioconductor-hom.dm.inp.db/meta.yaml b/recipes/bioconductor-hom.dm.inp.db/meta.yaml new file mode 100644 index 0000000000000..00acca0678104 --- /dev/null +++ b/recipes/bioconductor-hom.dm.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Dm.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 24599bd0267b6b6f83d9a27d42d72221 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Drosophila melanogaster from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.dm.inp.db/post-link.sh b/recipes/bioconductor-hom.dm.inp.db/post-link.sh new file mode 100644 index 0000000000000..30b0a6c8ec447 --- /dev/null +++ b/recipes/bioconductor-hom.dm.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Dm.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Dm.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Dm.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.dm.inp.db/bioconductor-hom.dm.inp.db_3.1.2_src_all.tar.gz" +) +MD5="24599bd0267b6b6f83d9a27d42d72221" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.dm.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.dm.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..0c0bcb753d6d3 --- /dev/null +++ b/recipes/bioconductor-hom.dm.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Dm.inp.db diff --git a/recipes/bioconductor-hom.dr.inp.db/meta.yaml b/recipes/bioconductor-hom.dr.inp.db/meta.yaml new file mode 100644 index 0000000000000..44b71d458c41f --- /dev/null +++ b/recipes/bioconductor-hom.dr.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Dr.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d3e588cb6116354605a024ed3e7f5c4e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Danio rerio from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.dr.inp.db/post-link.sh b/recipes/bioconductor-hom.dr.inp.db/post-link.sh new file mode 100644 index 0000000000000..ef366eb43829c --- /dev/null +++ b/recipes/bioconductor-hom.dr.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Dr.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Dr.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Dr.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.dr.inp.db/bioconductor-hom.dr.inp.db_3.1.2_src_all.tar.gz" +) +MD5="d3e588cb6116354605a024ed3e7f5c4e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.dr.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.dr.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..abe450ba2882c --- /dev/null +++ b/recipes/bioconductor-hom.dr.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Dr.inp.db diff --git a/recipes/bioconductor-hom.hs.inp.db/meta.yaml b/recipes/bioconductor-hom.hs.inp.db/meta.yaml index 4175f07801259..5f7cdb21bd5c1 100644 --- a/recipes/bioconductor-hom.hs.inp.db/meta.yaml +++ b/recipes/bioconductor-hom.hs.inp.db/meta.yaml @@ -1,35 +1,40 @@ {% set version = "3.1.2" %} {% set name = "hom.Hs.inp.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8dfe718726c80dcd990ddedde2e6f3027056d4fe4ee15bc6597b2880186b3d3a + md5: b0708148e9c6656527e004fbaf80c05c build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Homology information for Homo Sapiens from Inparanoid assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-hom.hs.inp.db + path: recipes/bioconductor-hom.hs.inp.db + version: 3.1.2 diff --git a/recipes/bioconductor-hom.hs.inp.db/post-link.sh b/recipes/bioconductor-hom.hs.inp.db/post-link.sh index eb334fce0dafa..e5527be05352b 100644 --- a/recipes/bioconductor-hom.hs.inp.db/post-link.sh +++ b/recipes/bioconductor-hom.hs.inp.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="hom.Hs.inp.db_3.1.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Hs.inp.db_3.1.2.tar.gz" "https://bioarchive.galaxyproject.org/hom.Hs.inp.db_3.1.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-hom.hs.inp.db/bioconductor-hom.hs.inp.db_3.1.2_src_all.tar.gz" diff --git a/recipes/bioconductor-hom.mm.inp.db/meta.yaml b/recipes/bioconductor-hom.mm.inp.db/meta.yaml new file mode 100644 index 0000000000000..6cbcd6927d1df --- /dev/null +++ b/recipes/bioconductor-hom.mm.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Mm.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 27d49db64f3f6049210456121f33d6c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Mus musculus from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.mm.inp.db/post-link.sh b/recipes/bioconductor-hom.mm.inp.db/post-link.sh new file mode 100644 index 0000000000000..1158c9512e897 --- /dev/null +++ b/recipes/bioconductor-hom.mm.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Mm.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Mm.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Mm.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.mm.inp.db/bioconductor-hom.mm.inp.db_3.1.2_src_all.tar.gz" +) +MD5="27d49db64f3f6049210456121f33d6c0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.mm.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.mm.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..91e9c021e37e5 --- /dev/null +++ b/recipes/bioconductor-hom.mm.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Mm.inp.db diff --git a/recipes/bioconductor-hom.rn.inp.db/meta.yaml b/recipes/bioconductor-hom.rn.inp.db/meta.yaml new file mode 100644 index 0000000000000..d2da3dfe43fd9 --- /dev/null +++ b/recipes/bioconductor-hom.rn.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Rn.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 17cf02b55681712da40405ffcd81ea5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Rattus norvegicus from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.rn.inp.db/post-link.sh b/recipes/bioconductor-hom.rn.inp.db/post-link.sh new file mode 100644 index 0000000000000..93272cbe64129 --- /dev/null +++ b/recipes/bioconductor-hom.rn.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Rn.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Rn.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Rn.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.rn.inp.db/bioconductor-hom.rn.inp.db_3.1.2_src_all.tar.gz" +) +MD5="17cf02b55681712da40405ffcd81ea5b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.rn.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.rn.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..17cd7f9556214 --- /dev/null +++ b/recipes/bioconductor-hom.rn.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Rn.inp.db diff --git a/recipes/bioconductor-hom.sc.inp.db/meta.yaml b/recipes/bioconductor-hom.sc.inp.db/meta.yaml new file mode 100644 index 0000000000000..16a9f5d5b3d68 --- /dev/null +++ b/recipes/bioconductor-hom.sc.inp.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.1.2" %} +{% set name = "hom.Sc.inp.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e3f58421e9067e8109e3e077b0109511 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Homology information for Saccharomyces cerevisiae from Inparanoid assembled using data from public repositories' + diff --git a/recipes/bioconductor-hom.sc.inp.db/post-link.sh b/recipes/bioconductor-hom.sc.inp.db/post-link.sh new file mode 100644 index 0000000000000..43bc2d9046e02 --- /dev/null +++ b/recipes/bioconductor-hom.sc.inp.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hom.Sc.inp.db_3.1.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hom.Sc.inp.db_3.1.2.tar.gz" + "https://bioarchive.galaxyproject.org/hom.Sc.inp.db_3.1.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hom.sc.inp.db/bioconductor-hom.sc.inp.db_3.1.2_src_all.tar.gz" +) +MD5="e3f58421e9067e8109e3e077b0109511" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hom.sc.inp.db/pre-unlink.sh b/recipes/bioconductor-hom.sc.inp.db/pre-unlink.sh new file mode 100644 index 0000000000000..6764df8b0c40d --- /dev/null +++ b/recipes/bioconductor-hom.sc.inp.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hom.Sc.inp.db diff --git a/recipes/bioconductor-homo.sapiens/conda_build_config.yaml b/recipes/bioconductor-homo.sapiens/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-homo.sapiens/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-homo.sapiens/meta.yaml b/recipes/bioconductor-homo.sapiens/meta.yaml index c818fa177a26b..5c1e57e4f3f18 100644 --- a/recipes/bioconductor-homo.sapiens/meta.yaml +++ b/recipes/bioconductor-homo.sapiens/meta.yaml @@ -1,43 +1,50 @@ {% set version = "1.3.1" %} {% set name = "Homo.sapiens" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 014809fc6ef6410be8dc1094c9cb083719f20d999065ae4bf388855be0913b94 + md5: 653b60cfcdaefd171729115cd629b585 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-organismdbi >=1.22.0,<1.24.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Contains the Homo.sapiens object to access data from several related annotation packages.' +extra: + parent_recipe: + name: bioconductor-homo.sapiens + path: recipes/bioconductor-homo.sapiens + version: 1.3.1 + diff --git a/recipes/bioconductor-homo.sapiens/post-link.sh b/recipes/bioconductor-homo.sapiens/post-link.sh index 771aae174bb97..64b4ec891c6ea 100644 --- a/recipes/bioconductor-homo.sapiens/post-link.sh +++ b/recipes/bioconductor-homo.sapiens/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="Homo.sapiens_1.3.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Homo.sapiens_1.3.1.tar.gz" + "https://bioarchive.galaxyproject.org/Homo.sapiens_1.3.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-homo.sapiens/bioconductor-homo.sapiens_1.3.1_src_all.tar.gz" ) MD5="653b60cfcdaefd171729115cd629b585" @@ -42,4 +44,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-hopach/build.sh b/recipes/bioconductor-hopach/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hopach/build.sh +++ b/recipes/bioconductor-hopach/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hopach/meta.yaml b/recipes/bioconductor-hopach/meta.yaml index b450e789184d8..568eb61392808 100644 --- a/recipes/bioconductor-hopach/meta.yaml +++ b/recipes/bioconductor-hopach/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "hopach" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c4562460a3dd571329f58b082f42a603f8490689af2618aabc350fe3e5188f49 + md5: 35465e16c6f9f85363b0e00701eb5e52 build: number: 0 rpaths: @@ -18,13 +18,13 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-cluster build: @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The HOPACH clustering algorithm builds a hierarchical tree of clusters by recursively partitioning a data set, while ordering and possibly collapsing clusters at each level. The algorithm uses the Mean/Median Split Silhouette (MSS) criteria to identify the level of the tree with maximally homogeneous clusters. It also runs the tree down to produce a final ordered list of the elements. The non-parametric bootstrap allows one to estimate the probability that each element belongs to each cluster (fuzzy clustering).' extra: identifiers: - biotools:hopach - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hopach + path: recipes/bioconductor-hopach + version: 2.40.0 + diff --git a/recipes/bioconductor-hpaanalyze/build.sh b/recipes/bioconductor-hpaanalyze/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-hpaanalyze/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hpaanalyze/meta.yaml b/recipes/bioconductor-hpaanalyze/meta.yaml new file mode 100644 index 0000000000000..1f865d5b9b3e2 --- /dev/null +++ b/recipes/bioconductor-hpaanalyze/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "HPAanalyze" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 211c3fa0f4c721603e9c913f2723bbf5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, devtools, BiocStyle +requirements: + host: + - 'bioconductor-hpar >=1.24.0,<1.25.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-readr + - r-reshape2 + - r-tibble + - r-tidyr + - r-xlconnect + - r-xml2 + run: + - 'bioconductor-hpar >=1.24.0,<1.25.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-magrittr + - r-readr + - r-reshape2 + - r-tibble + - r-tidyr + - r-xlconnect + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Provide functions for retrieving, exploratory analyzing and visualizing the Human Protein Atlas data.' + diff --git a/recipes/bioconductor-hpar/build.sh b/recipes/bioconductor-hpar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hpar/build.sh +++ b/recipes/bioconductor-hpar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hpar/meta.yaml b/recipes/bioconductor-hpar/meta.yaml index c5971981fab79..25fbfff925304 100644 --- a/recipes/bioconductor-hpar/meta.yaml +++ b/recipes/bioconductor-hpar/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.22.2" %} +{% set version = "1.24.0" %} {% set name = "hpar" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 088d47923e7b6c18a75b6be6cc0e1502fbff175dd2f4fad238d838adfe86e2ac + md5: d424723a0f21b8ad24e7280040c4cea7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, GO.db, knitr, BiocStyle, testthat requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The hpar package provides a simple R interface to and data from the Human Protein Atlas project.' extra: identifiers: - biotools:hpar - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hpar + path: recipes/bioconductor-hpar + version: 1.22.2 + diff --git a/recipes/bioconductor-hs25kresogen.db/meta.yaml b/recipes/bioconductor-hs25kresogen.db/meta.yaml new file mode 100644 index 0000000000000..829a383d20624 --- /dev/null +++ b/recipes/bioconductor-hs25kresogen.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "2.5.0" %} +{% set name = "hs25kresogen.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a3800d072ce0e5f6f5d8299538b99cca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'RNG_MRC Human Pangenomic 25k Set annotation data (chip hs25kresogen) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hs25kresogen.db/post-link.sh b/recipes/bioconductor-hs25kresogen.db/post-link.sh new file mode 100644 index 0000000000000..12649cd85a127 --- /dev/null +++ b/recipes/bioconductor-hs25kresogen.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hs25kresogen.db_2.5.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hs25kresogen.db_2.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/hs25kresogen.db_2.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hs25kresogen.db/bioconductor-hs25kresogen.db_2.5.0_src_all.tar.gz" +) +MD5="a3800d072ce0e5f6f5d8299538b99cca" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hs25kresogen.db/pre-unlink.sh b/recipes/bioconductor-hs25kresogen.db/pre-unlink.sh new file mode 100644 index 0000000000000..caa1bfadb5a14 --- /dev/null +++ b/recipes/bioconductor-hs25kresogen.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hs25kresogen.db diff --git a/recipes/bioconductor-hs6ug171.db/meta.yaml b/recipes/bioconductor-hs6ug171.db/meta.yaml new file mode 100644 index 0000000000000..1bda954b909a3 --- /dev/null +++ b/recipes/bioconductor-hs6ug171.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "Hs6UG171.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7aaf8a2441941f70247275c93735ed3b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package containing metadata for Hs6UG171 arrays assembled using data from public repositories' + diff --git a/recipes/bioconductor-hs6ug171.db/post-link.sh b/recipes/bioconductor-hs6ug171.db/post-link.sh new file mode 100644 index 0000000000000..871c7837a170e --- /dev/null +++ b/recipes/bioconductor-hs6ug171.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Hs6UG171.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Hs6UG171.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/Hs6UG171.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hs6ug171.db/bioconductor-hs6ug171.db_3.2.3_src_all.tar.gz" +) +MD5="7aaf8a2441941f70247275c93735ed3b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hs6ug171.db/pre-unlink.sh b/recipes/bioconductor-hs6ug171.db/pre-unlink.sh new file mode 100644 index 0000000000000..50fec4bc9cd85 --- /dev/null +++ b/recipes/bioconductor-hs6ug171.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Hs6UG171.db diff --git a/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml new file mode 100644 index 0000000000000..295d4513785f5 --- /dev/null +++ b/recipes/bioconductor-hsagilentdesign026652.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "HsAgilentDesign026652.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dcd2c748bf9d7c002611cd5cf2ff38c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Chips that use Agilent design number 026652 annotation data (chip HsAgilentDesign026652) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh b/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh new file mode 100644 index 0000000000000..2788bafa958a6 --- /dev/null +++ b/recipes/bioconductor-hsagilentdesign026652.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HsAgilentDesign026652.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HsAgilentDesign026652.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/HsAgilentDesign026652.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsagilentdesign026652.db/bioconductor-hsagilentdesign026652.db_3.2.3_src_all.tar.gz" +) +MD5="dcd2c748bf9d7c002611cd5cf2ff38c0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hsagilentdesign026652.db/pre-unlink.sh b/recipes/bioconductor-hsagilentdesign026652.db/pre-unlink.sh new file mode 100644 index 0000000000000..2d8eab6eb48a0 --- /dev/null +++ b/recipes/bioconductor-hsagilentdesign026652.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HsAgilentDesign026652.db diff --git a/recipes/bioconductor-hsmmsinglecell/meta.yaml b/recipes/bioconductor-hsmmsinglecell/meta.yaml index b8c5f82d337b0..f6cc524d44ade 100644 --- a/recipes/bioconductor-hsmmsinglecell/meta.yaml +++ b/recipes/bioconductor-hsmmsinglecell/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "0.114.0" %} +{% set version = "1.2.0" %} {% set name = "HSMMSingleCell" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 672e8202ea70c7098ce15b4383227310394da6faebbca4b353c90e0aa657e0a8 + md5: 13554a8eacb310fd9af3900ba9ce68b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Skeletal myoblasts undergo a well-characterized sequence of morphological and transcriptional changes during differentiation. In this experiment, primary human skeletal muscle myoblasts (HSMM) were expanded under high mitogen conditions (GM) and then differentiated by switching to low-mitogen media (DM). RNA-Seq libraries were sequenced from each of several hundred cells taken over a time-course of serum-induced differentiation. Between 49 and 77 cells were captured at each of four time points (0, 24, 48, 72 hours) following serum switch using the Fluidigm C1 microfluidic system. RNA from each cell was isolated and used to construct mRNA-Seq libraries, which were then sequenced to a depth of ~4 million reads per library, resulting in a complete gene expression profile for each cell.' - +extra: + parent_recipe: + name: bioconductor-hsmmsinglecell + path: recipes/bioconductor-hsmmsinglecell + version: 0.114.0 diff --git a/recipes/bioconductor-hsmmsinglecell/post-link.sh b/recipes/bioconductor-hsmmsinglecell/post-link.sh index 92778374059b3..467be71f23881 100644 --- a/recipes/bioconductor-hsmmsinglecell/post-link.sh +++ b/recipes/bioconductor-hsmmsinglecell/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="HSMMSingleCell_0.114.0.tar.gz" +FN="HSMMSingleCell_1.2.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/HSMMSingleCell_0.114.0.tar.gz" - "https://bioarchive.galaxyproject.org/HSMMSingleCell_0.114.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_0.114.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HSMMSingleCell_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/HSMMSingleCell_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hsmmsinglecell/bioconductor-hsmmsinglecell_1.2.0_src_all.tar.gz" ) -MD5="2b928efcb786a4486c79673d4ff457e3" +MD5="13554a8eacb310fd9af3900ba9ce68b9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-hspec/meta.yaml b/recipes/bioconductor-hspec/meta.yaml new file mode 100644 index 0000000000000..f49d7cd5ec90e --- /dev/null +++ b/recipes/bioconductor-hspec/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.99.1" %} +{% set name = "Hspec" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0ade3e3147c8f0086e9be2312cccdfeb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.' + diff --git a/recipes/bioconductor-hspec/post-link.sh b/recipes/bioconductor-hspec/post-link.sh new file mode 100644 index 0000000000000..92328dc7d37ab --- /dev/null +++ b/recipes/bioconductor-hspec/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Hspec_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Hspec_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/Hspec_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hspec/bioconductor-hspec_0.99.1_src_all.tar.gz" +) +MD5="0ade3e3147c8f0086e9be2312cccdfeb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hspec/pre-unlink.sh b/recipes/bioconductor-hspec/pre-unlink.sh new file mode 100644 index 0000000000000..ff6e57077c9da --- /dev/null +++ b/recipes/bioconductor-hspec/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Hspec diff --git a/recipes/bioconductor-hspeccdf/meta.yaml b/recipes/bioconductor-hspeccdf/meta.yaml new file mode 100644 index 0000000000000..e466a0c141ab5 --- /dev/null +++ b/recipes/bioconductor-hspeccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.99.1" %} +{% set name = "hspeccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 89f81adf91094710558ce6aec79fc7fd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HGU133Plus2_Hs_Hspec.cdf file.' + diff --git a/recipes/bioconductor-hspeccdf/post-link.sh b/recipes/bioconductor-hspeccdf/post-link.sh new file mode 100644 index 0000000000000..d3d7381d00016 --- /dev/null +++ b/recipes/bioconductor-hspeccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hspeccdf_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hspeccdf_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/hspeccdf_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hspeccdf/bioconductor-hspeccdf_0.99.1_src_all.tar.gz" +) +MD5="89f81adf91094710558ce6aec79fc7fd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hspeccdf/pre-unlink.sh b/recipes/bioconductor-hspeccdf/pre-unlink.sh new file mode 100644 index 0000000000000..f281a59fcdaea --- /dev/null +++ b/recipes/bioconductor-hspeccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hspeccdf diff --git a/recipes/bioconductor-hta20probeset.db/meta.yaml b/recipes/bioconductor-hta20probeset.db/meta.yaml new file mode 100644 index 0000000000000..6c520fdaf3f5f --- /dev/null +++ b/recipes/bioconductor-hta20probeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hta20probeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d2123b0ecd324626b06a920f947a114e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hta20 annotation data (chip hta20probeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hta20probeset.db/post-link.sh b/recipes/bioconductor-hta20probeset.db/post-link.sh new file mode 100644 index 0000000000000..d1348bcad7416 --- /dev/null +++ b/recipes/bioconductor-hta20probeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hta20probeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hta20probeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hta20probeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hta20probeset.db/bioconductor-hta20probeset.db_8.7.0_src_all.tar.gz" +) +MD5="d2123b0ecd324626b06a920f947a114e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hta20probeset.db/pre-unlink.sh b/recipes/bioconductor-hta20probeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..df23c05265219 --- /dev/null +++ b/recipes/bioconductor-hta20probeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hta20probeset.db diff --git a/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..924c80d4ef466 --- /dev/null +++ b/recipes/bioconductor-hta20transcriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hta20transcriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c7cdfe80bf2f7aa86fa3caff6da0c34c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hta20 annotation data (chip hta20transcriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh b/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..8a6c137e6f3ae --- /dev/null +++ b/recipes/bioconductor-hta20transcriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hta20transcriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hta20transcriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hta20transcriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hta20transcriptcluster.db/bioconductor-hta20transcriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="c7cdfe80bf2f7aa86fa3caff6da0c34c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hta20transcriptcluster.db/pre-unlink.sh b/recipes/bioconductor-hta20transcriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..07fc252ccd8e4 --- /dev/null +++ b/recipes/bioconductor-hta20transcriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hta20transcriptcluster.db diff --git a/recipes/bioconductor-hthgu133a.db/meta.yaml b/recipes/bioconductor-hthgu133a.db/meta.yaml new file mode 100644 index 0000000000000..40e3cd9d2a284 --- /dev/null +++ b/recipes/bioconductor-hthgu133a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hthgu133a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: df8c18dcb8d0adfb6f7a9306cbe9b162 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix HT Human Genome U133 Array Plate Set annotation data (chip hthgu133a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hthgu133a.db/post-link.sh b/recipes/bioconductor-hthgu133a.db/post-link.sh new file mode 100644 index 0000000000000..d4c076e83efc8 --- /dev/null +++ b/recipes/bioconductor-hthgu133a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133a.db/bioconductor-hthgu133a.db_3.2.3_src_all.tar.gz" +) +MD5="df8c18dcb8d0adfb6f7a9306cbe9b162" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133a.db/pre-unlink.sh b/recipes/bioconductor-hthgu133a.db/pre-unlink.sh new file mode 100644 index 0000000000000..3af0917830fea --- /dev/null +++ b/recipes/bioconductor-hthgu133a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133a.db diff --git a/recipes/bioconductor-hthgu133acdf/meta.yaml b/recipes/bioconductor-hthgu133acdf/meta.yaml new file mode 100644 index 0000000000000..ca3b1465c40c3 --- /dev/null +++ b/recipes/bioconductor-hthgu133acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b92e543867f1f0c08bfa9299e123d608 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_HG-U133A.cdf file.' + diff --git a/recipes/bioconductor-hthgu133acdf/post-link.sh b/recipes/bioconductor-hthgu133acdf/post-link.sh new file mode 100644 index 0000000000000..b582fa902c99d --- /dev/null +++ b/recipes/bioconductor-hthgu133acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133acdf/bioconductor-hthgu133acdf_2.18.0_src_all.tar.gz" +) +MD5="b92e543867f1f0c08bfa9299e123d608" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133acdf/pre-unlink.sh b/recipes/bioconductor-hthgu133acdf/pre-unlink.sh new file mode 100644 index 0000000000000..15e7469bb308b --- /dev/null +++ b/recipes/bioconductor-hthgu133acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133acdf diff --git a/recipes/bioconductor-hthgu133afrmavecs/meta.yaml b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml new file mode 100644 index 0000000000000..06768a388af1c --- /dev/null +++ b/recipes/bioconductor-hthgu133afrmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.3.0" %} +{% set name = "hthgu133afrmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be3f3d67a94dca3b080c184fba5ff6d8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-hthgu133afrmavecs/post-link.sh b/recipes/bioconductor-hthgu133afrmavecs/post-link.sh new file mode 100644 index 0000000000000..dbc26d673cbc4 --- /dev/null +++ b/recipes/bioconductor-hthgu133afrmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133afrmavecs_1.3.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133afrmavecs_1.3.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133afrmavecs_1.3.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133afrmavecs/bioconductor-hthgu133afrmavecs_1.3.0_src_all.tar.gz" +) +MD5="be3f3d67a94dca3b080c184fba5ff6d8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133afrmavecs/pre-unlink.sh b/recipes/bioconductor-hthgu133afrmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..b7e37370e517e --- /dev/null +++ b/recipes/bioconductor-hthgu133afrmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133afrmavecs diff --git a/recipes/bioconductor-hthgu133aprobe/meta.yaml b/recipes/bioconductor-hthgu133aprobe/meta.yaml new file mode 100644 index 0000000000000..a7752647e80a2 --- /dev/null +++ b/recipes/bioconductor-hthgu133aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cdc17ea670719f055ee75bea1415c754 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133A\_probe\_tab.' + diff --git a/recipes/bioconductor-hthgu133aprobe/post-link.sh b/recipes/bioconductor-hthgu133aprobe/post-link.sh new file mode 100644 index 0000000000000..cf01b9fab6df4 --- /dev/null +++ b/recipes/bioconductor-hthgu133aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133aprobe/bioconductor-hthgu133aprobe_2.18.0_src_all.tar.gz" +) +MD5="cdc17ea670719f055ee75bea1415c754" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133aprobe/pre-unlink.sh b/recipes/bioconductor-hthgu133aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..4f1dd287b778b --- /dev/null +++ b/recipes/bioconductor-hthgu133aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133aprobe diff --git a/recipes/bioconductor-hthgu133b.db/meta.yaml b/recipes/bioconductor-hthgu133b.db/meta.yaml new file mode 100644 index 0000000000000..8da72f6244661 --- /dev/null +++ b/recipes/bioconductor-hthgu133b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hthgu133b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a6dfceb47a306ec5365d8376dbb036c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix HT Human Genome U133 Array Plate Set annotation data (chip hthgu133b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hthgu133b.db/post-link.sh b/recipes/bioconductor-hthgu133b.db/post-link.sh new file mode 100644 index 0000000000000..3a789e7ed3e49 --- /dev/null +++ b/recipes/bioconductor-hthgu133b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133b.db/bioconductor-hthgu133b.db_3.2.3_src_all.tar.gz" +) +MD5="a6dfceb47a306ec5365d8376dbb036c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133b.db/pre-unlink.sh b/recipes/bioconductor-hthgu133b.db/pre-unlink.sh new file mode 100644 index 0000000000000..482fabec9c9cd --- /dev/null +++ b/recipes/bioconductor-hthgu133b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133b.db diff --git a/recipes/bioconductor-hthgu133bcdf/meta.yaml b/recipes/bioconductor-hthgu133bcdf/meta.yaml new file mode 100644 index 0000000000000..650d08e935c97 --- /dev/null +++ b/recipes/bioconductor-hthgu133bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 935ae53fb168d9c7890d71020ef4c366 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_HG-U133B.cdf file.' + diff --git a/recipes/bioconductor-hthgu133bcdf/post-link.sh b/recipes/bioconductor-hthgu133bcdf/post-link.sh new file mode 100644 index 0000000000000..2b664ba0318fa --- /dev/null +++ b/recipes/bioconductor-hthgu133bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133bcdf/bioconductor-hthgu133bcdf_2.18.0_src_all.tar.gz" +) +MD5="935ae53fb168d9c7890d71020ef4c366" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133bcdf/pre-unlink.sh b/recipes/bioconductor-hthgu133bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..60d0838de85a9 --- /dev/null +++ b/recipes/bioconductor-hthgu133bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133bcdf diff --git a/recipes/bioconductor-hthgu133bprobe/meta.yaml b/recipes/bioconductor-hthgu133bprobe/meta.yaml new file mode 100644 index 0000000000000..340d1fcfdcc31 --- /dev/null +++ b/recipes/bioconductor-hthgu133bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8a2e306638a81fdec3b10a014c04c6b9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133B\_probe\_tab.' + diff --git a/recipes/bioconductor-hthgu133bprobe/post-link.sh b/recipes/bioconductor-hthgu133bprobe/post-link.sh new file mode 100644 index 0000000000000..fdd57d7e64421 --- /dev/null +++ b/recipes/bioconductor-hthgu133bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133bprobe/bioconductor-hthgu133bprobe_2.18.0_src_all.tar.gz" +) +MD5="8a2e306638a81fdec3b10a014c04c6b9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133bprobe/pre-unlink.sh b/recipes/bioconductor-hthgu133bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..4d1785a5ddad1 --- /dev/null +++ b/recipes/bioconductor-hthgu133bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133bprobe diff --git a/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml new file mode 100644 index 0000000000000..809defa19deb1 --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133pluspmcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 56d15101d59decac7811caa15b349a9c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_HG-U133_Plus_PM.CDF file.' + diff --git a/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh b/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh new file mode 100644 index 0000000000000..5ea0f46ae7d0f --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133pluspmcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133pluspmcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133pluspmcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmcdf/bioconductor-hthgu133pluspmcdf_2.18.0_src_all.tar.gz" +) +MD5="56d15101d59decac7811caa15b349a9c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133pluspmcdf/pre-unlink.sh b/recipes/bioconductor-hthgu133pluspmcdf/pre-unlink.sh new file mode 100644 index 0000000000000..e94bb0bae3f11 --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133pluspmcdf diff --git a/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml new file mode 100644 index 0000000000000..2a8e2ff08ca14 --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hthgu133pluspmprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 74713e822a689007892d0eb92dbd456b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_HG-U133\_Plus\_PM\_probe\_tab.' + diff --git a/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh b/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh new file mode 100644 index 0000000000000..ab4bc051075f8 --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hthgu133pluspmprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hthgu133pluspmprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hthgu133pluspmprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hthgu133pluspmprobe/bioconductor-hthgu133pluspmprobe_2.18.0_src_all.tar.gz" +) +MD5="74713e822a689007892d0eb92dbd456b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hthgu133pluspmprobe/pre-unlink.sh b/recipes/bioconductor-hthgu133pluspmprobe/pre-unlink.sh new file mode 100644 index 0000000000000..8dab49d0a0ea0 --- /dev/null +++ b/recipes/bioconductor-hthgu133pluspmprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hthgu133pluspmprobe diff --git a/recipes/bioconductor-htmg430acdf/meta.yaml b/recipes/bioconductor-htmg430acdf/meta.yaml new file mode 100644 index 0000000000000..eb204849efeb7 --- /dev/null +++ b/recipes/bioconductor-htmg430acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: aef7a3c3af7d2624ee6fc6f2d22472e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_MG-430A.cdf file.' + diff --git a/recipes/bioconductor-htmg430acdf/post-link.sh b/recipes/bioconductor-htmg430acdf/post-link.sh new file mode 100644 index 0000000000000..b485226a75ffe --- /dev/null +++ b/recipes/bioconductor-htmg430acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430acdf/bioconductor-htmg430acdf_2.18.0_src_all.tar.gz" +) +MD5="aef7a3c3af7d2624ee6fc6f2d22472e2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430acdf/pre-unlink.sh b/recipes/bioconductor-htmg430acdf/pre-unlink.sh new file mode 100644 index 0000000000000..a9d42ed74a44e --- /dev/null +++ b/recipes/bioconductor-htmg430acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430acdf diff --git a/recipes/bioconductor-htmg430aprobe/meta.yaml b/recipes/bioconductor-htmg430aprobe/meta.yaml new file mode 100644 index 0000000000000..e0187372c652d --- /dev/null +++ b/recipes/bioconductor-htmg430aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e50cc49b8887b6ef8ee1152ec12d5010 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430A\_probe\_tab.' + diff --git a/recipes/bioconductor-htmg430aprobe/post-link.sh b/recipes/bioconductor-htmg430aprobe/post-link.sh new file mode 100644 index 0000000000000..9724848bc1db2 --- /dev/null +++ b/recipes/bioconductor-htmg430aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430aprobe/bioconductor-htmg430aprobe_2.18.0_src_all.tar.gz" +) +MD5="e50cc49b8887b6ef8ee1152ec12d5010" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430aprobe/pre-unlink.sh b/recipes/bioconductor-htmg430aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..67f8ac1d7ff27 --- /dev/null +++ b/recipes/bioconductor-htmg430aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430aprobe diff --git a/recipes/bioconductor-htmg430bcdf/meta.yaml b/recipes/bioconductor-htmg430bcdf/meta.yaml new file mode 100644 index 0000000000000..a4885eac8ce36 --- /dev/null +++ b/recipes/bioconductor-htmg430bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 53cc1408504a5f07b5655aa46b969157 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_MG-430B.cdf file.' + diff --git a/recipes/bioconductor-htmg430bcdf/post-link.sh b/recipes/bioconductor-htmg430bcdf/post-link.sh new file mode 100644 index 0000000000000..20c2519e577b5 --- /dev/null +++ b/recipes/bioconductor-htmg430bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430bcdf/bioconductor-htmg430bcdf_2.18.0_src_all.tar.gz" +) +MD5="53cc1408504a5f07b5655aa46b969157" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430bcdf/pre-unlink.sh b/recipes/bioconductor-htmg430bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..5665545edc893 --- /dev/null +++ b/recipes/bioconductor-htmg430bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430bcdf diff --git a/recipes/bioconductor-htmg430bprobe/meta.yaml b/recipes/bioconductor-htmg430bprobe/meta.yaml new file mode 100644 index 0000000000000..098d4151c678b --- /dev/null +++ b/recipes/bioconductor-htmg430bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f0e3eb56925d786762dee0c2dc82b530 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430B\_probe\_tab.' + diff --git a/recipes/bioconductor-htmg430bprobe/post-link.sh b/recipes/bioconductor-htmg430bprobe/post-link.sh new file mode 100644 index 0000000000000..ae8265e80e969 --- /dev/null +++ b/recipes/bioconductor-htmg430bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430bprobe/bioconductor-htmg430bprobe_2.18.0_src_all.tar.gz" +) +MD5="f0e3eb56925d786762dee0c2dc82b530" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430bprobe/pre-unlink.sh b/recipes/bioconductor-htmg430bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..34589c6511058 --- /dev/null +++ b/recipes/bioconductor-htmg430bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430bprobe diff --git a/recipes/bioconductor-htmg430pmcdf/meta.yaml b/recipes/bioconductor-htmg430pmcdf/meta.yaml new file mode 100644 index 0000000000000..82b68340a08a6 --- /dev/null +++ b/recipes/bioconductor-htmg430pmcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430pmcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 016a54b47adbbed7db989787646a0084 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_MG-430_PM.cdf file.' + diff --git a/recipes/bioconductor-htmg430pmcdf/post-link.sh b/recipes/bioconductor-htmg430pmcdf/post-link.sh new file mode 100644 index 0000000000000..df7e368434c5d --- /dev/null +++ b/recipes/bioconductor-htmg430pmcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430pmcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430pmcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430pmcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430pmcdf/bioconductor-htmg430pmcdf_2.18.0_src_all.tar.gz" +) +MD5="016a54b47adbbed7db989787646a0084" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430pmcdf/pre-unlink.sh b/recipes/bioconductor-htmg430pmcdf/pre-unlink.sh new file mode 100644 index 0000000000000..c92f1129ba607 --- /dev/null +++ b/recipes/bioconductor-htmg430pmcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430pmcdf diff --git a/recipes/bioconductor-htmg430pmprobe/meta.yaml b/recipes/bioconductor-htmg430pmprobe/meta.yaml new file mode 100644 index 0000000000000..374374e4068b4 --- /dev/null +++ b/recipes/bioconductor-htmg430pmprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htmg430pmprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f0e053fcc0ca4b5f8c539fc0a3fcb076 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_MG-430\_PM\_probe\_tab.' + diff --git a/recipes/bioconductor-htmg430pmprobe/post-link.sh b/recipes/bioconductor-htmg430pmprobe/post-link.sh new file mode 100644 index 0000000000000..0e4b6483c19cf --- /dev/null +++ b/recipes/bioconductor-htmg430pmprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htmg430pmprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htmg430pmprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htmg430pmprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htmg430pmprobe/bioconductor-htmg430pmprobe_2.18.0_src_all.tar.gz" +) +MD5="f0e053fcc0ca4b5f8c539fc0a3fcb076" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htmg430pmprobe/pre-unlink.sh b/recipes/bioconductor-htmg430pmprobe/pre-unlink.sh new file mode 100644 index 0000000000000..dd90f02c8e60d --- /dev/null +++ b/recipes/bioconductor-htmg430pmprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htmg430pmprobe diff --git a/recipes/bioconductor-htqpcr/build.sh b/recipes/bioconductor-htqpcr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-htqpcr/build.sh +++ b/recipes/bioconductor-htqpcr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htqpcr/conda_build_config.yaml b/recipes/bioconductor-htqpcr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-htqpcr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-htqpcr/meta.yaml b/recipes/bioconductor-htqpcr/meta.yaml index 2aa3be0bd6c60..3be074a46fc0b 100644 --- a/recipes/bioconductor-htqpcr/meta.yaml +++ b/recipes/bioconductor-htqpcr/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "HTqPCR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 18e3ac081022dc455f4f2f66f8a4f735fce90858d85fa3dc97e44137c1f5991c + md5: 6b49cf2e293bb387f20845b568bfc20b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: statmod requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-gplots - r-rcolorbrewer run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-gplots - r-rcolorbrewer @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of Ct values from high throughput quantitative real-time PCR (qPCR) assays across multiple conditions or replicates. The input data can be from spatially-defined formats such ABI TaqMan Low Density Arrays or OpenArray; LightCycler from Roche Applied Science; the CFX plates from Bio-Rad Laboratories; conventional 96- or 384-well plates; or microfluidic devices such as the Dynamic Arrays from Fluidigm Corporation. HTqPCR handles data loading, quality assessment, normalization, visualization and parametric or non-parametric testing for statistical significance in Ct values between features (e.g. genes, microRNAs).' extra: identifiers: - biotools:htqpcr + parent_recipe: + name: bioconductor-htqpcr + path: recipes/bioconductor-htqpcr + version: 1.34.0 + diff --git a/recipes/bioconductor-htrat230pmcdf/meta.yaml b/recipes/bioconductor-htrat230pmcdf/meta.yaml new file mode 100644 index 0000000000000..a6ba2f2592f46 --- /dev/null +++ b/recipes/bioconductor-htrat230pmcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htrat230pmcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c6683d16e8aacccd326f7a7eebb79b98 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_Rat230_PM.cdf file.' + diff --git a/recipes/bioconductor-htrat230pmcdf/post-link.sh b/recipes/bioconductor-htrat230pmcdf/post-link.sh new file mode 100644 index 0000000000000..a06a8143abd04 --- /dev/null +++ b/recipes/bioconductor-htrat230pmcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htrat230pmcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htrat230pmcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htrat230pmcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htrat230pmcdf/bioconductor-htrat230pmcdf_2.18.0_src_all.tar.gz" +) +MD5="c6683d16e8aacccd326f7a7eebb79b98" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htrat230pmcdf/pre-unlink.sh b/recipes/bioconductor-htrat230pmcdf/pre-unlink.sh new file mode 100644 index 0000000000000..551b3d703a6f9 --- /dev/null +++ b/recipes/bioconductor-htrat230pmcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htrat230pmcdf diff --git a/recipes/bioconductor-htrat230pmprobe/meta.yaml b/recipes/bioconductor-htrat230pmprobe/meta.yaml new file mode 100644 index 0000000000000..813779eea32ff --- /dev/null +++ b/recipes/bioconductor-htrat230pmprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htrat230pmprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e4deeca2dc406367ac4a347e370267cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat230\_PM\_probe\_tab.' + diff --git a/recipes/bioconductor-htrat230pmprobe/post-link.sh b/recipes/bioconductor-htrat230pmprobe/post-link.sh new file mode 100644 index 0000000000000..e7ac0e6982ada --- /dev/null +++ b/recipes/bioconductor-htrat230pmprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htrat230pmprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htrat230pmprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htrat230pmprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htrat230pmprobe/bioconductor-htrat230pmprobe_2.18.0_src_all.tar.gz" +) +MD5="e4deeca2dc406367ac4a347e370267cf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htrat230pmprobe/pre-unlink.sh b/recipes/bioconductor-htrat230pmprobe/pre-unlink.sh new file mode 100644 index 0000000000000..208666bb9d887 --- /dev/null +++ b/recipes/bioconductor-htrat230pmprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htrat230pmprobe diff --git a/recipes/bioconductor-htratfocuscdf/meta.yaml b/recipes/bioconductor-htratfocuscdf/meta.yaml new file mode 100644 index 0000000000000..8c422b7d1da79 --- /dev/null +++ b/recipes/bioconductor-htratfocuscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htratfocuscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 04b4952f7d8b607a7eb0f779c08c57dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HT_Rat-Focus.cdf file.' + diff --git a/recipes/bioconductor-htratfocuscdf/post-link.sh b/recipes/bioconductor-htratfocuscdf/post-link.sh new file mode 100644 index 0000000000000..76c08fab70b7c --- /dev/null +++ b/recipes/bioconductor-htratfocuscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htratfocuscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htratfocuscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htratfocuscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htratfocuscdf/bioconductor-htratfocuscdf_2.18.0_src_all.tar.gz" +) +MD5="04b4952f7d8b607a7eb0f779c08c57dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htratfocuscdf/pre-unlink.sh b/recipes/bioconductor-htratfocuscdf/pre-unlink.sh new file mode 100644 index 0000000000000..3d47023147f4d --- /dev/null +++ b/recipes/bioconductor-htratfocuscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htratfocuscdf diff --git a/recipes/bioconductor-htratfocusprobe/meta.yaml b/recipes/bioconductor-htratfocusprobe/meta.yaml new file mode 100644 index 0000000000000..11173b6a688c5 --- /dev/null +++ b/recipes/bioconductor-htratfocusprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "htratfocusprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 26a0963d8aff314a4a1f2c47e9147a8a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HT\_Rat-Focus\_probe\_tab.' + diff --git a/recipes/bioconductor-htratfocusprobe/post-link.sh b/recipes/bioconductor-htratfocusprobe/post-link.sh new file mode 100644 index 0000000000000..b6f93ef3d94bb --- /dev/null +++ b/recipes/bioconductor-htratfocusprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="htratfocusprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/htratfocusprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/htratfocusprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-htratfocusprobe/bioconductor-htratfocusprobe_2.18.0_src_all.tar.gz" +) +MD5="26a0963d8aff314a4a1f2c47e9147a8a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-htratfocusprobe/pre-unlink.sh b/recipes/bioconductor-htratfocusprobe/pre-unlink.sh new file mode 100644 index 0000000000000..182124f578d9c --- /dev/null +++ b/recipes/bioconductor-htratfocusprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ htratfocusprobe diff --git a/recipes/bioconductor-htsanalyzer/build.sh b/recipes/bioconductor-htsanalyzer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-htsanalyzer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htsanalyzer/meta.yaml b/recipes/bioconductor-htsanalyzer/meta.yaml new file mode 100644 index 0000000000000..40338081c3381 --- /dev/null +++ b/recipes/bioconductor-htsanalyzer/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "2.34.0" %} +{% set name = "HTSanalyzeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 29d69fa45e56724f4586828c74dbe748 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: KEGG.db, GO.db, org.Dm.eg.db, GOstats, org.Ce.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Hs.eg.db, snow +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-bionet >=1.42.0,<1.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - r-base + - r-igraph + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-bionet >=1.42.0,<1.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - r-base + - r-igraph +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides classes and methods for gene set over-representation, enrichment and network analyses on high-throughput screens. The over-representation analysis is performed based on hypergeometric tests. The enrichment analysis is based on the GSEA algorithm (Subramanian et al. PNAS 2005). The network analysis identifies enriched subnetworks based on algorithms from the BioNet package (Beisser et al., Bioinformatics 2010). A pipeline is also specifically designed for cellHTS2 object to perform integrative network analyses of high-throughput RNA interference screens. The users can build their own analysis pipeline for their own data set based on this package.' + diff --git a/recipes/bioconductor-htseqgenie/build.sh b/recipes/bioconductor-htseqgenie/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-htseqgenie/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htseqgenie/meta.yaml b/recipes/bioconductor-htseqgenie/meta.yaml new file mode 100644 index 0000000000000..101be05bb4de3 --- /dev/null +++ b/recipes/bioconductor-htseqgenie/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "4.12.0" %} +{% set name = "HTSeqGenie" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7e4ef25284d34c49ec0c01d8502f4622 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: TxDb.Hsapiens.UCSC.hg19.knownGene, LungCancerLines, org.Hs.eg.db +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gmapr >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - r-base + - 'r-cairo >=1.5.5' + - 'r-hwriter >=1.3.0' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gmapr >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - r-base + - 'r-cairo >=1.5.5' + - 'r-hwriter >=1.3.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Libraries to perform NGS analysis.' + diff --git a/recipes/bioconductor-htseqtools/build.sh b/recipes/bioconductor-htseqtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-htseqtools/build.sh +++ b/recipes/bioconductor-htseqtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htseqtools/meta.yaml b/recipes/bioconductor-htseqtools/meta.yaml index 29941bc0362d5..a4236d59b6fce 100644 --- a/recipes/bioconductor-htseqtools/meta.yaml +++ b/recipes/bioconductor-htseqtools/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "1.28.3" %} +{% set version = "1.30.0" %} {% set name = "htSeqTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e7ee1b65265dc44256ec0618a907ae095a19c9aa3723a15229aa3f22011530a1 + md5: e62c9dd3fa250ff61a92ee38400b23b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'We provide efficient, easy-to-use tools for High-Throughput Sequencing (ChIP-seq, RNAseq etc.). These include MDS plots (analogues to PCA), detecting inefficient immuno-precipitation or over-amplification artifacts, tools to identify and test for genomic regions with large accumulation of reads, and visualization of coverage profiles.' extra: identifiers: - biotools:htseqtools - doi:10.1093/bioinformatics/btr700 + parent_recipe: + name: bioconductor-htseqtools + path: recipes/bioconductor-htseqtools + version: 1.28.3 + diff --git a/recipes/bioconductor-htsfilter/build.sh b/recipes/bioconductor-htsfilter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-htsfilter/build.sh +++ b/recipes/bioconductor-htsfilter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-htsfilter/meta.yaml b/recipes/bioconductor-htsfilter/meta.yaml index bee9c945a5de7..b907f3656cc2b 100644 --- a/recipes/bioconductor-htsfilter/meta.yaml +++ b/recipes/bioconductor-htsfilter/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "HTSFilter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c4597ad7589c74ace67fd5c7c0540bafc796c7f0dd081a450d2e2bb64f4deb44 + md5: 11e7bab944c5572bd842847ac7d46555 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: EDASeq (>= 2.1.4), BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements a filtering procedure for replicated transcriptome sequencing data based on a global Jaccard similarity index in order to identify genes with low, constant levels of expression across one or more experimental conditions.' extra: identifiers: - biotools:htsfilter + parent_recipe: + name: bioconductor-htsfilter + path: recipes/bioconductor-htsfilter + version: 1.20.0 + diff --git a/recipes/bioconductor-hu35ksuba.db/meta.yaml b/recipes/bioconductor-hu35ksuba.db/meta.yaml new file mode 100644 index 0000000000000..5cb1d4690004f --- /dev/null +++ b/recipes/bioconductor-hu35ksuba.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hu35ksuba.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eef6de6790e904d0b63a3ec8faba2962 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome HU35K Set annotation data (chip hu35ksuba) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hu35ksuba.db/post-link.sh b/recipes/bioconductor-hu35ksuba.db/post-link.sh new file mode 100644 index 0000000000000..3e53f149c4d6d --- /dev/null +++ b/recipes/bioconductor-hu35ksuba.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksuba.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksuba.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksuba.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksuba.db/bioconductor-hu35ksuba.db_3.2.3_src_all.tar.gz" +) +MD5="eef6de6790e904d0b63a3ec8faba2962" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksuba.db/pre-unlink.sh b/recipes/bioconductor-hu35ksuba.db/pre-unlink.sh new file mode 100644 index 0000000000000..a939d9fd140ad --- /dev/null +++ b/recipes/bioconductor-hu35ksuba.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksuba.db diff --git a/recipes/bioconductor-hu35ksubacdf/meta.yaml b/recipes/bioconductor-hu35ksubacdf/meta.yaml new file mode 100644 index 0000000000000..d2679d898000d --- /dev/null +++ b/recipes/bioconductor-hu35ksubacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c8b82c4755eb62818ca0dbf22de5d25e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu35KsubA.CDF file.' + diff --git a/recipes/bioconductor-hu35ksubacdf/post-link.sh b/recipes/bioconductor-hu35ksubacdf/post-link.sh new file mode 100644 index 0000000000000..649ce0d4a73cc --- /dev/null +++ b/recipes/bioconductor-hu35ksubacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubacdf/bioconductor-hu35ksubacdf_2.18.0_src_all.tar.gz" +) +MD5="c8b82c4755eb62818ca0dbf22de5d25e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubacdf/pre-unlink.sh b/recipes/bioconductor-hu35ksubacdf/pre-unlink.sh new file mode 100644 index 0000000000000..696e3129ecda0 --- /dev/null +++ b/recipes/bioconductor-hu35ksubacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubacdf diff --git a/recipes/bioconductor-hu35ksubaprobe/meta.yaml b/recipes/bioconductor-hu35ksubaprobe/meta.yaml new file mode 100644 index 0000000000000..2546e7e12281a --- /dev/null +++ b/recipes/bioconductor-hu35ksubaprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubaprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 49bd19ec3b6404211f2e410e473fa644 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubA\_probe\_tab.' + diff --git a/recipes/bioconductor-hu35ksubaprobe/post-link.sh b/recipes/bioconductor-hu35ksubaprobe/post-link.sh new file mode 100644 index 0000000000000..0576a32f18cf3 --- /dev/null +++ b/recipes/bioconductor-hu35ksubaprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubaprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubaprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubaprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubaprobe/bioconductor-hu35ksubaprobe_2.18.0_src_all.tar.gz" +) +MD5="49bd19ec3b6404211f2e410e473fa644" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubaprobe/pre-unlink.sh b/recipes/bioconductor-hu35ksubaprobe/pre-unlink.sh new file mode 100644 index 0000000000000..9596b9c4e6b80 --- /dev/null +++ b/recipes/bioconductor-hu35ksubaprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubaprobe diff --git a/recipes/bioconductor-hu35ksubb.db/meta.yaml b/recipes/bioconductor-hu35ksubb.db/meta.yaml new file mode 100644 index 0000000000000..1c9e56d1e5b32 --- /dev/null +++ b/recipes/bioconductor-hu35ksubb.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hu35ksubb.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b49fc7bda2b0879d1be1ac0061a7ea98 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubb) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hu35ksubb.db/post-link.sh b/recipes/bioconductor-hu35ksubb.db/post-link.sh new file mode 100644 index 0000000000000..8ce724fdf457f --- /dev/null +++ b/recipes/bioconductor-hu35ksubb.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubb.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubb.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubb.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubb.db/bioconductor-hu35ksubb.db_3.2.3_src_all.tar.gz" +) +MD5="b49fc7bda2b0879d1be1ac0061a7ea98" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubb.db/pre-unlink.sh b/recipes/bioconductor-hu35ksubb.db/pre-unlink.sh new file mode 100644 index 0000000000000..cec815cea7e26 --- /dev/null +++ b/recipes/bioconductor-hu35ksubb.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubb.db diff --git a/recipes/bioconductor-hu35ksubbcdf/meta.yaml b/recipes/bioconductor-hu35ksubbcdf/meta.yaml new file mode 100644 index 0000000000000..56cfe616d4da8 --- /dev/null +++ b/recipes/bioconductor-hu35ksubbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d873b6c521e926b331f799baf10a4e13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu35KsubB.CDF file.' + diff --git a/recipes/bioconductor-hu35ksubbcdf/post-link.sh b/recipes/bioconductor-hu35ksubbcdf/post-link.sh new file mode 100644 index 0000000000000..fe0640ed70d26 --- /dev/null +++ b/recipes/bioconductor-hu35ksubbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbcdf/bioconductor-hu35ksubbcdf_2.18.0_src_all.tar.gz" +) +MD5="d873b6c521e926b331f799baf10a4e13" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubbcdf/pre-unlink.sh b/recipes/bioconductor-hu35ksubbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..5cbde6a0b580d --- /dev/null +++ b/recipes/bioconductor-hu35ksubbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubbcdf diff --git a/recipes/bioconductor-hu35ksubbprobe/meta.yaml b/recipes/bioconductor-hu35ksubbprobe/meta.yaml new file mode 100644 index 0000000000000..725a53a556e6a --- /dev/null +++ b/recipes/bioconductor-hu35ksubbprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubbprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0a63051d0faf38a56f17d5865cbed9b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubB\_probe\_tab.' + diff --git a/recipes/bioconductor-hu35ksubbprobe/post-link.sh b/recipes/bioconductor-hu35ksubbprobe/post-link.sh new file mode 100644 index 0000000000000..890681497c673 --- /dev/null +++ b/recipes/bioconductor-hu35ksubbprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubbprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubbprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubbprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubbprobe/bioconductor-hu35ksubbprobe_2.18.0_src_all.tar.gz" +) +MD5="0a63051d0faf38a56f17d5865cbed9b1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubbprobe/pre-unlink.sh b/recipes/bioconductor-hu35ksubbprobe/pre-unlink.sh new file mode 100644 index 0000000000000..1499eb8a6e391 --- /dev/null +++ b/recipes/bioconductor-hu35ksubbprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubbprobe diff --git a/recipes/bioconductor-hu35ksubc.db/meta.yaml b/recipes/bioconductor-hu35ksubc.db/meta.yaml new file mode 100644 index 0000000000000..ebb4e1b835abc --- /dev/null +++ b/recipes/bioconductor-hu35ksubc.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hu35ksubc.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f3c215dc2ddbab7ddcdbf015495f87b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubc) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hu35ksubc.db/post-link.sh b/recipes/bioconductor-hu35ksubc.db/post-link.sh new file mode 100644 index 0000000000000..814126788be8a --- /dev/null +++ b/recipes/bioconductor-hu35ksubc.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubc.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubc.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubc.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubc.db/bioconductor-hu35ksubc.db_3.2.3_src_all.tar.gz" +) +MD5="f3c215dc2ddbab7ddcdbf015495f87b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubc.db/pre-unlink.sh b/recipes/bioconductor-hu35ksubc.db/pre-unlink.sh new file mode 100644 index 0000000000000..2592b66c6666b --- /dev/null +++ b/recipes/bioconductor-hu35ksubc.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubc.db diff --git a/recipes/bioconductor-hu35ksubccdf/meta.yaml b/recipes/bioconductor-hu35ksubccdf/meta.yaml new file mode 100644 index 0000000000000..9f96cf6ba8556 --- /dev/null +++ b/recipes/bioconductor-hu35ksubccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: de96e69680c5f8747c99d170272d7c3c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu35KsubC.CDF file.' + diff --git a/recipes/bioconductor-hu35ksubccdf/post-link.sh b/recipes/bioconductor-hu35ksubccdf/post-link.sh new file mode 100644 index 0000000000000..b7f7adce1f279 --- /dev/null +++ b/recipes/bioconductor-hu35ksubccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubccdf/bioconductor-hu35ksubccdf_2.18.0_src_all.tar.gz" +) +MD5="de96e69680c5f8747c99d170272d7c3c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubccdf/pre-unlink.sh b/recipes/bioconductor-hu35ksubccdf/pre-unlink.sh new file mode 100644 index 0000000000000..7faf13c8f4798 --- /dev/null +++ b/recipes/bioconductor-hu35ksubccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubccdf diff --git a/recipes/bioconductor-hu35ksubcprobe/meta.yaml b/recipes/bioconductor-hu35ksubcprobe/meta.yaml new file mode 100644 index 0000000000000..d2bcf4a019640 --- /dev/null +++ b/recipes/bioconductor-hu35ksubcprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubcprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b10453ea061b09172192bd21baa9083d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubC\_probe\_tab.' + diff --git a/recipes/bioconductor-hu35ksubcprobe/post-link.sh b/recipes/bioconductor-hu35ksubcprobe/post-link.sh new file mode 100644 index 0000000000000..95ccbcaa70f03 --- /dev/null +++ b/recipes/bioconductor-hu35ksubcprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubcprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubcprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubcprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubcprobe/bioconductor-hu35ksubcprobe_2.18.0_src_all.tar.gz" +) +MD5="b10453ea061b09172192bd21baa9083d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubcprobe/pre-unlink.sh b/recipes/bioconductor-hu35ksubcprobe/pre-unlink.sh new file mode 100644 index 0000000000000..832411319b2c4 --- /dev/null +++ b/recipes/bioconductor-hu35ksubcprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubcprobe diff --git a/recipes/bioconductor-hu35ksubd.db/meta.yaml b/recipes/bioconductor-hu35ksubd.db/meta.yaml new file mode 100644 index 0000000000000..dfdc4007ceac0 --- /dev/null +++ b/recipes/bioconductor-hu35ksubd.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hu35ksubd.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9b8f09012d27c7b41e0d20321d83a625 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human Genome HU35K Set annotation data (chip hu35ksubd) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hu35ksubd.db/post-link.sh b/recipes/bioconductor-hu35ksubd.db/post-link.sh new file mode 100644 index 0000000000000..61e06db03d603 --- /dev/null +++ b/recipes/bioconductor-hu35ksubd.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubd.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubd.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubd.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubd.db/bioconductor-hu35ksubd.db_3.2.3_src_all.tar.gz" +) +MD5="9b8f09012d27c7b41e0d20321d83a625" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubd.db/pre-unlink.sh b/recipes/bioconductor-hu35ksubd.db/pre-unlink.sh new file mode 100644 index 0000000000000..e608ef6a555d7 --- /dev/null +++ b/recipes/bioconductor-hu35ksubd.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubd.db diff --git a/recipes/bioconductor-hu35ksubdcdf/meta.yaml b/recipes/bioconductor-hu35ksubdcdf/meta.yaml new file mode 100644 index 0000000000000..6a0664ebebf79 --- /dev/null +++ b/recipes/bioconductor-hu35ksubdcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubdcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f6423426969f306fb0d5171e75b5380 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu35KsubD.CDF file.' + diff --git a/recipes/bioconductor-hu35ksubdcdf/post-link.sh b/recipes/bioconductor-hu35ksubdcdf/post-link.sh new file mode 100644 index 0000000000000..30c64240813da --- /dev/null +++ b/recipes/bioconductor-hu35ksubdcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubdcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubdcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubdcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdcdf/bioconductor-hu35ksubdcdf_2.18.0_src_all.tar.gz" +) +MD5="6f6423426969f306fb0d5171e75b5380" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubdcdf/pre-unlink.sh b/recipes/bioconductor-hu35ksubdcdf/pre-unlink.sh new file mode 100644 index 0000000000000..8617fd3baf6fc --- /dev/null +++ b/recipes/bioconductor-hu35ksubdcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubdcdf diff --git a/recipes/bioconductor-hu35ksubdprobe/meta.yaml b/recipes/bioconductor-hu35ksubdprobe/meta.yaml new file mode 100644 index 0000000000000..310407e598b66 --- /dev/null +++ b/recipes/bioconductor-hu35ksubdprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu35ksubdprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 430a9b8ccd646d8cb06e6c1d750eec23 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu35KsubD\_probe\_tab.' + diff --git a/recipes/bioconductor-hu35ksubdprobe/post-link.sh b/recipes/bioconductor-hu35ksubdprobe/post-link.sh new file mode 100644 index 0000000000000..c753393abbdcd --- /dev/null +++ b/recipes/bioconductor-hu35ksubdprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu35ksubdprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu35ksubdprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu35ksubdprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu35ksubdprobe/bioconductor-hu35ksubdprobe_2.18.0_src_all.tar.gz" +) +MD5="430a9b8ccd646d8cb06e6c1d750eec23" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu35ksubdprobe/pre-unlink.sh b/recipes/bioconductor-hu35ksubdprobe/pre-unlink.sh new file mode 100644 index 0000000000000..7c0bf9bae8ae5 --- /dev/null +++ b/recipes/bioconductor-hu35ksubdprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu35ksubdprobe diff --git a/recipes/bioconductor-hu6800.db/meta.yaml b/recipes/bioconductor-hu6800.db/meta.yaml new file mode 100644 index 0000000000000..1ad8da797731e --- /dev/null +++ b/recipes/bioconductor-hu6800.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "hu6800.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7783c1539639aec9d3d736e38b4f028c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix HuGeneFL Genome Array annotation data (chip hu6800) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hu6800.db/post-link.sh b/recipes/bioconductor-hu6800.db/post-link.sh new file mode 100644 index 0000000000000..33ac218e91abb --- /dev/null +++ b/recipes/bioconductor-hu6800.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800.db/bioconductor-hu6800.db_3.2.3_src_all.tar.gz" +) +MD5="7783c1539639aec9d3d736e38b4f028c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800.db/pre-unlink.sh b/recipes/bioconductor-hu6800.db/pre-unlink.sh new file mode 100644 index 0000000000000..251ed876854cb --- /dev/null +++ b/recipes/bioconductor-hu6800.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800.db diff --git a/recipes/bioconductor-hu6800cdf/meta.yaml b/recipes/bioconductor-hu6800cdf/meta.yaml new file mode 100644 index 0000000000000..b1bae16a7485f --- /dev/null +++ b/recipes/bioconductor-hu6800cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fa2b2ab8f3aba517c63ad2e65873d2f0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu6800.CDF file.' + diff --git a/recipes/bioconductor-hu6800cdf/post-link.sh b/recipes/bioconductor-hu6800cdf/post-link.sh new file mode 100644 index 0000000000000..1e9ce7333bc18 --- /dev/null +++ b/recipes/bioconductor-hu6800cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800cdf/bioconductor-hu6800cdf_2.18.0_src_all.tar.gz" +) +MD5="fa2b2ab8f3aba517c63ad2e65873d2f0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800cdf/pre-unlink.sh b/recipes/bioconductor-hu6800cdf/pre-unlink.sh new file mode 100644 index 0000000000000..9a7f76046a2c9 --- /dev/null +++ b/recipes/bioconductor-hu6800cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800cdf diff --git a/recipes/bioconductor-hu6800probe/meta.yaml b/recipes/bioconductor-hu6800probe/meta.yaml new file mode 100644 index 0000000000000..2785838d967f9 --- /dev/null +++ b/recipes/bioconductor-hu6800probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7a2383bd870cbc0628c210174e911250 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Hu6800\_probe\_tab.' + diff --git a/recipes/bioconductor-hu6800probe/post-link.sh b/recipes/bioconductor-hu6800probe/post-link.sh new file mode 100644 index 0000000000000..b7a1d066298c9 --- /dev/null +++ b/recipes/bioconductor-hu6800probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800probe/bioconductor-hu6800probe_2.18.0_src_all.tar.gz" +) +MD5="7a2383bd870cbc0628c210174e911250" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800probe/pre-unlink.sh b/recipes/bioconductor-hu6800probe/pre-unlink.sh new file mode 100644 index 0000000000000..8bdc426df489e --- /dev/null +++ b/recipes/bioconductor-hu6800probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800probe diff --git a/recipes/bioconductor-hu6800subacdf/meta.yaml b/recipes/bioconductor-hu6800subacdf/meta.yaml new file mode 100644 index 0000000000000..b0fe73828933a --- /dev/null +++ b/recipes/bioconductor-hu6800subacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800subacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9e8ec301e066e400564976cd9750297e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu6800subA.CDF file.' + diff --git a/recipes/bioconductor-hu6800subacdf/post-link.sh b/recipes/bioconductor-hu6800subacdf/post-link.sh new file mode 100644 index 0000000000000..17eeaf0bf0e17 --- /dev/null +++ b/recipes/bioconductor-hu6800subacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800subacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800subacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subacdf/bioconductor-hu6800subacdf_2.18.0_src_all.tar.gz" +) +MD5="9e8ec301e066e400564976cd9750297e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800subacdf/pre-unlink.sh b/recipes/bioconductor-hu6800subacdf/pre-unlink.sh new file mode 100644 index 0000000000000..065f0d07ec2cd --- /dev/null +++ b/recipes/bioconductor-hu6800subacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800subacdf diff --git a/recipes/bioconductor-hu6800subbcdf/meta.yaml b/recipes/bioconductor-hu6800subbcdf/meta.yaml new file mode 100644 index 0000000000000..f3ed189d2168a --- /dev/null +++ b/recipes/bioconductor-hu6800subbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800subbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 529aad5e4e73594c8cb66274d7e4adc5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu6800subB.CDF file.' + diff --git a/recipes/bioconductor-hu6800subbcdf/post-link.sh b/recipes/bioconductor-hu6800subbcdf/post-link.sh new file mode 100644 index 0000000000000..78a9c7db436b2 --- /dev/null +++ b/recipes/bioconductor-hu6800subbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800subbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800subbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subbcdf/bioconductor-hu6800subbcdf_2.18.0_src_all.tar.gz" +) +MD5="529aad5e4e73594c8cb66274d7e4adc5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800subbcdf/pre-unlink.sh b/recipes/bioconductor-hu6800subbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..16a0b6933f461 --- /dev/null +++ b/recipes/bioconductor-hu6800subbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800subbcdf diff --git a/recipes/bioconductor-hu6800subccdf/meta.yaml b/recipes/bioconductor-hu6800subccdf/meta.yaml new file mode 100644 index 0000000000000..5291dcd8b4171 --- /dev/null +++ b/recipes/bioconductor-hu6800subccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800subccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 020fe3a6bdf44efbde15432b968433e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu6800subC.CDF file.' + diff --git a/recipes/bioconductor-hu6800subccdf/post-link.sh b/recipes/bioconductor-hu6800subccdf/post-link.sh new file mode 100644 index 0000000000000..398ed39c5c183 --- /dev/null +++ b/recipes/bioconductor-hu6800subccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800subccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800subccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subccdf/bioconductor-hu6800subccdf_2.18.0_src_all.tar.gz" +) +MD5="020fe3a6bdf44efbde15432b968433e8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800subccdf/pre-unlink.sh b/recipes/bioconductor-hu6800subccdf/pre-unlink.sh new file mode 100644 index 0000000000000..764340d8168ef --- /dev/null +++ b/recipes/bioconductor-hu6800subccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800subccdf diff --git a/recipes/bioconductor-hu6800subdcdf/meta.yaml b/recipes/bioconductor-hu6800subdcdf/meta.yaml new file mode 100644 index 0000000000000..84b7a517966ef --- /dev/null +++ b/recipes/bioconductor-hu6800subdcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hu6800subdcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7966c21babb23e18cca4faafc8720f0a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Hu6800subD.CDF file.' + diff --git a/recipes/bioconductor-hu6800subdcdf/post-link.sh b/recipes/bioconductor-hu6800subdcdf/post-link.sh new file mode 100644 index 0000000000000..d44375860876c --- /dev/null +++ b/recipes/bioconductor-hu6800subdcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hu6800subdcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hu6800subdcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hu6800subdcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hu6800subdcdf/bioconductor-hu6800subdcdf_2.18.0_src_all.tar.gz" +) +MD5="7966c21babb23e18cca4faafc8720f0a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hu6800subdcdf/pre-unlink.sh b/recipes/bioconductor-hu6800subdcdf/pre-unlink.sh new file mode 100644 index 0000000000000..10a2bcb350d76 --- /dev/null +++ b/recipes/bioconductor-hu6800subdcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hu6800subdcdf diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml new file mode 100644 index 0000000000000..7582f6bfbcd13 --- /dev/null +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.1.0" %} +{% set name = "huex.1.0.st.v2frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 982935d07b526ff555790e309fe4147e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.9.2.' + diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh b/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh new file mode 100644 index 0000000000000..838cbc805e61a --- /dev/null +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="huex.1.0.st.v2frmavecs_1.1.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex.1.0.st.v2frmavecs_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/huex.1.0.st.v2frmavecs_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex.1.0.st.v2frmavecs/bioconductor-huex.1.0.st.v2frmavecs_1.1.0_src_all.tar.gz" +) +MD5="982935d07b526ff555790e309fe4147e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huex.1.0.st.v2frmavecs/pre-unlink.sh b/recipes/bioconductor-huex.1.0.st.v2frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..7051afa9125e2 --- /dev/null +++ b/recipes/bioconductor-huex.1.0.st.v2frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ huex.1.0.st.v2frmavecs diff --git a/recipes/bioconductor-huex10stprobeset.db/meta.yaml b/recipes/bioconductor-huex10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..c425fce713d63 --- /dev/null +++ b/recipes/bioconductor-huex10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "huex10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 52cf39820872de4ac5529aa1192328b5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix huex10 annotation data (chip huex10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-huex10stprobeset.db/post-link.sh b/recipes/bioconductor-huex10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..740f0f83686da --- /dev/null +++ b/recipes/bioconductor-huex10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="huex10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/huex10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex10stprobeset.db/bioconductor-huex10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="52cf39820872de4ac5529aa1192328b5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huex10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-huex10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..fe94c43501dde --- /dev/null +++ b/recipes/bioconductor-huex10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ huex10stprobeset.db diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..832a4fc48bb8e --- /dev/null +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "huex10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7fb762002b5792c64ccafbd7bacf92a4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix huex10 annotation data (chip huex10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..5f18eace0a560 --- /dev/null +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="huex10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/huex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/huex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huex10sttranscriptcluster.db/bioconductor-huex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="7fb762002b5792c64ccafbd7bacf92a4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huex10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-huex10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..023a56b93743b --- /dev/null +++ b/recipes/bioconductor-huex10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ huex10sttranscriptcluster.db diff --git a/recipes/bioconductor-huexexonprobesetlocation/meta.yaml b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml new file mode 100644 index 0000000000000..4b096e121b7b5 --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocation/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.15.0" %} +{% set name = "HuExExonProbesetLocation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 11bf1b88d9e90711b4064497f611da4f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' + diff --git a/recipes/bioconductor-huexexonprobesetlocation/post-link.sh b/recipes/bioconductor-huexexonprobesetlocation/post-link.sh new file mode 100644 index 0000000000000..c679be39ecaac --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HuExExonProbesetLocation_1.15.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocation_1.15.0.tar.gz" + "https://bioarchive.galaxyproject.org/HuExExonProbesetLocation_1.15.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocation/bioconductor-huexexonprobesetlocation_1.15.0_src_all.tar.gz" +) +MD5="11bf1b88d9e90711b4064497f611da4f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huexexonprobesetlocation/pre-unlink.sh b/recipes/bioconductor-huexexonprobesetlocation/pre-unlink.sh new file mode 100644 index 0000000000000..f8b65c28a9d04 --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HuExExonProbesetLocation diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml new file mode 100644 index 0000000000000..692d104786df3 --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.0.2" %} +{% set name = "HuExExonProbesetLocationHg18" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bb00b7f5e4db2b04dca5951aa6bd073e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationDbi version 1.8.0. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg18.' + diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh b/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh new file mode 100644 index 0000000000000..21b3015a4040b --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HuExExonProbesetLocationHg18_0.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocationHg18_0.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg18_0.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg18/bioconductor-huexexonprobesetlocationhg18_0.0.2_src_all.tar.gz" +) +MD5="bb00b7f5e4db2b04dca5951aa6bd073e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huexexonprobesetlocationhg18/pre-unlink.sh b/recipes/bioconductor-huexexonprobesetlocationhg18/pre-unlink.sh new file mode 100644 index 0000000000000..bbffc8d3740a7 --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg18/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HuExExonProbesetLocationHg18 diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml new file mode 100644 index 0000000000000..c844b6205656d --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.0.3" %} +{% set name = "HuExExonProbesetLocationHg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1a3843c95c82dc71a043d902961ba33a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationDbi version 1.11.8. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible. Genome release hg19.' + diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh b/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh new file mode 100644 index 0000000000000..5574f462d0508 --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HuExExonProbesetLocationHg19_0.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuExExonProbesetLocationHg19_0.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/HuExExonProbesetLocationHg19_0.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huexexonprobesetlocationhg19/bioconductor-huexexonprobesetlocationhg19_0.0.3_src_all.tar.gz" +) +MD5="1a3843c95c82dc71a043d902961ba33a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huexexonprobesetlocationhg19/pre-unlink.sh b/recipes/bioconductor-huexexonprobesetlocationhg19/pre-unlink.sh new file mode 100644 index 0000000000000..5c45dbcefe3db --- /dev/null +++ b/recipes/bioconductor-huexexonprobesetlocationhg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HuExExonProbesetLocationHg19 diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml new file mode 100644 index 0000000000000..8c395885680de --- /dev/null +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.1.0" %} +{% set name = "hugene.1.0.st.v1frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 711a69e6fa6dd3737a90615222416dfc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.13.0.' + diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh new file mode 100644 index 0000000000000..fcb874a4b59dc --- /dev/null +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene.1.0.st.v1frmavecs/bioconductor-hugene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" +) +MD5="711a69e6fa6dd3737a90615222416dfc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene.1.0.st.v1frmavecs/pre-unlink.sh b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..c05320b65ef5a --- /dev/null +++ b/recipes/bioconductor-hugene.1.0.st.v1frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene.1.0.st.v1frmavecs diff --git a/recipes/bioconductor-hugene10stprobeset.db/meta.yaml b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..d9f9ce18286fa --- /dev/null +++ b/recipes/bioconductor-hugene10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8c138a26b4aa0391edd69ef6abed3247 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene10 annotation data (chip hugene10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene10stprobeset.db/post-link.sh b/recipes/bioconductor-hugene10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..841660800995e --- /dev/null +++ b/recipes/bioconductor-hugene10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stprobeset.db/bioconductor-hugene10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="8c138a26b4aa0391edd69ef6abed3247" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-hugene10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..1799abfbca7d1 --- /dev/null +++ b/recipes/bioconductor-hugene10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene10stprobeset.db diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..e079583c1957e --- /dev/null +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d38c7a0fb26410d420e72c6aacf622ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene10 annotation data (chip hugene10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..c6a1614582e54 --- /dev/null +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10sttranscriptcluster.db/bioconductor-hugene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="d38c7a0fb26410d420e72c6aacf622ad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-hugene10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..469e0301365dc --- /dev/null +++ b/recipes/bioconductor-hugene10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene10sttranscriptcluster.db diff --git a/recipes/bioconductor-hugene10stv1cdf/meta.yaml b/recipes/bioconductor-hugene10stv1cdf/meta.yaml new file mode 100644 index 0000000000000..9382986852961 --- /dev/null +++ b/recipes/bioconductor-hugene10stv1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hugene10stv1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f1fb1c7076ac40b9e709f18e645d6181 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the HuGene-1_0-st-v1.cdf file.' + diff --git a/recipes/bioconductor-hugene10stv1cdf/post-link.sh b/recipes/bioconductor-hugene10stv1cdf/post-link.sh new file mode 100644 index 0000000000000..8e3598454058b --- /dev/null +++ b/recipes/bioconductor-hugene10stv1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene10stv1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stv1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene10stv1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1cdf/bioconductor-hugene10stv1cdf_2.18.0_src_all.tar.gz" +) +MD5="f1fb1c7076ac40b9e709f18e645d6181" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene10stv1cdf/pre-unlink.sh b/recipes/bioconductor-hugene10stv1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..e555e275c385a --- /dev/null +++ b/recipes/bioconductor-hugene10stv1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene10stv1cdf diff --git a/recipes/bioconductor-hugene10stv1probe/meta.yaml b/recipes/bioconductor-hugene10stv1probe/meta.yaml new file mode 100644 index 0000000000000..5745a6c2c8007 --- /dev/null +++ b/recipes/bioconductor-hugene10stv1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "hugene10stv1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6ed3c17dd026acf008658a5994044c62 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was HuGene-1\_0-st-v1\_probe\_tab.' + diff --git a/recipes/bioconductor-hugene10stv1probe/post-link.sh b/recipes/bioconductor-hugene10stv1probe/post-link.sh new file mode 100644 index 0000000000000..6b97c38911d93 --- /dev/null +++ b/recipes/bioconductor-hugene10stv1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene10stv1probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene10stv1probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene10stv1probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene10stv1probe/bioconductor-hugene10stv1probe_2.18.0_src_all.tar.gz" +) +MD5="6ed3c17dd026acf008658a5994044c62" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene10stv1probe/pre-unlink.sh b/recipes/bioconductor-hugene10stv1probe/pre-unlink.sh new file mode 100644 index 0000000000000..a2ddbb86e2775 --- /dev/null +++ b/recipes/bioconductor-hugene10stv1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene10stv1probe diff --git a/recipes/bioconductor-hugene11stprobeset.db/meta.yaml b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..a983289653101 --- /dev/null +++ b/recipes/bioconductor-hugene11stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene11stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 315c1dff0ba5240c6c5432d0dcc11eb1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene11 annotation data (chip hugene11stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene11stprobeset.db/post-link.sh b/recipes/bioconductor-hugene11stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..5917c1a8504f4 --- /dev/null +++ b/recipes/bioconductor-hugene11stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene11stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene11stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene11stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene11stprobeset.db/bioconductor-hugene11stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="315c1dff0ba5240c6c5432d0dcc11eb1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene11stprobeset.db/pre-unlink.sh b/recipes/bioconductor-hugene11stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..dedb05d7c94ee --- /dev/null +++ b/recipes/bioconductor-hugene11stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene11stprobeset.db diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..ebc35c034e3cc --- /dev/null +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene11sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0d366281eac2cba4b1fcfbe48596975a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene11 annotation data (chip hugene11sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..691aeccc0f017 --- /dev/null +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene11sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene11sttranscriptcluster.db/bioconductor-hugene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="0d366281eac2cba4b1fcfbe48596975a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene11sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-hugene11sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..f7824e05ebea7 --- /dev/null +++ b/recipes/bioconductor-hugene11sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene11sttranscriptcluster.db diff --git a/recipes/bioconductor-hugene20stprobeset.db/meta.yaml b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..00ead16f1383f --- /dev/null +++ b/recipes/bioconductor-hugene20stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene20stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 17e599fe0f885f17de29a6174324054d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene20 annotation data (chip hugene20stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene20stprobeset.db/post-link.sh b/recipes/bioconductor-hugene20stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..e52dd27da0589 --- /dev/null +++ b/recipes/bioconductor-hugene20stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene20stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene20stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene20stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene20stprobeset.db/bioconductor-hugene20stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="17e599fe0f885f17de29a6174324054d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene20stprobeset.db/pre-unlink.sh b/recipes/bioconductor-hugene20stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..5f0a7ad2a49b9 --- /dev/null +++ b/recipes/bioconductor-hugene20stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene20stprobeset.db diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..ca5f6e1e25dca --- /dev/null +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene20sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 85b23453d8e7c6c92673deaa7a82e51e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene20 annotation data (chip hugene20sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..993b4c34b82e3 --- /dev/null +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene20sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene20sttranscriptcluster.db/bioconductor-hugene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="85b23453d8e7c6c92673deaa7a82e51e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene20sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-hugene20sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..0a3f86af4de16 --- /dev/null +++ b/recipes/bioconductor-hugene20sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene20sttranscriptcluster.db diff --git a/recipes/bioconductor-hugene21stprobeset.db/meta.yaml b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..886142c6167fa --- /dev/null +++ b/recipes/bioconductor-hugene21stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene21stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ad101fb652b87da23d17547268019bb8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene21 annotation data (chip hugene21stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene21stprobeset.db/post-link.sh b/recipes/bioconductor-hugene21stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..b8f5b85770420 --- /dev/null +++ b/recipes/bioconductor-hugene21stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene21stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene21stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene21stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene21stprobeset.db/bioconductor-hugene21stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="ad101fb652b87da23d17547268019bb8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene21stprobeset.db/pre-unlink.sh b/recipes/bioconductor-hugene21stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..e91099be9ffaf --- /dev/null +++ b/recipes/bioconductor-hugene21stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene21stprobeset.db diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..5170d241edeeb --- /dev/null +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "hugene21sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7d4d913f3e48f3eab45e036323d223b5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix hugene21 annotation data (chip hugene21sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..60f703ac2c110 --- /dev/null +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hugene21sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hugene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/hugene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hugene21sttranscriptcluster.db/bioconductor-hugene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="7d4d913f3e48f3eab45e036323d223b5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hugene21sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-hugene21sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..98fc2ccabfe8a --- /dev/null +++ b/recipes/bioconductor-hugene21sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hugene21sttranscriptcluster.db diff --git a/recipes/bioconductor-human.db0/meta.yaml b/recipes/bioconductor-human.db0/meta.yaml new file mode 100644 index 0000000000000..f52462c189d18 --- /dev/null +++ b/recipes/bioconductor-human.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "human.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e34a53909394d8987f03e57345ab91f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for human, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-human.db0/post-link.sh b/recipes/bioconductor-human.db0/post-link.sh new file mode 100644 index 0000000000000..ee678d0251862 --- /dev/null +++ b/recipes/bioconductor-human.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/human.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human.db0/bioconductor-human.db0_3.7.1_src_all.tar.gz" +) +MD5="e34a53909394d8987f03e57345ab91f5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human.db0/pre-unlink.sh b/recipes/bioconductor-human.db0/pre-unlink.sh new file mode 100644 index 0000000000000..fe7ab4b65432c --- /dev/null +++ b/recipes/bioconductor-human.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human.db0 diff --git a/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml new file mode 100644 index 0000000000000..6f8c43fcdfcbe --- /dev/null +++ b/recipes/bioconductor-human1mduov3bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.4" %} +{% set name = "human1mduov3bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0ff9f1e8bcc6348d6777bbb982ae0325 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 1M Duo arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh b/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh new file mode 100644 index 0000000000000..e518af4ec4607 --- /dev/null +++ b/recipes/bioconductor-human1mduov3bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human1mduov3bCrlmm_1.0.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human1mduov3bCrlmm_1.0.4.tar.gz" + "https://bioarchive.galaxyproject.org/human1mduov3bCrlmm_1.0.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human1mduov3bcrlmm/bioconductor-human1mduov3bcrlmm_1.0.4_src_all.tar.gz" +) +MD5="0ff9f1e8bcc6348d6777bbb982ae0325" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human1mduov3bcrlmm/pre-unlink.sh b/recipes/bioconductor-human1mduov3bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..e2d9e2dd2bbd6 --- /dev/null +++ b/recipes/bioconductor-human1mduov3bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human1mduov3bCrlmm diff --git a/recipes/bioconductor-human1mv1ccrlmm/meta.yaml b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml new file mode 100644 index 0000000000000..639095433b5a1 --- /dev/null +++ b/recipes/bioconductor-human1mv1ccrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "human1mv1cCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b9f638c7b0ede50cb070f1bae85eb4dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata fast genotyping Illumina 1M arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human1mv1ccrlmm/post-link.sh b/recipes/bioconductor-human1mv1ccrlmm/post-link.sh new file mode 100644 index 0000000000000..31a25eee41212 --- /dev/null +++ b/recipes/bioconductor-human1mv1ccrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human1mv1cCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human1mv1cCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/human1mv1cCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human1mv1ccrlmm/bioconductor-human1mv1ccrlmm_1.0.3_src_all.tar.gz" +) +MD5="b9f638c7b0ede50cb070f1bae85eb4dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human1mv1ccrlmm/pre-unlink.sh b/recipes/bioconductor-human1mv1ccrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..2221c03e096bc --- /dev/null +++ b/recipes/bioconductor-human1mv1ccrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human1mv1cCrlmm diff --git a/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml new file mode 100644 index 0000000000000..53d20512e80b1 --- /dev/null +++ b/recipes/bioconductor-human370quadv3ccrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "human370quadv3cCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 33c3ccc3793ed95647418b746a5177f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 370kQuad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh b/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh new file mode 100644 index 0000000000000..cd0816350a5d0 --- /dev/null +++ b/recipes/bioconductor-human370quadv3ccrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human370quadv3cCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human370quadv3cCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/human370quadv3cCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human370quadv3ccrlmm/bioconductor-human370quadv3ccrlmm_1.0.3_src_all.tar.gz" +) +MD5="33c3ccc3793ed95647418b746a5177f9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human370quadv3ccrlmm/pre-unlink.sh b/recipes/bioconductor-human370quadv3ccrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..a318062ca9a31 --- /dev/null +++ b/recipes/bioconductor-human370quadv3ccrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human370quadv3cCrlmm diff --git a/recipes/bioconductor-human370v1ccrlmm/meta.yaml b/recipes/bioconductor-human370v1ccrlmm/meta.yaml new file mode 100644 index 0000000000000..25913a5b016b1 --- /dev/null +++ b/recipes/bioconductor-human370v1ccrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.2" %} +{% set name = "human370v1cCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ec4192f533faee2b14484de02548075 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 370k arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human370v1ccrlmm/post-link.sh b/recipes/bioconductor-human370v1ccrlmm/post-link.sh new file mode 100644 index 0000000000000..18d0d73426068 --- /dev/null +++ b/recipes/bioconductor-human370v1ccrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human370v1cCrlmm_1.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human370v1cCrlmm_1.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/human370v1cCrlmm_1.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human370v1ccrlmm/bioconductor-human370v1ccrlmm_1.0.2_src_all.tar.gz" +) +MD5="9ec4192f533faee2b14484de02548075" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human370v1ccrlmm/pre-unlink.sh b/recipes/bioconductor-human370v1ccrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..c8709c792c2cf --- /dev/null +++ b/recipes/bioconductor-human370v1ccrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human370v1cCrlmm diff --git a/recipes/bioconductor-human550v3bcrlmm/meta.yaml b/recipes/bioconductor-human550v3bcrlmm/meta.yaml new file mode 100644 index 0000000000000..320d2654e202e --- /dev/null +++ b/recipes/bioconductor-human550v3bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.4" %} +{% set name = "human550v3bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 20e6b008fab5e1084354c87ad50d18a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 550k arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human550v3bcrlmm/post-link.sh b/recipes/bioconductor-human550v3bcrlmm/post-link.sh new file mode 100644 index 0000000000000..6d1d215b76df5 --- /dev/null +++ b/recipes/bioconductor-human550v3bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human550v3bCrlmm_1.0.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human550v3bCrlmm_1.0.4.tar.gz" + "https://bioarchive.galaxyproject.org/human550v3bCrlmm_1.0.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human550v3bcrlmm/bioconductor-human550v3bcrlmm_1.0.4_src_all.tar.gz" +) +MD5="20e6b008fab5e1084354c87ad50d18a8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human550v3bcrlmm/pre-unlink.sh b/recipes/bioconductor-human550v3bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..4e0bcba9fd9c1 --- /dev/null +++ b/recipes/bioconductor-human550v3bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human550v3bCrlmm diff --git a/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml new file mode 100644 index 0000000000000..5966f0123cbce --- /dev/null +++ b/recipes/bioconductor-human610quadv1bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "human610quadv1bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 609cf09410774e084ee6a3286652bb1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 610kQuad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh b/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh new file mode 100644 index 0000000000000..471605a515a7e --- /dev/null +++ b/recipes/bioconductor-human610quadv1bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human610quadv1bCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human610quadv1bCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/human610quadv1bCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human610quadv1bcrlmm/bioconductor-human610quadv1bcrlmm_1.0.3_src_all.tar.gz" +) +MD5="609cf09410774e084ee6a3286652bb1a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human610quadv1bcrlmm/pre-unlink.sh b/recipes/bioconductor-human610quadv1bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..4f9beee52c567 --- /dev/null +++ b/recipes/bioconductor-human610quadv1bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human610quadv1bCrlmm diff --git a/recipes/bioconductor-human650v3acrlmm/meta.yaml b/recipes/bioconductor-human650v3acrlmm/meta.yaml new file mode 100644 index 0000000000000..ae0766acf461e --- /dev/null +++ b/recipes/bioconductor-human650v3acrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "human650v3aCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4b0de367ccc0f7499dcffe21ef1893c2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 650k arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human650v3acrlmm/post-link.sh b/recipes/bioconductor-human650v3acrlmm/post-link.sh new file mode 100644 index 0000000000000..c1d785c012602 --- /dev/null +++ b/recipes/bioconductor-human650v3acrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human650v3aCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human650v3aCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/human650v3aCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human650v3acrlmm/bioconductor-human650v3acrlmm_1.0.3_src_all.tar.gz" +) +MD5="4b0de367ccc0f7499dcffe21ef1893c2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human650v3acrlmm/pre-unlink.sh b/recipes/bioconductor-human650v3acrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..6a329c46dc4e7 --- /dev/null +++ b/recipes/bioconductor-human650v3acrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human650v3aCrlmm diff --git a/recipes/bioconductor-human660quadv1acrlmm/meta.yaml b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml new file mode 100644 index 0000000000000..d668d2c7ad048 --- /dev/null +++ b/recipes/bioconductor-human660quadv1acrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "human660quadv1aCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5fd2d94a462e150c888f13c5c0975c36 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina 660kQuad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-human660quadv1acrlmm/post-link.sh b/recipes/bioconductor-human660quadv1acrlmm/post-link.sh new file mode 100644 index 0000000000000..99899f2226e1a --- /dev/null +++ b/recipes/bioconductor-human660quadv1acrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="human660quadv1aCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/human660quadv1aCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/human660quadv1aCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-human660quadv1acrlmm/bioconductor-human660quadv1acrlmm_1.0.3_src_all.tar.gz" +) +MD5="5fd2d94a462e150c888f13c5c0975c36" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-human660quadv1acrlmm/pre-unlink.sh b/recipes/bioconductor-human660quadv1acrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..ead580cef681b --- /dev/null +++ b/recipes/bioconductor-human660quadv1acrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ human660quadv1aCrlmm diff --git a/recipes/bioconductor-humanaffydata/meta.yaml b/recipes/bioconductor-humanaffydata/meta.yaml new file mode 100644 index 0000000000000..71a0c0253f13d --- /dev/null +++ b/recipes/bioconductor-humanaffydata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.8.0" %} +{% set name = "HumanAffyData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dfe3425fce62815fdd066bd003bfb4d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Re-analysis of human gene expression data generated on the Affymetrix HG U133PlusV2 (EH176) and Affymetrix HG U133A (EH177) platforms. The original data were normalized using robust multiarray averaging (RMA) to obtain an integrated gene expression atlas across diverse biological sample types and conditions. The entire compendia comprisee 9395 arrays for EH176 and 5372 arrays for EH177.' + diff --git a/recipes/bioconductor-humanaffydata/post-link.sh b/recipes/bioconductor-humanaffydata/post-link.sh new file mode 100644 index 0000000000000..09de247d325bb --- /dev/null +++ b/recipes/bioconductor-humanaffydata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HumanAffyData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/HumanAffyData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/HumanAffyData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanaffydata/bioconductor-humanaffydata_1.8.0_src_all.tar.gz" +) +MD5="dfe3425fce62815fdd066bd003bfb4d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanaffydata/pre-unlink.sh b/recipes/bioconductor-humanaffydata/pre-unlink.sh new file mode 100644 index 0000000000000..9b882d6c4b996 --- /dev/null +++ b/recipes/bioconductor-humanaffydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HumanAffyData diff --git a/recipes/bioconductor-humanchrloc/meta.yaml b/recipes/bioconductor-humanchrloc/meta.yaml new file mode 100644 index 0000000000000..15a7bd98eee31 --- /dev/null +++ b/recipes/bioconductor-humanchrloc/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.1.6" %} +{% set name = "humanCHRLOC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 113450c0822000c9b4e8a0141cf4b819 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'Annotation data file for humanCHRLOC assembled using data from public data repositories' + diff --git a/recipes/bioconductor-humanchrloc/post-link.sh b/recipes/bioconductor-humanchrloc/post-link.sh new file mode 100644 index 0000000000000..b5e4f2cbe5e79 --- /dev/null +++ b/recipes/bioconductor-humanchrloc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanCHRLOC_2.1.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanCHRLOC_2.1.6.tar.gz" + "https://bioarchive.galaxyproject.org/humanCHRLOC_2.1.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanchrloc/bioconductor-humanchrloc_2.1.6_src_all.tar.gz" +) +MD5="113450c0822000c9b4e8a0141cf4b819" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanchrloc/pre-unlink.sh b/recipes/bioconductor-humanchrloc/pre-unlink.sh new file mode 100644 index 0000000000000..e08dd58f95c29 --- /dev/null +++ b/recipes/bioconductor-humanchrloc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanCHRLOC diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml new file mode 100644 index 0000000000000..32430d9c4ca84 --- /dev/null +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.1" %} +{% set name = "humancytosnp12v2p1hCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: edf80245ddb28afb9fbaa6668187bf3a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina CytoSNP 12 arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh new file mode 100644 index 0000000000000..32ca50f70c929 --- /dev/null +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/humancytosnp12v2p1hCrlmm_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humancytosnp12v2p1hcrlmm/bioconductor-humancytosnp12v2p1hcrlmm_1.0.1_src_all.tar.gz" +) +MD5="edf80245ddb28afb9fbaa6668187bf3a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humancytosnp12v2p1hcrlmm/pre-unlink.sh b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..0a760c4a61c02 --- /dev/null +++ b/recipes/bioconductor-humancytosnp12v2p1hcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humancytosnp12v2p1hCrlmm diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml new file mode 100644 index 0000000000000..92395b4249dc4 --- /dev/null +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.3" %} +{% set name = "humanomni1quadv1bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e81b2603f37d4cda3f28cd69a7296a23 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina Omni1 Quad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh new file mode 100644 index 0000000000000..2683ea367ee42 --- /dev/null +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanomni1quadv1bCrlmm_1.0.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni1quadv1bCrlmm_1.0.3.tar.gz" + "https://bioarchive.galaxyproject.org/humanomni1quadv1bCrlmm_1.0.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni1quadv1bcrlmm/bioconductor-humanomni1quadv1bcrlmm_1.0.3_src_all.tar.gz" +) +MD5="e81b2603f37d4cda3f28cd69a7296a23" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanomni1quadv1bcrlmm/pre-unlink.sh b/recipes/bioconductor-humanomni1quadv1bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..a947caf69ff41 --- /dev/null +++ b/recipes/bioconductor-humanomni1quadv1bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanomni1quadv1bCrlmm diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml new file mode 100644 index 0000000000000..683e2ecd110f7 --- /dev/null +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.2" %} +{% set name = "humanomni25quadv1bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2ee1fa7bf712d7f81a167079c975d49f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina Omni2.5 Quad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh new file mode 100644 index 0000000000000..dd604ca05dd13 --- /dev/null +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanomni25quadv1bCrlmm_1.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni25quadv1bCrlmm_1.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/humanomni25quadv1bCrlmm_1.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni25quadv1bcrlmm/bioconductor-humanomni25quadv1bcrlmm_1.0.2_src_all.tar.gz" +) +MD5="2ee1fa7bf712d7f81a167079c975d49f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanomni25quadv1bcrlmm/pre-unlink.sh b/recipes/bioconductor-humanomni25quadv1bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..3c82e74d48db6 --- /dev/null +++ b/recipes/bioconductor-humanomni25quadv1bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanomni25quadv1bCrlmm diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml new file mode 100644 index 0000000000000..57393d552fad5 --- /dev/null +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.0" %} +{% set name = "humanomni5quadv1bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3ac4d6867c3d5590a6308d6edff0912b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina Omni5 Quad arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh b/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh new file mode 100644 index 0000000000000..63ae406e36b5d --- /dev/null +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanomni5quadv1bCrlmm_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomni5quadv1bCrlmm_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/humanomni5quadv1bCrlmm_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomni5quadv1bcrlmm/bioconductor-humanomni5quadv1bcrlmm_1.0.0_src_all.tar.gz" +) +MD5="3ac4d6867c3d5590a6308d6edff0912b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanomni5quadv1bcrlmm/pre-unlink.sh b/recipes/bioconductor-humanomni5quadv1bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..444d8a0f9f9ae --- /dev/null +++ b/recipes/bioconductor-humanomni5quadv1bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanomni5quadv1bCrlmm diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml new file mode 100644 index 0000000000000..d8c5b4dd12cd9 --- /dev/null +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.1" %} +{% set name = "humanomniexpress12v1bCrlmm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: abdb730fc230db669e588e024ee7624b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package with metadata for genotyping Illumina Omni Express 12 arrays using the ''crlmm'' package.' + diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh b/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh new file mode 100644 index 0000000000000..b232aec3bfa92 --- /dev/null +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanomniexpress12v1bCrlmm_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/humanomniexpress12v1bCrlmm_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/humanomniexpress12v1bCrlmm_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanomniexpress12v1bcrlmm/bioconductor-humanomniexpress12v1bcrlmm_1.0.1_src_all.tar.gz" +) +MD5="abdb730fc230db669e588e024ee7624b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanomniexpress12v1bcrlmm/pre-unlink.sh b/recipes/bioconductor-humanomniexpress12v1bcrlmm/pre-unlink.sh new file mode 100644 index 0000000000000..bbbecb950ccff --- /dev/null +++ b/recipes/bioconductor-humanomniexpress12v1bcrlmm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanomniexpress12v1bCrlmm diff --git a/recipes/bioconductor-humanstemcell/meta.yaml b/recipes/bioconductor-humanstemcell/meta.yaml new file mode 100644 index 0000000000000..894f7e1532d08 --- /dev/null +++ b/recipes/bioconductor-humanstemcell/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.22.0" %} +{% set name = "humanStemCell" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c51c8672331f6416b56f0224b5e7494 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix time course experiment on human stem cells (two time points: undifferentiated and differentiated).' + diff --git a/recipes/bioconductor-humanstemcell/post-link.sh b/recipes/bioconductor-humanstemcell/post-link.sh new file mode 100644 index 0000000000000..c215c2bba704f --- /dev/null +++ b/recipes/bioconductor-humanstemcell/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="humanStemCell_0.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/humanStemCell_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/humanStemCell_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-humanstemcell/bioconductor-humanstemcell_0.22.0_src_all.tar.gz" +) +MD5="9c51c8672331f6416b56f0224b5e7494" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-humanstemcell/pre-unlink.sh b/recipes/bioconductor-humanstemcell/pre-unlink.sh new file mode 100644 index 0000000000000..efbd421350bcb --- /dev/null +++ b/recipes/bioconductor-humanstemcell/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ humanStemCell diff --git a/recipes/bioconductor-huo22.db/meta.yaml b/recipes/bioconductor-huo22.db/meta.yaml new file mode 100644 index 0000000000000..85a08ebd8f0d6 --- /dev/null +++ b/recipes/bioconductor-huo22.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "HuO22.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ddabf6c01f94c1dfd6ab35b40852828a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Genomics Shared Resource HuO22 Annotation Data (HuO22) assembled using data from public repositories' + diff --git a/recipes/bioconductor-huo22.db/post-link.sh b/recipes/bioconductor-huo22.db/post-link.sh new file mode 100644 index 0000000000000..0db267ca18a94 --- /dev/null +++ b/recipes/bioconductor-huo22.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="HuO22.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/HuO22.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/HuO22.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-huo22.db/bioconductor-huo22.db_3.2.3_src_all.tar.gz" +) +MD5="ddabf6c01f94c1dfd6ab35b40852828a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-huo22.db/pre-unlink.sh b/recipes/bioconductor-huo22.db/pre-unlink.sh new file mode 100644 index 0000000000000..3c951162ec94a --- /dev/null +++ b/recipes/bioconductor-huo22.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ HuO22.db diff --git a/recipes/bioconductor-hwgcod.db/meta.yaml b/recipes/bioconductor-hwgcod.db/meta.yaml new file mode 100644 index 0000000000000..c26f4d9f8cf51 --- /dev/null +++ b/recipes/bioconductor-hwgcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "hwgcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a46bf1a242853bbab26351a11b18030a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Human Whole Genome Bioarray (~55 000 human genes) annotation data (chip hwgcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-hwgcod.db/post-link.sh b/recipes/bioconductor-hwgcod.db/post-link.sh new file mode 100644 index 0000000000000..4c399353cef52 --- /dev/null +++ b/recipes/bioconductor-hwgcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="hwgcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/hwgcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/hwgcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-hwgcod.db/bioconductor-hwgcod.db_3.4.0_src_all.tar.gz" +) +MD5="a46bf1a242853bbab26351a11b18030a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-hwgcod.db/pre-unlink.sh b/recipes/bioconductor-hwgcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..05b1f73b01432 --- /dev/null +++ b/recipes/bioconductor-hwgcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ hwgcod.db diff --git a/recipes/bioconductor-hybridmtest/build.sh b/recipes/bioconductor-hybridmtest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hybridmtest/build.sh +++ b/recipes/bioconductor-hybridmtest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hybridmtest/meta.yaml b/recipes/bioconductor-hybridmtest/meta.yaml index 5ef1474b28b12..644a3b5662700 100644 --- a/recipes/bioconductor-hybridmtest/meta.yaml +++ b/recipes/bioconductor-hybridmtest/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "HybridMTest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ed79e3d2df7e52193e251efbe5ed5b62380fcf5b0340776c0036ca084bef9251 + md5: 37e8b32af15775b684fd95f27b08a29c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fdrtool - r-mass - r-survival run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fdrtool - r-mass @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL Version 2 or later' summary: 'Performs hybrid multiple testing that incorporates method selection and assumption evaluations into the analysis using empirical Bayes probability (EBP) estimates obtained by Grenander density estimation. For instance, for 3-group comparison analysis, Hybrid Multiple testing considers EBPs as weighted EBPs between F-test and H-test with EBPs from Shapiro Wilk test of normality as weigth. Instead of just using EBPs from F-test only or using H-test only, this methodology combines both types of EBPs through EBPs from Shapiro Wilk test of normality. This methodology uses then the law of total EBPs.' extra: identifiers: - biotools:hybridmtest - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hybridmtest + path: recipes/bioconductor-hybridmtest + version: 1.24.0 + diff --git a/recipes/bioconductor-hyperdraw/build.sh b/recipes/bioconductor-hyperdraw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hyperdraw/build.sh +++ b/recipes/bioconductor-hyperdraw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hyperdraw/meta.yaml b/recipes/bioconductor-hyperdraw/meta.yaml index 36dc7ecb8ab78..6afe94a0a5d56 100644 --- a/recipes/bioconductor-hyperdraw/meta.yaml +++ b/recipes/bioconductor-hyperdraw/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "hyperdraw" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecc1fc2a682b262eb72d80d8ace1159c1a1a8c99a7fa93c63c3dae2bb75e8ece + md5: 585067dc2db3c0ccf3d69733092811c8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# SystemRequirements: graphviz requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions for visualizing hypergraphs.' extra: identifiers: - biotools:hyperdraw - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hyperdraw + path: recipes/bioconductor-hyperdraw + version: 1.32.0 + diff --git a/recipes/bioconductor-hypergraph/build.sh b/recipes/bioconductor-hypergraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-hypergraph/build.sh +++ b/recipes/bioconductor-hypergraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-hypergraph/meta.yaml b/recipes/bioconductor-hypergraph/meta.yaml index 9629da00621c8..694a64f0e500d 100644 --- a/recipes/bioconductor-hypergraph/meta.yaml +++ b/recipes/bioconductor-hypergraph/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "hypergraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 35d530dd00739ac6a5d39aaec79b88c3088535cb94850091a2404dc278cac0fe + md5: f26b3809c03897878b51a9f9e7fd11a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that implements some simple capabilities for representing and manipulating hypergraphs.' extra: identifiers: - biotools:hypergraph - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-hypergraph + path: recipes/bioconductor-hypergraph + version: 1.52.0 + diff --git a/recipes/bioconductor-iaseq/build.sh b/recipes/bioconductor-iaseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iaseq/build.sh +++ b/recipes/bioconductor-iaseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iaseq/meta.yaml b/recipes/bioconductor-iaseq/meta.yaml index ff2503f36762a..a84700abd0cea 100644 --- a/recipes/bioconductor-iaseq/meta.yaml +++ b/recipes/bioconductor-iaseq/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "iASeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5bc4b06bc9a00541500f59b47ea69ca649a06f6893f5c6d70e29e2a537ba93fb + md5: e6b9e4315f60d5530a2ed3985e9da304 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'It fits correlation motif model to multiple RNAseq or ChIPseq studies to improve detection of allele-specific events and describe correlation patterns across studies.' extra: identifiers: - biotools:iaseq - doi:10.1186/1471-2164-13-681 + parent_recipe: + name: bioconductor-iaseq + path: recipes/bioconductor-iaseq + version: 1.24.0 + diff --git a/recipes/bioconductor-iasva/build.sh b/recipes/bioconductor-iasva/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iasva/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iasva/meta.yaml b/recipes/bioconductor-iasva/meta.yaml new file mode 100644 index 0000000000000..7ed350accb157 --- /dev/null +++ b/recipes/bioconductor-iasva/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "iasva" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2e7572ca526ebf0b88442e25908ed305 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, rmarkdown, sva, Rtsne, pheatmap, corrplot, DescTools, RColorBrewer +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-irlba + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-irlba +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Iteratively Adjusted Surrogate Variable Analysis (IA-SVA) is a statistical framework to uncover hidden sources of variation even when these sources are correlated. IA-SVA provides a flexible methodology to i) identify a hidden factor for unwanted heterogeneity while adjusting for all known factors; ii) test the significance of the putative hidden factor for explaining the unmodeled variation in the data; and iii), if significant, use the estimated factor as an additional known factor in the next iteration to uncover further hidden factors.' + diff --git a/recipes/bioconductor-ibbig/build.sh b/recipes/bioconductor-ibbig/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ibbig/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ibbig/meta.yaml b/recipes/bioconductor-ibbig/meta.yaml new file mode 100644 index 0000000000000..13deb6e5be674 --- /dev/null +++ b/recipes/bioconductor-ibbig/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.26.0" %} +{% set name = "iBBiG" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a8d9db691a24a412fd0e1bbbd10e635b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: methods +requirements: + host: + - r-ade4 + - r-base + - r-biclust + - r-xtable + run: + - r-ade4 + - r-base + - r-biclust + - r-xtable + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'iBBiG is a bi-clustering algorithm which is optimizes for binary data analysis. We apply it to meta-gene set analysis of large numbers of gene expression datasets. The iterative algorithm extracts groups of phenotypes from multiple studies that are associated with similar gene sets. iBBiG does not require prior knowledge of the number or scale of clusters and allows discovery of clusters with diverse sizes' + diff --git a/recipes/bioconductor-ibh/build.sh b/recipes/bioconductor-ibh/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ibh/build.sh +++ b/recipes/bioconductor-ibh/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ibh/meta.yaml b/recipes/bioconductor-ibh/meta.yaml index 049a252ec16f3..6c78dcd5fc07b 100644 --- a/recipes/bioconductor-ibh/meta.yaml +++ b/recipes/bioconductor-ibh/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "ibh" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dfa0ff19dcc58c02413ebbb59e861f732bea30cd02baf4391f44569c549490ce + md5: 2f9f043d554d46a1ce0146c3b59d556a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: yeastCC, stats requirements: host: - - 'bioconductor-simpintlists >=1.16.0,<1.18.0' + - 'bioconductor-simpintlists >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-simpintlists >=1.16.0,<1.18.0' + - 'bioconductor-simpintlists >=1.18.0,<1.19.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains methods for calculating Interaction Based Homogeneity to evaluate fitness of gene lists to an interaction network which is useful for evaluation of clustering results and gene list analysis. BioGRID interactions are used in the calculation. The user can also provide their own interactions.' extra: identifiers: - biotools:ibh - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ibh + path: recipes/bioconductor-ibh + version: 1.28.0 + diff --git a/recipes/bioconductor-ibmq/build.sh b/recipes/bioconductor-ibmq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ibmq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ibmq/meta.yaml b/recipes/bioconductor-ibmq/meta.yaml new file mode 100644 index 0000000000000..82e5c44645ac5 --- /dev/null +++ b/recipes/bioconductor-ibmq/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.22.0" %} +{% set name = "iBMQ" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 18f8a0260516df35cf64a3dc6d8cf403 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# SystemRequirements: GSL and OpenMP +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-ggplot2 >=0.9.2' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-ggplot2 >=0.9.2' + build: + - {{ compiler('c') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'integrated Bayesian Modeling of eQTL data' + diff --git a/recipes/bioconductor-icare/build.sh b/recipes/bioconductor-icare/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-icare/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icare/meta.yaml b/recipes/bioconductor-icare/meta.yaml new file mode 100644 index 0000000000000..76e020f045763 --- /dev/null +++ b/recipes/bioconductor-icare/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.10.2" %} +{% set name = "iCARE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c450b066a76a00c07fba5ec1475518d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + - r-gtools + - r-hmisc + - r-plotrix + run: + - r-base + - r-gtools + - r-hmisc + - r-plotrix + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'An R package to compute Individualized Coherent Absolute Risk Estimators.' + diff --git a/recipes/bioconductor-icens/build.sh b/recipes/bioconductor-icens/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-icens/build.sh +++ b/recipes/bioconductor-icens/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icens/meta.yaml b/recipes/bioconductor-icens/meta.yaml index 05d6f4e2f5da0..6598ebcaab361 100644 --- a/recipes/bioconductor-icens/meta.yaml +++ b/recipes/bioconductor-icens/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "Icens" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 74bc104fb871de276531fabef56643d2e2a05bcb3feec3077865a558b92a78f7 + md5: 6b85482eca0f13261be84bae8285c419 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Many functions for computing the NPMLE for censored and truncated data.' extra: identifiers: - biotools:icens - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-icens + path: recipes/bioconductor-icens + version: 1.52.0 + diff --git a/recipes/bioconductor-icetea/build.sh b/recipes/bioconductor-icetea/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-icetea/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icetea/meta.yaml b/recipes/bioconductor-icetea/meta.yaml new file mode 100644 index 0000000000000..1fa24f86176f6 --- /dev/null +++ b/recipes/bioconductor-icetea/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "icetea" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0c4660744294e5b10e06637c30e7962f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, Rsubread (>= 1.29.0), testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.4.0,<3.5.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene >=3.4.0,<3.5.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'icetea (Integrating Cap Enrichment with Transcript Expression Analysis) provides functions for end-to-end analysis of multiple 5''-profiling methods such as CAGE, RAMPAGE and MAPCap, beginning from raw reads to detection of transcription start sites using replicates. It also allows performing differential TSS detection between group of samples, therefore, integrating the mRNA cap enrichment information with transcript expression analysis.' + diff --git a/recipes/bioconductor-icheck/build.sh b/recipes/bioconductor-icheck/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-icheck/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icheck/meta.yaml b/recipes/bioconductor-icheck/meta.yaml new file mode 100644 index 0000000000000..8f61be2995602 --- /dev/null +++ b/recipes/bioconductor-icheck/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.12.0" %} +{% set name = "iCheck" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e13b3395b8c803eb0f0f12b16ef9c9f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geneselectmmd >=2.26.0,<2.27.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-gplots + - r-lmtest + - r-mass + - r-randomforest + - r-rgl + - r-scatterplot3d + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geneselectmmd >=2.26.0,<2.27.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-gplots + - r-lmtest + - r-mass + - r-randomforest + - r-rgl + - r-scatterplot3d +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'QC pipeline and data analysis tools for high-dimensional Illumina mRNA expression data.' + diff --git a/recipes/bioconductor-ichip/build.sh b/recipes/bioconductor-ichip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ichip/build.sh +++ b/recipes/bioconductor-ichip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ichip/meta.yaml b/recipes/bioconductor-ichip/meta.yaml index 6bbce08657571..dff1c5d3566b8 100644 --- a/recipes/bioconductor-ichip/meta.yaml +++ b/recipes/bioconductor-ichip/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "iChip" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9230c90087696bb4d35f0e9221b2f288a30da0b398f01614270d2e41c9189342 + md5: db251b763a1f7693401bcb60141bef87 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'This package uses hidden Ising models to identify enriched genomic regions in ChIP-chip data. It can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.' + summary: 'Hidden Ising models are implemented to identify enriched genomic regions in ChIP-chip data. They can be used to analyze the data from multiple platforms (e.g., Affymetrix, Agilent, and NimbleGen), and the data with single to multiple replicates.' extra: identifiers: - biotools:ichip - doi:10.1093/bioinformatics/btq032 + parent_recipe: + name: bioconductor-ichip + path: recipes/bioconductor-ichip + version: 1.34.0 + diff --git a/recipes/bioconductor-iclusterplus/build.sh b/recipes/bioconductor-iclusterplus/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iclusterplus/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iclusterplus/meta.yaml b/recipes/bioconductor-iclusterplus/meta.yaml new file mode 100644 index 0000000000000..81acd6732ffb0 --- /dev/null +++ b/recipes/bioconductor-iclusterplus/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.18.0" %} +{% set name = "iClusterPlus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 651bb943711a5b111ac411d248784f84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Integrative clustering of multiple genomic data using a joint latent variable model.' + diff --git a/recipes/bioconductor-icnv/build.sh b/recipes/bioconductor-icnv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-icnv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icnv/meta.yaml b/recipes/bioconductor-icnv/meta.yaml new file mode 100644 index 0000000000000..86ec5e6c2224d --- /dev/null +++ b/recipes/bioconductor-icnv/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "iCNV" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c140064422b14e8c35b3a815f93ea945 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, WES.1KG.WUGSC +requirements: + host: + - 'bioconductor-codex >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-dplyr + - r-fields + - r-ggplot2 + - r-rlang + - r-tidyr + - r-truncnorm + run: + - 'bioconductor-codex >=1.14.0,<1.15.0' + - r-base + - r-data.table + - r-dplyr + - r-fields + - r-ggplot2 + - r-rlang + - r-tidyr + - r-truncnorm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Integrative copy number variation (CNV) detection from multiple platform and experimental design.' + diff --git a/recipes/bioconductor-icobra/build.sh b/recipes/bioconductor-icobra/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-icobra/build.sh +++ b/recipes/bioconductor-icobra/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-icobra/meta.yaml b/recipes/bioconductor-icobra/meta.yaml index 4064a76a4fc30..f19558833aef2 100644 --- a/recipes/bioconductor-icobra/meta.yaml +++ b/recipes/bioconductor-icobra/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "iCOBRA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 47bae461e90a3dbf971c96bc2a545fa4957d1c8149005e1c55b8cf191eb83339 + md5: 144995f01f0fd56500c6d211ae072a31 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-dt @@ -31,7 +33,7 @@ requirements: - r-shinydashboard - r-upsetr run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dplyr - r-dt @@ -47,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package provides functions for calculation and visualization of performance metrics for evaluation of ranking and binary classification (assignment) methods. It also contains a shiny application for interactive exploration of results.' extra: identifiers: - biotools:icobra + parent_recipe: + name: bioconductor-icobra + path: recipes/bioconductor-icobra + version: 1.8.0 + diff --git a/recipes/bioconductor-ideal/build.sh b/recipes/bioconductor-ideal/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ideal/build.sh +++ b/recipes/bioconductor-ideal/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ideal/meta.yaml b/recipes/bioconductor-ideal/meta.yaml index 5318385622a52..2f4aa8929b063 100644 --- a/recipes/bioconductor-ideal/meta.yaml +++ b/recipes/bioconductor-ideal/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "ideal" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c5f3d116a78fc815cd99dd4b7b7640b0b7db3ad046cc26b92de3d75319aabc77 + md5: 33ff8c3c3257c04588768124494540da build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, airway, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, DEFormats, edgeR requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-ihw >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pcaexplorer >=2.6.0,<2.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-ihw >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pcaexplorer >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-d3heatmap - r-dplyr @@ -40,7 +42,6 @@ requirements: - r-gplots - r-knitr - r-pheatmap - - r-plyr - r-rentrez - r-rintrojs - r-rmarkdown @@ -51,20 +52,20 @@ requirements: - r-stringr - r-upsetr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-ihw >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pcaexplorer >=2.6.0,<2.8.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-ihw >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pcaexplorer >=2.8.0,<2.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-d3heatmap - r-dplyr @@ -73,7 +74,6 @@ requirements: - r-gplots - r-knitr - r-pheatmap - - r-plyr - r-rentrez - r-rintrojs - r-rmarkdown @@ -87,8 +87,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides functions for an Interactive Differential Expression AnaLysis of RNA-sequencing datasets, to extract quickly and effectively information downstream the step of differential expression. A Shiny application encapsulates the whole package.' - +extra: + parent_recipe: + name: bioconductor-ideal + path: recipes/bioconductor-ideal + version: 1.4.0 diff --git a/recipes/bioconductor-ideoviz/build.sh b/recipes/bioconductor-ideoviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ideoviz/build.sh +++ b/recipes/bioconductor-ideoviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ideoviz/meta.yaml b/recipes/bioconductor-ideoviz/meta.yaml index 633af7f0f97c2..20223a99ed3df 100644 --- a/recipes/bioconductor-ideoviz/meta.yaml +++ b/recipes/bioconductor-ideoviz/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "IdeoViz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9fb75f79df3b3f9ae2603fcceb12a9657842124e22c4f035f26246e86710a17e + md5: 9dc076de1e7d704ef8f359bc184c1b84 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-rcolorbrewer test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Plots data associated with arbitrary genomic intervals along chromosomal ideogram.' extra: identifiers: - biotools:ideoviz - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ideoviz + path: recipes/bioconductor-ideoviz + version: 1.16.0 + diff --git a/recipes/bioconductor-idiogram/build.sh b/recipes/bioconductor-idiogram/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-idiogram/build.sh +++ b/recipes/bioconductor-idiogram/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-idiogram/meta.yaml b/recipes/bioconductor-idiogram/meta.yaml index 5c6e7f7c1cb7d..bb3d221fe364d 100644 --- a/recipes/bioconductor-idiogram/meta.yaml +++ b/recipes/bioconductor-idiogram/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "idiogram" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d7ae785f13ac7270f927561a16703209e26c822f2682dca2783b789702911e0d + md5: d066bd7ee141691de135e4b6a5aebdda build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hu6800.db, hgu95av2.db, golubEsets requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-plotrix run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-plotrix test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A package for plotting genomic data by chromosomal location' extra: identifiers: - biotools:idiogram - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-idiogram + path: recipes/bioconductor-idiogram + version: 1.56.0 + diff --git a/recipes/bioconductor-idmappinganalysis/build.sh b/recipes/bioconductor-idmappinganalysis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-idmappinganalysis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-idmappinganalysis/meta.yaml b/recipes/bioconductor-idmappinganalysis/meta.yaml new file mode 100644 index 0000000000000..63b5a92f02c84 --- /dev/null +++ b/recipes/bioconductor-idmappinganalysis/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.26.0" %} +{% set name = "IdMappingAnalysis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c8890afd6e21106448dc0d3bc8b4d50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-boot + - r-mclust + - 'r-r.oo >=1.13.0' + - r-rchoicedialogs + - r-rcolorbrewer + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-boot + - r-mclust + - 'r-r.oo >=1.13.0' + - r-rchoicedialogs + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identifier mapping performance analysis' + diff --git a/recipes/bioconductor-idmappingretrieval/build.sh b/recipes/bioconductor-idmappingretrieval/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-idmappingretrieval/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-idmappingretrieval/meta.yaml b/recipes/bioconductor-idmappingretrieval/meta.yaml new file mode 100644 index 0000000000000..a72ebccf2f476 --- /dev/null +++ b/recipes/bioconductor-idmappingretrieval/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.30.0" %} +{% set name = "IdMappingRetrieval" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7da2fe9ac3cf79adc91f06e3a343cf86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affycompatible >=1.42.0,<1.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-envisionquery >=1.30.0,<1.31.0' + - r-base + - r-r.methodss3 + - r-r.oo + - r-rchoicedialogs + - r-rcurl + - r-xml + run: + - 'bioconductor-affycompatible >=1.42.0,<1.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-envisionquery >=1.30.0,<1.31.0' + - r-base + - r-r.methodss3 + - r-r.oo + - r-rchoicedialogs + - r-rcurl + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Data retrieval for identifier mapping performance analysis' + diff --git a/recipes/bioconductor-igc/build.sh b/recipes/bioconductor-igc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-igc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-igc/meta.yaml b/recipes/bioconductor-igc/meta.yaml new file mode 100644 index 0000000000000..68c56a26cda44 --- /dev/null +++ b/recipes/bioconductor-igc/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.12.0" %} +{% set name = "iGC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1914525e82325febd676e0700ec780e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + - r-data.table + - r-plyr + run: + - r-base + - r-data.table + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package is intended to identify differentially expressed genes driven by Copy Number Alterations from samples with both gene expression and CNA data.' + diff --git a/recipes/bioconductor-igvr/build.sh b/recipes/bioconductor-igvr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-igvr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-igvr/meta.yaml b/recipes/bioconductor-igvr/meta.yaml new file mode 100644 index 0000000000000..9beb8b4aa0501 --- /dev/null +++ b/recipes/bioconductor-igvr/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "igvR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9e2eac0566ea2b2810e66375f24c9917 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-browserviz >=2.4.0,<2.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-httpuv + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-browserviz >=2.4.0,<2.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-httpuv +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Access to igv.js, the Integrative Genomics Viewer running in a web browser.' + diff --git a/recipes/bioconductor-ihw/build.sh b/recipes/bioconductor-ihw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ihw/build.sh +++ b/recipes/bioconductor-ihw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ihw/meta.yaml b/recipes/bioconductor-ihw/meta.yaml index 23de3cae91305..8363e5f91efbb 100644 --- a/recipes/bioconductor-ihw/meta.yaml +++ b/recipes/bioconductor-ihw/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "IHW" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5127685a6aba22ff330415c45feb4c80de3021c75c2665406c063d8a27f3da4e + md5: 70fb102a4fb16b6bee1fbb925588957c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ggplot2, dplyr, gridExtra, scales, DESeq2, airway, testthat, Matrix, BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-lpsymphony >=1.8.0,<1.10.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-lpsymphony >=1.10.0,<1.11.0' - r-base - r-fdrtool - r-slam run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-lpsymphony >=1.8.0,<1.10.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-lpsymphony >=1.10.0,<1.11.0' - r-base - r-fdrtool - r-slam @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Independent hypothesis weighting (IHW) is a multiple testing procedure that increases power compared to the method of Benjamini and Hochberg by assigning data-driven weights to each hypothesis. The input to IHW is a two-column table of p-values and covariates. The covariate can be any continuous-valued or categorical variable that is thought to be informative on the statistical properties of each hypothesis test, while it is independent of the p-value under the null hypothesis.' extra: identifiers: - biotools:IHW - doi:10.1038/nmeth.3885 + parent_recipe: + name: bioconductor-ihw + path: recipes/bioconductor-ihw + version: 1.8.0 + diff --git a/recipes/bioconductor-ihwpaper/meta.yaml b/recipes/bioconductor-ihwpaper/meta.yaml new file mode 100644 index 0000000000000..487797b375f0b --- /dev/null +++ b/recipes/bioconductor-ihwpaper/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.10.0" %} +{% set name = "IHWpaper" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 941b62cdbd35bd8c0327712b47963bf2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, RColorBrewer, wesanderson, scales, gridExtra, BiocStyle, knitr, rmarkdown, airway, pasilla, DESeq, locfdr, tidyr, ggbio, latex2exp +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-ihw >=1.10.0,<1.11.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cowplot + - r-dplyr + - r-fdrtool + - r-ggplot2 + - r-rcpp + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-ihw >=1.10.0,<1.11.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cowplot + - r-dplyr + - r-fdrtool + - r-ggplot2 + - r-rcpp + - wget + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package conveniently wraps all functions needed to reproduce the figures in the IHW paper (https://www.nature.com/articles/nmeth.3885) and the latest arXiv preprint available under http://arxiv.org/abs/1701.05179. Thus it is a companion package to the Bioconductor IHW package.' + diff --git a/recipes/bioconductor-ihwpaper/post-link.sh b/recipes/bioconductor-ihwpaper/post-link.sh new file mode 100644 index 0000000000000..94a844f1b8312 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IHWpaper_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/IHWpaper_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/IHWpaper_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ihwpaper/bioconductor-ihwpaper_1.10.0_src_all.tar.gz" +) +MD5="941b62cdbd35bd8c0327712b47963bf2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ihwpaper/pre-unlink.sh b/recipes/bioconductor-ihwpaper/pre-unlink.sh new file mode 100644 index 0000000000000..d1f84af0b03c7 --- /dev/null +++ b/recipes/bioconductor-ihwpaper/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IHWpaper diff --git a/recipes/bioconductor-illumina450probevariants.db/meta.yaml b/recipes/bioconductor-illumina450probevariants.db/meta.yaml new file mode 100644 index 0000000000000..b0048d21320b8 --- /dev/null +++ b/recipes/bioconductor-illumina450probevariants.db/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "Illumina450ProbeVariants.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f1a96cc966c6de6c687ad024efdc6551 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Includes details on variants for each probe on the 450k bead chip for each of the four populations (Asian, American, African and European)' + diff --git a/recipes/bioconductor-illumina450probevariants.db/post-link.sh b/recipes/bioconductor-illumina450probevariants.db/post-link.sh new file mode 100644 index 0000000000000..78a598fb80dd8 --- /dev/null +++ b/recipes/bioconductor-illumina450probevariants.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Illumina450ProbeVariants.db_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Illumina450ProbeVariants.db_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/Illumina450ProbeVariants.db_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illumina450probevariants.db/bioconductor-illumina450probevariants.db_1.18.0_src_all.tar.gz" +) +MD5="f1a96cc966c6de6c687ad024efdc6551" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illumina450probevariants.db/pre-unlink.sh b/recipes/bioconductor-illumina450probevariants.db/pre-unlink.sh new file mode 100644 index 0000000000000..7ce9ae22ab501 --- /dev/null +++ b/recipes/bioconductor-illumina450probevariants.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Illumina450ProbeVariants.db diff --git a/recipes/bioconductor-illuminadatatestfiles/meta.yaml b/recipes/bioconductor-illuminadatatestfiles/meta.yaml new file mode 100644 index 0000000000000..2bfc13b3beb1e --- /dev/null +++ b/recipes/bioconductor-illuminadatatestfiles/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "IlluminaDataTestFiles" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4038cc1acc8bcd01c8b18d1de6ff1ffd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Example data for Illumina microarray output files, for testing purposes' + diff --git a/recipes/bioconductor-illuminadatatestfiles/post-link.sh b/recipes/bioconductor-illuminadatatestfiles/post-link.sh new file mode 100644 index 0000000000000..8b88a3f1d1a79 --- /dev/null +++ b/recipes/bioconductor-illuminadatatestfiles/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaDataTestFiles_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/IlluminaDataTestFiles_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaDataTestFiles_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminadatatestfiles/bioconductor-illuminadatatestfiles_1.20.0_src_all.tar.gz" +) +MD5="4038cc1acc8bcd01c8b18d1de6ff1ffd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminadatatestfiles/pre-unlink.sh b/recipes/bioconductor-illuminadatatestfiles/pre-unlink.sh new file mode 100644 index 0000000000000..71c4c76cd7539 --- /dev/null +++ b/recipes/bioconductor-illuminadatatestfiles/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaDataTestFiles diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml new file mode 100644 index 0000000000000..482eb31d6aa8c --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.4.8" %} +{% set name = "IlluminaHumanMethylation27k.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 70586bda9db01d598723bb439c315367 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Illumina Human Methylation 27k annotation data (chip IlluminaHumanMethylation27k) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh new file mode 100644 index 0000000000000..f77b2518f7dc3 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylation27k.db_1.4.8.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27k.db_1.4.8.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27k.db_1.4.8.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27k.db/bioconductor-illuminahumanmethylation27k.db_1.4.8_src_all.tar.gz" +) +MD5="70586bda9db01d598723bb439c315367" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylation27k.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylation27k.db/pre-unlink.sh new file mode 100644 index 0000000000000..e12b7c654fb27 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27k.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylation27k.db diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml new file mode 100644 index 0000000000000..383e5030151d9 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.6.0" %} +{% set name = "IlluminaHumanMethylation27kanno.ilmn12.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 765851336506120467c2e3cc6beef7ed +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An annotation package for Illumina''s EPIC methylation arrays.' + diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh new file mode 100644 index 0000000000000..7fab5c103af01 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" +) +MD5="765851336506120467c2e3cc6beef7ed" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..35e86192b158f --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylation27kanno.ilmn12.hg19 diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml new file mode 100644 index 0000000000000..81c8a4e138fbb --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.4.0" %} +{% set name = "IlluminaHumanMethylation27kmanifest" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c4cdda637dccf85f193342c7262b02a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Manifest for Illumina''s 27k array data' + diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh new file mode 100644 index 0000000000000..8448c496ed3f5 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation27kmanifest_0.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation27kmanifest/bioconductor-illuminahumanmethylation27kmanifest_0.4.0_src_all.tar.gz" +) +MD5="c4cdda637dccf85f193342c7262b02a6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylation27kmanifest/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylation27kmanifest/pre-unlink.sh new file mode 100644 index 0000000000000..4dd10b152965f --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation27kmanifest/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylation27kmanifest diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml index d45cb451c9f6f..b4fcfb7a86d04 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylation450kanno.ilmn12.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 249b8fd62add3c95b5047b597cff0868d26a98862a47cebd656edcd175a73b15 + md5: 2f569646ca8adc49863224b1cd076a79 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Manifests and annotation for Illumina''s 450k array data.' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + path: recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 + version: 0.6.0 diff --git a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh index a6ce3c30c4b34..1e55d9061ba88 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kanno.ilmn12.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19/bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19_0.6.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml index 6d1a038af1b39..e02db38fa54f9 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.4.0" %} {% set name = "IlluminaHumanMethylation450kmanifest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 41b2e54bac3feafc7646fe40bce3aa2b92c10871b0a13657c5736517792fa763 + md5: 664d1f5a3892974334faa26757269509 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Manifest for Illumina''s 450k array data' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylation450kmanifest + path: recipes/bioconductor-illuminahumanmethylation450kmanifest + version: 0.4.0 diff --git a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh index 93ab2a247224d..b5cff1b1e535d 100644 --- a/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylation450kmanifest/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kmanifest_0.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kmanifest/bioconductor-illuminahumanmethylation450kmanifest_0.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml new file mode 100644 index 0000000000000..ffc364ef5f939 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.0.6" %} +{% set name = "IlluminaHumanMethylation450kprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 84c31861fcbaddbf2a9c500b8d8d767d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'Probe sequences from Illumina (ftp.illumina.com) for hm450 probes' + diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh b/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh new file mode 100644 index 0000000000000..92c4d47a92126 --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" + "https://bioarchive.galaxyproject.org/IlluminaHumanMethylation450kprobe_2.0.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylation450kprobe/bioconductor-illuminahumanmethylation450kprobe_2.0.6_src_all.tar.gz" +) +MD5="84c31861fcbaddbf2a9c500b8d8d767d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanmethylation450kprobe/pre-unlink.sh b/recipes/bioconductor-illuminahumanmethylation450kprobe/pre-unlink.sh new file mode 100644 index 0000000000000..d413875f45e8d --- /dev/null +++ b/recipes/bioconductor-illuminahumanmethylation450kprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ IlluminaHumanMethylation450kprobe diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml index 3f7c6f290ecfa..60d058c48725b 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b2.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4decdbc78a6a8d02bf8aecb0d6e1d81134ae9dbc2375add52574f07829e8cd69 + md5: 6a8e2398a0f930aa7828a1412fb21e88 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 + version: 0.6.0 diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh index 1dd8c36173496..66a13f17b4b27 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b2.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19_0.6.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml index d5a59d8760983..6ec157eac18aa 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b3.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 062aa3c78e3fc518849adc73b8540aa50f85ecab8ef91b535b48a1bfeedab3e5 + md5: 2dac8e889486386eaea1bb7ce1beea2e build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19 + version: 0.6.0 diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh index 62576b4fca412..aadbcfde1e02a 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b3.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b3.hg19_0.6.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml index c93082f153b61..cfcd41c62696d 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.6.0" %} {% set name = "IlluminaHumanMethylationEPICanno.ilm10b4.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2c8128126b63e7fa805a5f3b02449367dca9c3be3eb5f6300acc718826590719 + md5: 2d0c05917bcbf9ba1e354380d4e17a77 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'An annotation package for Illumina''s EPIC methylation arrays.' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 + path: recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 + version: 0.6.0 diff --git a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh index 104cb7c559697..d105dc46d6d84 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICanno.ilm10b4.hg19_0.6.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19/bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19_0.6.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml index 12d23577c5465..34db3248ebf45 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.3.0" %} {% set name = "IlluminaHumanMethylationEPICmanifest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e39a69d98486cec981e97c56f45bbe47d2ccb5bbb66a1b16fa0685575493902a + md5: c6b0268de177badfe0b8184002da7e16 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A manifest package for Illumina''s EPIC methylation arrays.' - +extra: + parent_recipe: + name: bioconductor-illuminahumanmethylationepicmanifest + path: recipes/bioconductor-illuminahumanmethylationepicmanifest + version: 0.3.0 diff --git a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh index 1c63aaeebc559..8bc687b1951c0 100644 --- a/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh +++ b/recipes/bioconductor-illuminahumanmethylationepicmanifest/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://bioarchive.galaxyproject.org/IlluminaHumanMethylationEPICmanifest_0.3.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminahumanmethylationepicmanifest/bioconductor-illuminahumanmethylationepicmanifest_0.3.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminahumanv1.db/meta.yaml b/recipes/bioconductor-illuminahumanv1.db/meta.yaml new file mode 100644 index 0000000000000..8834351218b83 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanv1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2c362256b7be2861b8bf6e0d1fe46786 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanWG6v1 annotation data (chip illuminaHumanv1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanv1.db/post-link.sh b/recipes/bioconductor-illuminahumanv1.db/post-link.sh new file mode 100644 index 0000000000000..a83022aa3b15b --- /dev/null +++ b/recipes/bioconductor-illuminahumanv1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanv1.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv1.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanv1.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv1.db/bioconductor-illuminahumanv1.db_1.26.0_src_all.tar.gz" +) +MD5="2c362256b7be2861b8bf6e0d1fe46786" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanv1.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanv1.db/pre-unlink.sh new file mode 100644 index 0000000000000..aa720110598f1 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanv1.db diff --git a/recipes/bioconductor-illuminahumanv2.db/meta.yaml b/recipes/bioconductor-illuminahumanv2.db/meta.yaml new file mode 100644 index 0000000000000..c2a0d079f84ab --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanv2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 006de5f671a9a68fb27a6b6bce39c555 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanWG6v2 annotation data (chip illuminaHumanv2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanv2.db/post-link.sh b/recipes/bioconductor-illuminahumanv2.db/post-link.sh new file mode 100644 index 0000000000000..79dec2a0ead37 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanv2.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv2.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanv2.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2.db/bioconductor-illuminahumanv2.db_1.26.0_src_all.tar.gz" +) +MD5="006de5f671a9a68fb27a6b6bce39c555" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanv2.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanv2.db/pre-unlink.sh new file mode 100644 index 0000000000000..814cdc3fd51b6 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanv2.db diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml new file mode 100644 index 0000000000000..fde117dea0e93 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2beadid.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.8.0" %} +{% set name = "illuminaHumanv2BeadID.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b5a2b2deaa9a9b245a141043e7bc5270 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanWGv2 annotation data (chip illuminaHumanv2BeadID) assembled using data from public repositories to be used with data summarized from bead-level data with numeric ArrayAddressIDs as keys. Illumina probes with a No match or Bad quality score were removed prior to annotation. See http://www.compbio.group.cam.ac.uk/Resources/Annotation/index.html and Barbosa-Morais et al (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Research.' + diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh b/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh new file mode 100644 index 0000000000000..606074b49e8d7 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2beadid.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanv2BeadID.db_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv2BeadID.db_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanv2BeadID.db_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv2beadid.db/bioconductor-illuminahumanv2beadid.db_1.8.0_src_all.tar.gz" +) +MD5="b5a2b2deaa9a9b245a141043e7bc5270" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanv2beadid.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanv2beadid.db/pre-unlink.sh new file mode 100644 index 0000000000000..bfee7aeb4d551 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv2beadid.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanv2BeadID.db diff --git a/recipes/bioconductor-illuminahumanv3.db/meta.yaml b/recipes/bioconductor-illuminahumanv3.db/meta.yaml new file mode 100644 index 0000000000000..cec8c296b4a01 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv3.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanv3.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7d9e7534f0b60f0e3e7473e545ef373d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanHT12v3 annotation data (chip illuminaHumanv3) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanv3.db/post-link.sh b/recipes/bioconductor-illuminahumanv3.db/post-link.sh new file mode 100644 index 0000000000000..2b00a6e75a4ed --- /dev/null +++ b/recipes/bioconductor-illuminahumanv3.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanv3.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv3.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanv3.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv3.db/bioconductor-illuminahumanv3.db_1.26.0_src_all.tar.gz" +) +MD5="7d9e7534f0b60f0e3e7473e545ef373d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanv3.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanv3.db/pre-unlink.sh new file mode 100644 index 0000000000000..78c7c17f1ef94 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv3.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanv3.db diff --git a/recipes/bioconductor-illuminahumanv4.db/meta.yaml b/recipes/bioconductor-illuminahumanv4.db/meta.yaml new file mode 100644 index 0000000000000..6093d254597fd --- /dev/null +++ b/recipes/bioconductor-illuminahumanv4.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanv4.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 42d554559ac0106dc71317ffaf466421 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanHT12v4 annotation data (chip illuminaHumanv4) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanv4.db/post-link.sh b/recipes/bioconductor-illuminahumanv4.db/post-link.sh new file mode 100644 index 0000000000000..0b0f34ab2ebd1 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv4.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanv4.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanv4.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanv4.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanv4.db/bioconductor-illuminahumanv4.db_1.26.0_src_all.tar.gz" +) +MD5="42d554559ac0106dc71317ffaf466421" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanv4.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanv4.db/pre-unlink.sh new file mode 100644 index 0000000000000..13aa3db782eb4 --- /dev/null +++ b/recipes/bioconductor-illuminahumanv4.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanv4.db diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml new file mode 100644 index 0000000000000..2a671acc880f4 --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanWGDASLv3.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 32e8e24555c16f6d0148438d4a841ab8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanHT12WGDASLv3 annotation data (chip illuminaHumanWGDASLv3) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh b/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh new file mode 100644 index 0000000000000..42e1c474cf816 --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanWGDASLv3.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanWGDASLv3.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv3.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv3.db/bioconductor-illuminahumanwgdaslv3.db_1.26.0_src_all.tar.gz" +) +MD5="32e8e24555c16f6d0148438d4a841ab8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanwgdaslv3.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanwgdaslv3.db/pre-unlink.sh new file mode 100644 index 0000000000000..80ef6bff7aa0a --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv3.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanWGDASLv3.db diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml new file mode 100644 index 0000000000000..20f067eca038a --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaHumanWGDASLv4.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4cc1f192de838f2b6c1b148706d354ca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina HumanWGDASLv4 annotation data (chip illuminaHumanWGDASLv4) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh b/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh new file mode 100644 index 0000000000000..7dd1cf86e09d5 --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaHumanWGDASLv4.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaHumanWGDASLv4.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaHumanWGDASLv4.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminahumanwgdaslv4.db/bioconductor-illuminahumanwgdaslv4.db_1.26.0_src_all.tar.gz" +) +MD5="4cc1f192de838f2b6c1b148706d354ca" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminahumanwgdaslv4.db/pre-unlink.sh b/recipes/bioconductor-illuminahumanwgdaslv4.db/pre-unlink.sh new file mode 100644 index 0000000000000..d0901ead1d15f --- /dev/null +++ b/recipes/bioconductor-illuminahumanwgdaslv4.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaHumanWGDASLv4.db diff --git a/recipes/bioconductor-illuminaio/build.sh b/recipes/bioconductor-illuminaio/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-illuminaio/build.sh +++ b/recipes/bioconductor-illuminaio/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-illuminaio/meta.yaml b/recipes/bioconductor-illuminaio/meta.yaml index 4b18cf9fc2b1b..62a60b19d02e0 100644 --- a/recipes/bioconductor-illuminaio/meta.yaml +++ b/recipes/bioconductor-illuminaio/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "0.22.0" %} +{% set version = "0.24.0" %} {% set name = "illuminaio" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d0d9fca7d238e6045d4f613db26443bf87d44a9a4c367e73bfe9ff19ae047211 + md5: 739638c3a278019ba705240fb8818a65 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, IlluminaDataTestFiles (>= 1.0.2), BiocStyle requirements: host: - r-base @@ -30,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Tools for parsing Illumina''s microarray output files, including IDAT.' extra: identifiers: - biotools:illuminaio + parent_recipe: + name: bioconductor-illuminaio + path: recipes/bioconductor-illuminaio + version: 0.22.0 + diff --git a/recipes/bioconductor-illuminamousev1.db/meta.yaml b/recipes/bioconductor-illuminamousev1.db/meta.yaml new file mode 100644 index 0000000000000..b34f8c9032046 --- /dev/null +++ b/recipes/bioconductor-illuminamousev1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaMousev1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 13818c3b9acabe75550492bbe638fc05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina MouseWG6v1 annotation data (chip illuminaMousev1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminamousev1.db/post-link.sh b/recipes/bioconductor-illuminamousev1.db/post-link.sh new file mode 100644 index 0000000000000..05602c2702dc9 --- /dev/null +++ b/recipes/bioconductor-illuminamousev1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaMousev1.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev1.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaMousev1.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1.db/bioconductor-illuminamousev1.db_1.26.0_src_all.tar.gz" +) +MD5="13818c3b9acabe75550492bbe638fc05" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminamousev1.db/pre-unlink.sh b/recipes/bioconductor-illuminamousev1.db/pre-unlink.sh new file mode 100644 index 0000000000000..a92dc00087c03 --- /dev/null +++ b/recipes/bioconductor-illuminamousev1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaMousev1.db diff --git a/recipes/bioconductor-illuminamousev1p1.db/meta.yaml b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml new file mode 100644 index 0000000000000..219bd7086290e --- /dev/null +++ b/recipes/bioconductor-illuminamousev1p1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaMousev1p1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f6a4af01480a6f8d1d2d9b9b64a2b073 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina MouseWG6v1p1 annotation data (chip illuminaMousev1p1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminamousev1p1.db/post-link.sh b/recipes/bioconductor-illuminamousev1p1.db/post-link.sh new file mode 100644 index 0000000000000..011e3158b850b --- /dev/null +++ b/recipes/bioconductor-illuminamousev1p1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaMousev1p1.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev1p1.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaMousev1p1.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminamousev1p1.db/bioconductor-illuminamousev1p1.db_1.26.0_src_all.tar.gz" +) +MD5="f6a4af01480a6f8d1d2d9b9b64a2b073" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminamousev1p1.db/pre-unlink.sh b/recipes/bioconductor-illuminamousev1p1.db/pre-unlink.sh new file mode 100644 index 0000000000000..dfd0b9f317af2 --- /dev/null +++ b/recipes/bioconductor-illuminamousev1p1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaMousev1p1.db diff --git a/recipes/bioconductor-illuminamousev2.db/meta.yaml b/recipes/bioconductor-illuminamousev2.db/meta.yaml index 4f3420a7f9797..919e2315a124e 100644 --- a/recipes/bioconductor-illuminamousev2.db/meta.yaml +++ b/recipes/bioconductor-illuminamousev2.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "1.26.0" %} {% set name = "illuminaMousev2.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 03864df588d7261db6923d0d7cccdd9bbb753ce60e4cdf92ba2bc3ea1318916f + md5: fba228a71f264f976d8cdb035861974d build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Illumina MouseWG6v2 annotation data (chip illuminaMousev2) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-illuminamousev2.db + path: recipes/bioconductor-illuminamousev2.db + version: 1.26.0 diff --git a/recipes/bioconductor-illuminamousev2.db/post-link.sh b/recipes/bioconductor-illuminamousev2.db/post-link.sh index 86dc41728ebce..231bf226d946f 100644 --- a/recipes/bioconductor-illuminamousev2.db/post-link.sh +++ b/recipes/bioconductor-illuminamousev2.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="illuminaMousev2.db_1.26.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaMousev2.db_1.26.0.tar.gz" "https://bioarchive.galaxyproject.org/illuminaMousev2.db_1.26.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-illuminamousev2.db/bioconductor-illuminamousev2.db_1.26.0_src_all.tar.gz" diff --git a/recipes/bioconductor-illuminaratv1.db/meta.yaml b/recipes/bioconductor-illuminaratv1.db/meta.yaml new file mode 100644 index 0000000000000..b13e0b6dc8397 --- /dev/null +++ b/recipes/bioconductor-illuminaratv1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.26.0" %} +{% set name = "illuminaRatv1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5de2324d7b96c0cdb3301ef269341aa8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Ratv1 annotation data (chip illuminaRatv1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-illuminaratv1.db/post-link.sh b/recipes/bioconductor-illuminaratv1.db/post-link.sh new file mode 100644 index 0000000000000..670ed09d90e03 --- /dev/null +++ b/recipes/bioconductor-illuminaratv1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="illuminaRatv1.db_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/illuminaRatv1.db_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/illuminaRatv1.db_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-illuminaratv1.db/bioconductor-illuminaratv1.db_1.26.0_src_all.tar.gz" +) +MD5="5de2324d7b96c0cdb3301ef269341aa8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-illuminaratv1.db/pre-unlink.sh b/recipes/bioconductor-illuminaratv1.db/pre-unlink.sh new file mode 100644 index 0000000000000..a7af7e0bbf599 --- /dev/null +++ b/recipes/bioconductor-illuminaratv1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ illuminaRatv1.db diff --git a/recipes/bioconductor-imagehts/build.sh b/recipes/bioconductor-imagehts/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-imagehts/build.sh +++ b/recipes/bioconductor-imagehts/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-imagehts/conda_build_config.yaml b/recipes/bioconductor-imagehts/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-imagehts/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-imagehts/meta.yaml b/recipes/bioconductor-imagehts/meta.yaml index 6376dfcb80559..9f2669b4d5a83 100644 --- a/recipes/bioconductor-imagehts/meta.yaml +++ b/recipes/bioconductor-imagehts/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "imageHTS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 39a5dc9d30b9c0d22cc63bd9ec3976c66daa362168a3ec484f55df895fe8ef0e + md5: 19f67d974501ad1563397cb4d465ef2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, MASS requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-e1071 - r-hwriter run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-e1071 - r-hwriter @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2.1 summary: 'imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces. Designed to operate in distributed environments, imageHTS provides a standardized access to remote data and facilitates the dissemination of high-throughput microscopy-based datasets.' extra: identifiers: - biotools:imagehts - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-imagehts + path: recipes/bioconductor-imagehts + version: 1.30.0 + diff --git a/recipes/bioconductor-imas/build.sh b/recipes/bioconductor-imas/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-imas/build.sh +++ b/recipes/bioconductor-imas/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-imas/meta.yaml b/recipes/bioconductor-imas/meta.yaml index 08217ede7197e..7984c70352a28 100644 --- a/recipes/bioconductor-imas/meta.yaml +++ b/recipes/bioconductor-imas/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "IMAS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cef75e8992be51b77d0053e960560d2865bcf9d44fd6f2a6415b1eaebbb7c752 + md5: 58867e3f9d00eb28cd7368186e3cebb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-ivas >=2.0.0,<2.2.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-ivas >=2.2.0,<2.3.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -40,17 +42,17 @@ requirements: - r-matrix - r-survival run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-ivas >=2.0.0,<2.2.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-ivas >=2.2.0,<2.3.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -65,8 +67,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Integrative analysis of Multi-omics data for Alternative splicing.' - +extra: + parent_recipe: + name: bioconductor-imas + path: recipes/bioconductor-imas + version: 1.4.0 diff --git a/recipes/bioconductor-imetagene/build.sh b/recipes/bioconductor-imetagene/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-imetagene/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-imetagene/meta.yaml b/recipes/bioconductor-imetagene/meta.yaml new file mode 100644 index 0000000000000..c09c264448034 --- /dev/null +++ b/recipes/bioconductor-imetagene/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.12.0" %} +{% set name = "Imetagene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2e924c04928d481ee78f0fdf35f51eeb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-metagene >=2.14.0,<2.15.0' + - r-base + - r-d3heatmap + - r-ggplot2 + - r-shiny + - r-shinybs + - r-shinyfiles + - r-shinythemes + run: + - 'bioconductor-metagene >=2.14.0,<2.15.0' + - r-base + - r-d3heatmap + - r-ggplot2 + - r-shiny + - r-shinybs + - r-shinyfiles + - r-shinythemes +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic-2.0 | file LICENSE' + summary: 'This package provide a graphical user interface to the metagene package. This will allow people with minimal R experience to easily complete metagene analysis.' + diff --git a/recipes/bioconductor-imman/build.sh b/recipes/bioconductor-imman/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-imman/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-imman/meta.yaml b/recipes/bioconductor-imman/meta.yaml new file mode 100644 index 0000000000000..9643ad2649c6c --- /dev/null +++ b/recipes/bioconductor-imman/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "IMMAN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cd457c7494ce1cb6339920531190bb73 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-igraph + - r-seqinr + run: + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-igraph + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Reconstructing Interlog Protein Network (IPN) integrated from several Protein protein Interaction Networks (PPINs). Using this package, overlaying different PPINs to mine conserved common networks between diverse species will be applicable.' + diff --git a/recipes/bioconductor-immunespacer/build.sh b/recipes/bioconductor-immunespacer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-immunespacer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-immunespacer/meta.yaml b/recipes/bioconductor-immunespacer/meta.yaml new file mode 100644 index 0000000000000..53c2bde3276e6 --- /dev/null +++ b/recipes/bioconductor-immunespacer/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.10.1" %} +{% set name = "ImmuneSpaceR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd551477bc4ed5e3d81cf7cb239d3717 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-curl + - r-data.table + - r-ggplot2 + - r-gplots + - r-gtools + - 'r-heatmaply >=0.7.0' + - r-httr + - r-pheatmap + - r-plotly + - r-r6 + - r-reshape2 + - r-rjson + - 'r-rlabkey >=2.1.136' + - r-rmarkdown + - r-scales + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-curl + - r-data.table + - r-ggplot2 + - r-gplots + - r-gtools + - 'r-heatmaply >=0.7.0' + - r-httr + - r-pheatmap + - r-plotly + - r-r6 + - r-reshape2 + - r-rjson + - 'r-rlabkey >=2.1.136' + - r-rmarkdown + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Provides a convenient API for accessing data sets within ImmuneSpace (www.immunespace.org), the data repository and analysis platform of the Human Immunology Project Consortium (HIPC).' + diff --git a/recipes/bioconductor-immunoclust/build.sh b/recipes/bioconductor-immunoclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-immunoclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-immunoclust/meta.yaml b/recipes/bioconductor-immunoclust/meta.yaml new file mode 100644 index 0000000000000..0bc3844db71fa --- /dev/null +++ b/recipes/bioconductor-immunoclust/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.14.1" %} +{% set name = "immunoClust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de57ef8eaee13ab9a1c3dd9bbea5f857 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-lattice + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-lattice + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Model based clustering and meta-clustering of Flow Cytometry Data' + diff --git a/recipes/bioconductor-impcdata/build.sh b/recipes/bioconductor-impcdata/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-impcdata/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-impcdata/meta.yaml b/recipes/bioconductor-impcdata/meta.yaml new file mode 100644 index 0000000000000..7189435c00ed6 --- /dev/null +++ b/recipes/bioconductor-impcdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "IMPCdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7a7078db25def7231965af0a6604b598 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-rjson + run: + - r-base + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Package contains methods for data retrieval from IMPC Database.' + diff --git a/recipes/bioconductor-impulsede/build.sh b/recipes/bioconductor-impulsede/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-impulsede/build.sh +++ b/recipes/bioconductor-impulsede/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-impulsede/meta.yaml b/recipes/bioconductor-impulsede/meta.yaml index c00418258aef8..5f0a248e692ed 100644 --- a/recipes/bioconductor-impulsede/meta.yaml +++ b/recipes/bioconductor-impulsede/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "ImpulseDE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9246bcaaba1c6ea8cf52ca4b85dbdcb6a632ff56761dc7e54bacaee5450cc68c + md5: 99b95fd2df1ea360f4555129a1d845bb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: longitudinal, knitr requirements: host: - r-amap @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'ImpulseDE is suited to capture single impulse-like patterns in high throughput time series datasets. By fitting a representative impulse model to each gene, it reports differentially expressed genes whether across time points in a single experiment or between two time courses from two experiments. To optimize the running time, the code makes use of clustering steps and multi-threading.' extra: identifiers: - biotools:impulsede - doi:10.1093/bioinformatics/btw665 + parent_recipe: + name: bioconductor-impulsede + path: recipes/bioconductor-impulsede + version: 1.6.0 + diff --git a/recipes/bioconductor-impulsede2/build.sh b/recipes/bioconductor-impulsede2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-impulsede2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-impulsede2/meta.yaml b/recipes/bioconductor-impulsede2/meta.yaml new file mode 100644 index 0000000000000..9d058fb8ac49b --- /dev/null +++ b/recipes/bioconductor-impulsede2/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.6.0" %} +{% set name = "ImpulseDE2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1ab384e936b22d4bd426369da18e6e8b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-cowplot + - r-ggplot2 + - r-knitr + - r-matrix + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-cowplot + - r-ggplot2 + - r-knitr + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'ImpulseDE2 is a differential expression algorithm for longitudinal count data sets which arise in sequencing experiments such as RNA-seq, ChIP-seq, ATAC-seq and DNaseI-seq. ImpulseDE2 is based on a negative binomial noise model with dispersion trend smoothing by DESeq2 and uses the impulse model to constrain the mean expression trajectory of each gene. The impulse model was empirically found to fit global expression changes in cells after environmental and developmental stimuli and is therefore appropriate in most cell biological scenarios. The constraint on the mean expression trajectory prevents overfitting to small expression fluctuations. Secondly, ImpulseDE2 has higher statistical testing power than generalized linear model-based differential expression algorithms which fit time as a categorial variable if more than six time points are sampled because of the fixed number of parameters.' + diff --git a/recipes/bioconductor-impute/build.sh b/recipes/bioconductor-impute/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-impute/build.sh +++ b/recipes/bioconductor-impute/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-impute/meta.yaml b/recipes/bioconductor-impute/meta.yaml index 49c95c6bde504..857e82695a348 100644 --- a/recipes/bioconductor-impute/meta.yaml +++ b/recipes/bioconductor-impute/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "impute" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 19129a57c912280fae17c345174d3d6dd93c79875e300dc7b24f608a95bb6cb4 + md5: f9e8aa154a5e8069fe4cc12c61355e63 build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Imputation for microarray data (currently KNN only)' extra: identifiers: - biotools:impute - doi:10.1007/978-3-642-57489-4_7 + parent_recipe: + name: bioconductor-impute + path: recipes/bioconductor-impute + version: 1.54.0 + diff --git a/recipes/bioconductor-indac.db/meta.yaml b/recipes/bioconductor-indac.db/meta.yaml new file mode 100644 index 0000000000000..0aafd3f7f8f94 --- /dev/null +++ b/recipes/bioconductor-indac.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "indac.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cba72edcf7278033151e0eac077d8ff8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'INDAC FlyChip_long_oligonucleotide_002 (FL002) annotation data (chip indac) assembled using data from public repositories' + diff --git a/recipes/bioconductor-indac.db/post-link.sh b/recipes/bioconductor-indac.db/post-link.sh new file mode 100644 index 0000000000000..a6f24806aa4dd --- /dev/null +++ b/recipes/bioconductor-indac.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="indac.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/indac.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/indac.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-indac.db/bioconductor-indac.db_3.2.3_src_all.tar.gz" +) +MD5="cba72edcf7278033151e0eac077d8ff8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-indac.db/pre-unlink.sh b/recipes/bioconductor-indac.db/pre-unlink.sh new file mode 100644 index 0000000000000..54b3313022e10 --- /dev/null +++ b/recipes/bioconductor-indac.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ indac.db diff --git a/recipes/bioconductor-indeed/build.sh b/recipes/bioconductor-indeed/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-indeed/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-indeed/meta.yaml b/recipes/bioconductor-indeed/meta.yaml new file mode 100644 index 0000000000000..1b390fe3e35c5 --- /dev/null +++ b/recipes/bioconductor-indeed/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "INDEED" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5438bb5d85aa0489e92f2876736954e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.19), rmarkdown (>= 1.8), testthat (>= 2.0.0) +requirements: + host: + - r-base + - 'r-devtools >=1.13.0' + - 'r-glasso >=1.8' + run: + - r-base + - 'r-devtools >=1.13.0' + - 'r-glasso >=1.8' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An Implementation of Integrated Differential Expression and Differential Network Analysis of Omic Data. The differential network is obtained based on partial correlation or correlation.' + diff --git a/recipes/bioconductor-inpas/build.sh b/recipes/bioconductor-inpas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-inpas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inpas/meta.yaml b/recipes/bioconductor-inpas/meta.yaml new file mode 100644 index 0000000000000..bbb0bf0d914b2 --- /dev/null +++ b/recipes/bioconductor-inpas/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.14.1" %} +{% set name = "InPAS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec41c3f0144286126e8edecb617fd2ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, org.Hs.eg.db, org.Mm.eg.db, TxDb.Hsapiens.UCSC.hg19.knownGene, TxDb.Mmusculus.UCSC.mm10.knownGene, rtracklayer, knitr +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-cleanupdtseq >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-depmixs4 + - r-seqinr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-cleanupdtseq >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-depmixs4 + - r-seqinr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Alternative polyadenylation (APA) is one of the important post-transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites from RNAseq data. It leverages cleanUpdTSeq to fine tune identified APA sites.' + diff --git a/recipes/bioconductor-inpower/build.sh b/recipes/bioconductor-inpower/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-inpower/build.sh +++ b/recipes/bioconductor-inpower/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inpower/meta.yaml b/recipes/bioconductor-inpower/meta.yaml index dae8e59314d5f..b63149150c6b1 100644 --- a/recipes/bioconductor-inpower/meta.yaml +++ b/recipes/bioconductor-inpower/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "INPower" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3f1e0515b673117e6cdc4d3437e30a795ee17ecb4300ed55f1f5797e160b271a + md5: be5f4b9a24bea8cb1b0942152d79f49c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 + file LICENSE' summary: 'An R package for computing the number of susceptibility SNPs and power of future studies' extra: identifiers: - biotools:inpower - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-inpower + path: recipes/bioconductor-inpower + version: 1.16.0 + diff --git a/recipes/bioconductor-inspect/build.sh b/recipes/bioconductor-inspect/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-inspect/build.sh +++ b/recipes/bioconductor-inspect/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inspect/meta.yaml b/recipes/bioconductor-inspect/meta.yaml index bc8aa02aebbc9..35c5d8fabf759 100644 --- a/recipes/bioconductor-inspect/meta.yaml +++ b/recipes/bioconductor-inspect/meta.yaml @@ -1,48 +1,50 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "INSPEcT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1751702fbb09e762ae2a196aa11021d157e2bf602377b1dece5ccf1a3dbf60be + md5: fe9fe90244776aac0fe97a065eb29614 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, TxDb.Mmusculus.UCSC.mm9.knownGene requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-desolve - r-proc - r-rootsolve run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-desolve - r-proc @@ -51,9 +53,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'INSPEcT (INference of Synthesis, Processing and dEgradation rates in Time-Course experiments) analyses 4sU-seq and RNA-seq time-course data in order to evaluate synthesis, processing and degradation rates and asses via modeling the rates that determines changes in mature mRNA levels.' extra: identifiers: - biotools:inspect + parent_recipe: + name: bioconductor-inspect + path: recipes/bioconductor-inspect + version: 1.10.0 + diff --git a/recipes/bioconductor-intad/build.sh b/recipes/bioconductor-intad/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-intad/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-intad/meta.yaml b/recipes/bioconductor-intad/meta.yaml new file mode 100644 index 0000000000000..c4bd90c28a9c6 --- /dev/null +++ b/recipes/bioconductor-intad/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "InTAD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 661266e30d603c82bd28949f9493084f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggpubr + - r-mclust + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggpubr + - r-mclust +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'The package is focused on the detection of correlation between expressed genes and selected epigenomic signals i.e. enhancers obtained from ChIP-seq data within topologically associated domains (TADs). Various parameters can be controlled to investigate the influence of external factors and visualization plots are available for each analysis step.' + diff --git a/recipes/bioconductor-intansv/build.sh b/recipes/bioconductor-intansv/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-intansv/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-intansv/meta.yaml b/recipes/bioconductor-intansv/meta.yaml new file mode 100644 index 0000000000000..48cd8bb0e011b --- /dev/null +++ b/recipes/bioconductor-intansv/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.22.0" %} +{% set name = "intansv" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1286b959d63fb61017de3f1244738a42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-plyr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides efficient tools to read and integrate structural variations predicted by popular softwares. Annotation and visulation of structural variations are also implemented in the package.' + diff --git a/recipes/bioconductor-interactionset/build.sh b/recipes/bioconductor-interactionset/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-interactionset/build.sh +++ b/recipes/bioconductor-interactionset/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interactionset/conda_build_config.yaml b/recipes/bioconductor-interactionset/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-interactionset/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-interactionset/meta.yaml b/recipes/bioconductor-interactionset/meta.yaml index cca74b999fef1..81fba2f2f0cf3 100644 --- a/recipes/bioconductor-interactionset/meta.yaml +++ b/recipes/bioconductor-interactionset/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "InteractionSet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 164dd6d8ed315881a6e3a202e3afc12dbed617ba988788529600b178b0cacf76 + md5: 9aa7ddaaad56bef6685c95ae3950141a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-matrix - r-rcpp run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-matrix - r-rcpp @@ -45,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides the GInteractions, InteractionSet and ContactMatrix objects and associated methods for storing and manipulating genomic interaction data from Hi-C and ChIA-PET experiments.' extra: identifiers: - biotools:interactionset + parent_recipe: + name: bioconductor-interactionset + path: recipes/bioconductor-interactionset + version: 1.8.0 + diff --git a/recipes/bioconductor-interactivedisplay/build.sh b/recipes/bioconductor-interactivedisplay/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-interactivedisplay/build.sh +++ b/recipes/bioconductor-interactivedisplay/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interactivedisplay/meta.yaml b/recipes/bioconductor-interactivedisplay/meta.yaml index b024944a3ef0a..3fcb3d918d0aa 100644 --- a/recipes/bioconductor-interactivedisplay/meta.yaml +++ b/recipes/bioconductor-interactivedisplay/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "interactiveDisplay" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d22f03cabf6e9cff77b9389b9f3458d6099384d65d0049f6554466a2bc0a12b6 + md5: 34c2b077ccf7ef2b8048e802cb499e32 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, hgu95av2.db, knitr, GenomicRanges, SummarizedExperiment, GOstats, ggbio, GO.db, Gviz, rtracklayer, metagenomeSeq, gplots, vegan, Biobase requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' - r-base - r-ggplot2 - r-gridsvg @@ -31,10 +33,10 @@ requirements: - r-shiny - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-interactivedisplaybase >=1.18.0,<1.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-interactivedisplaybase >=1.20.0,<1.21.0' - r-base - r-ggplot2 - r-gridsvg @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The interactiveDisplay package contains the methods needed to generate interactive Shiny based display methods for Bioconductor objects.' extra: identifiers: - biotools:interactivedisplay - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-interactivedisplay + path: recipes/bioconductor-interactivedisplay + version: 1.18.0 + diff --git a/recipes/bioconductor-interactivedisplaybase/build.sh b/recipes/bioconductor-interactivedisplaybase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-interactivedisplaybase/build.sh +++ b/recipes/bioconductor-interactivedisplaybase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interactivedisplaybase/meta.yaml b/recipes/bioconductor-interactivedisplaybase/meta.yaml index 648b45e47ba83..5868f126584a9 100644 --- a/recipes/bioconductor-interactivedisplaybase/meta.yaml +++ b/recipes/bioconductor-interactivedisplaybase/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "interactiveDisplayBase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e59499d2ed37e4dc136eecdd9bf924387aa269571266d3245175ee14c7478517 + md5: 9fde04ff11ca32a7c8d7a5e59e10efae build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-shiny run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-shiny test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The interactiveDisplayBase package contains the the basic methods needed to generate interactive Shiny based display methods for Bioconductor objects.' extra: identifiers: - biotools:interactivedisplaybase - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-interactivedisplaybase + path: recipes/bioconductor-interactivedisplaybase + version: 1.18.0 + diff --git a/recipes/bioconductor-interest/build.sh b/recipes/bioconductor-interest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-interest/build.sh +++ b/recipes/bioconductor-interest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interest/meta.yaml b/recipes/bioconductor-interest/meta.yaml index 8e27b34f9861f..be0f0dea12df4 100644 --- a/recipes/bioconductor-interest/meta.yaml +++ b/recipes/bioconductor-interest/meta.yaml @@ -1,56 +1,58 @@ -{% set version = "1.4.1" %} +{% set version = "1.6.1" %} {% set name = "IntEREst" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cb2ebcacbd951c029c9ceb32360baa9dda9109d95eeed94b5d38ac4b52e56754 + md5: 3af0d22cde14690b2e71d4ca3da6a53e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: clinfun, knitr, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-dexseq >=1.26.0,<1.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dexseq >=1.28.0,<1.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dbi - r-rmysql - r-seqinr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-dexseq >=1.26.0,<1.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dexseq >=1.28.0,<1.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dbi - r-rmysql @@ -59,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package performs Intron-Exon Retention analysis on RNA-seq data (.bam files).' extra: identifiers: - doi:10.18129/B9.bioc.IntEREst + parent_recipe: + name: bioconductor-interest + path: recipes/bioconductor-interest + version: 1.4.1 + diff --git a/recipes/bioconductor-interminer/build.sh b/recipes/bioconductor-interminer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-interminer/build.sh +++ b/recipes/bioconductor-interminer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-interminer/meta.yaml b/recipes/bioconductor-interminer/meta.yaml index 4e769511d9564..6b8e03cb2e7ef 100644 --- a/recipes/bioconductor-interminer/meta.yaml +++ b/recipes/bioconductor-interminer/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "InterMineR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4261d607ec70ed1375b2f95c6af746db23dd59ce847999fc12be4b5052e3ce69 + md5: 18fdbd559ba46ea9e78e352c9ca09543 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, Gviz, knitr, rmarkdown, GeneAnswers, GO.db, org.Hs.eg.db requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-httr - r-igraph @@ -32,11 +34,11 @@ requirements: - r-xml - r-xml2 run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-httr - r-igraph @@ -49,8 +51,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Databases based on the InterMine platform such as FlyMine, modMine (modENCODE), RatMine, YeastMine, HumanMine and TargetMine are integrated databases of genomic, expression and protein data for various organisms. Integrating data makes it possible to run sophisticated data mining queries that span domains of biological knowledge. This R package provides interfaces with these databases through webservices. It makes most from the correspondence of the data frame object in R and the table object in databases, while hiding the details of data exchange through XML or JSON.' - +extra: + parent_recipe: + name: bioconductor-interminer + path: recipes/bioconductor-interminer + version: 1.2.1 diff --git a/recipes/bioconductor-intramirexplorer/build.sh b/recipes/bioconductor-intramirexplorer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-intramirexplorer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-intramirexplorer/meta.yaml b/recipes/bioconductor-intramirexplorer/meta.yaml new file mode 100644 index 0000000000000..01ce683f22b42 --- /dev/null +++ b/recipes/bioconductor-intramirexplorer/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.4.0" %} +{% set name = "IntramiRExploreR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9dacefac5bab443f1f1e9fb9327c02c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RDAVIDWebService, gProfileR, topGO, KEGGprofile, org.Dm.eg.db, rmarkdown, testthat +requirements: + host: + - 'bioconductor-fgnet >=3.16.0,<3.17.0' + - r-base + - 'r-igraph >=1.0.1' + - 'r-knitr >=1.12.3' + run: + - 'bioconductor-fgnet >=3.16.0,<3.17.0' + - r-base + - 'r-igraph >=1.0.1' + - 'r-knitr >=1.12.3' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Intra-miR-ExploreR, an integrative miRNA target prediction bioinformatics tool, identifies targets combining expression and biophysical interactions of a given microRNA (miR). Using the tool, we have identified targets for 92 intragenic miRs in D. melanogaster, using available microarray expression data, from Affymetrix 1 and Affymetrix2 microarray array platforms, providing a global perspective of intragenic miR targets in Drosophila. Predicted targets are grouped according to biological functions using the DAVID Gene Ontology tool and are ranked based on a biologically relevant scoring system, enabling the user to identify functionally relevant targets for a given miR.' + diff --git a/recipes/bioconductor-inversion/build.sh b/recipes/bioconductor-inversion/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-inversion/build.sh +++ b/recipes/bioconductor-inversion/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-inversion/meta.yaml b/recipes/bioconductor-inversion/meta.yaml index bf46b9a1638d7..34c46e70e474c 100644 --- a/recipes/bioconductor-inversion/meta.yaml +++ b/recipes/bioconductor-inversion/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "inveRsion" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4d6ac9f478fe77da8aa220c0d8dac0949ff99f5e3eeddfbc273f82ebb2d3ef9b + md5: a412874157e3ce4f3c4ecea6fe37318f build: number: 0 rpaths: @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package to find genetic inversions in genotype (SNP array) data.' extra: identifiers: - biotools:inversion - doi:10.1186/1471-2105-13-28 + parent_recipe: + name: bioconductor-inversion + path: recipes/bioconductor-inversion + version: 1.28.0 + diff --git a/recipes/bioconductor-ioniser/build.sh b/recipes/bioconductor-ioniser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ioniser/build.sh +++ b/recipes/bioconductor-ioniser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ioniser/meta.yaml b/recipes/bioconductor-ioniser/meta.yaml index 7786a3139bae6..bc7b99544562f 100644 --- a/recipes/bioconductor-ioniser/meta.yaml +++ b/recipes/bioconductor-ioniser/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "2.4.0" %} +{% set version = "2.6.0" %} {% set name = "IONiseR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3e0711320179a7a2f3971cb33842bbfc5f98a1ddb3d0b0891780e281fa76322d + md5: 61e911d51f0caa89932208c837ab6342 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, gridExtra, testthat, minionSummaryData requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-bit64 - r-dplyr @@ -33,12 +35,12 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-bit64 - r-dplyr @@ -51,10 +53,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.' extra: identifiers: - biotools:ioniser - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ioniser + path: recipes/bioconductor-ioniser + version: 2.4.0 + diff --git a/recipes/bioconductor-iontreedata/meta.yaml b/recipes/bioconductor-iontreedata/meta.yaml new file mode 100644 index 0000000000000..b0e2a60356ead --- /dev/null +++ b/recipes/bioconductor-iontreedata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "iontreeData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 212d5af9852edd8e2d0505ba6f208185 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Raw MS2, MS3 scans from direct infusion mass spectrometry (DIMS) and a demo ion tree database ''mzDB'' derived from the DIMS data are included. The demo database is used to show the functionalities provided by the ''iontree'' package, not for the purpose of compound identification by any means.' + diff --git a/recipes/bioconductor-iontreedata/post-link.sh b/recipes/bioconductor-iontreedata/post-link.sh new file mode 100644 index 0000000000000..76b7c8f24b888 --- /dev/null +++ b/recipes/bioconductor-iontreedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="iontreeData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/iontreeData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/iontreeData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-iontreedata/bioconductor-iontreedata_1.18.0_src_all.tar.gz" +) +MD5="212d5af9852edd8e2d0505ba6f208185" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-iontreedata/pre-unlink.sh b/recipes/bioconductor-iontreedata/pre-unlink.sh new file mode 100644 index 0000000000000..5e49f3c3f105d --- /dev/null +++ b/recipes/bioconductor-iontreedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ iontreeData diff --git a/recipes/bioconductor-ipac/build.sh b/recipes/bioconductor-ipac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ipac/build.sh +++ b/recipes/bioconductor-ipac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ipac/meta.yaml b/recipes/bioconductor-ipac/meta.yaml index 656362e67f268..d5dd6414117eb 100644 --- a/recipes/bioconductor-ipac/meta.yaml +++ b/recipes/bioconductor-ipac/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.24.2" %} +{% set version = "1.26.0" %} {% set name = "iPAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f5a446e34d6139f6f05be29a9cb8a448fc2ad65e642a923a998a409d92cee21c + md5: 11d1424c3e0f5f1d56e7a97e038d5c08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-gdata - r-scatterplot3d run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-gdata - r-scatterplot3d @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'iPAC is a novel tool to identify somatic amino acid mutation clustering within proteins while taking into account protein structure.' extra: identifiers: - biotools:ipac - doi:10.1186/1471-2105-14-190 + parent_recipe: + name: bioconductor-ipac + path: recipes/bioconductor-ipac + version: 1.24.2 + diff --git a/recipes/bioconductor-ipddb/build.sh b/recipes/bioconductor-ipddb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ipddb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ipddb/meta.yaml b/recipes/bioconductor-ipddb/meta.yaml new file mode 100644 index 0000000000000..6fd289d8ff754 --- /dev/null +++ b/recipes/bioconductor-ipddb/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "ipdDb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2fb18bc886d7261c082f6aef486d862f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-assertthat + - r-base + - r-dbi + - r-rsqlite + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-assertthat + - r-base + - r-dbi + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'All alleles from the IPD IMGT/HLA and IPD KIR database for Homo sapiens. Reference: Robinson J, Maccari G, Marsh SGE, Walter L, Blokhuis J, Bimber B, Parham P, De Groot NG, Bontrop RE, Guethlein LA, and Hammond JA KIR Nomenclature in non-human species Immunogenetics (2018), in preparation.' + diff --git a/recipes/bioconductor-ipo/build.sh b/recipes/bioconductor-ipo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ipo/build.sh +++ b/recipes/bioconductor-ipo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ipo/meta.yaml b/recipes/bioconductor-ipo/meta.yaml index d8c3e0108e47e..7f065fec0aa27 100644 --- a/recipes/bioconductor-ipo/meta.yaml +++ b/recipes/bioconductor-ipo/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "IPO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f13e09841eb4c83d7fe3e2dd5b98d11bb29ea386c068215177087ee9e7d06c39 + md5: 79c8b2f8502a530c2374bc2208ada7f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, msdata, mtbls2, faahKO, knitr requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-rsm run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-rsm test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'The outcome of XCMS data processing strongly depends on the parameter settings. IPO (`Isotopologue Parameter Optimization`) is a parameter optimization tool that is applicable for different kinds of samples and liquid chromatography coupled to high resolution mass spectrometry devices, fast and free of labeling steps. IPO uses natural, stable 13C isotopes to calculate a peak picking score. Retention time correction is optimized by minimizing the relative retention time differences within features and grouping parameters are optimized by maximizing the number of features showing exactly one peak from each injection of a pooled sample. The different parameter settings are achieved by design of experiment. The resulting scores are evaluated using response surface models.' extra: identifiers: - biotools:ipo + parent_recipe: + name: bioconductor-ipo + path: recipes/bioconductor-ipo + version: 1.6.0 + diff --git a/recipes/bioconductor-ippd/build.sh b/recipes/bioconductor-ippd/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ippd/build.sh +++ b/recipes/bioconductor-ippd/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ippd/meta.yaml b/recipes/bioconductor-ippd/meta.yaml index af896e0fe6fac..a66bcc5ba0f7d 100644 --- a/recipes/bioconductor-ippd/meta.yaml +++ b/recipes/bioconductor-ippd/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "IPPD" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 47c671a0beea2cb498d6d3e07d043805837afbc3dd4e8f38cd0f74a3a6f65dfe + md5: ae63fe883f60495d5f67784e28e11a6f build: number: 0 rpaths: @@ -38,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (version 2 or later)' summary: 'The package provides functionality to extract isotopic peak patterns from raw mass spectra. This is done by fitting a large set of template basis functions to the raw spectrum using either nonnegative least squares or least absolute deviation fittting. The package offers a flexible function which tries to estimate model parameters in a way tailored to the peak shapes in the data. The package also provides functionality to process LCMS runs.' extra: identifiers: - biotools:ippd - doi:10.1186/1471-2105-13-291 + parent_recipe: + name: bioconductor-ippd + path: recipes/bioconductor-ippd + version: 1.28.0 + diff --git a/recipes/bioconductor-iranges/build.sh b/recipes/bioconductor-iranges/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iranges/build.sh +++ b/recipes/bioconductor-iranges/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iranges/meta.yaml b/recipes/bioconductor-iranges/meta.yaml index 5d851e588b922..27f8976c11d75 100644 --- a/recipes/bioconductor-iranges/meta.yaml +++ b/recipes/bioconductor-iranges/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "2.14.12" %} +{% set version = "2.16.0" %} {% set name = "IRanges" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 768285a716728bd8e506ce9bd3552f39f2673c66caf6fc5603c037f930d628ab + md5: f37fa0b9438adf9af358844bf1f87c02 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: XVector, GenomicRanges, Rsamtools, GenomicAlignments, GenomicFeatures, BSgenome.Celegans.UCSC.ce2, pasillaBamSubset, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base build: - {{ compiler('c') }} @@ -32,9 +33,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides efficient low-level and highly reusable S4 classes for storing, manipulating and aggregating over annotated ranges of integers. Implements an algebra of range operations, including efficient algorithms for finding overlaps and nearest neighbors. Defines efficient list-like classes for storing, transforming and aggregating large grouped data, i.e., collections of atomic vectors and DataFrames.' extra: identifiers: - biotools:iranges + parent_recipe: + name: bioconductor-iranges + path: recipes/bioconductor-iranges + version: 2.14.12 + diff --git a/recipes/bioconductor-isee/build.sh b/recipes/bioconductor-isee/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-isee/build.sh +++ b/recipes/bioconductor-isee/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isee/meta.yaml b/recipes/bioconductor-isee/meta.yaml index 12eda85eab1db..c5c073becd436 100644 --- a/recipes/bioconductor-isee/meta.yaml +++ b/recipes/bioconductor-isee/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.0.1" %} +{% set version = "1.2.0" %} {% set name = "iSEE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2b50c65a41fbb62f95f98375903af933504b0cab09ce785c5537259da3ee0fd7 + md5: 170e94a6acf704baad9742320af6c599 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, scater, DelayedArray (>= 0.7.44), Rtsne, irlba, RColorBrewer, viridis, org.Mm.eg.db, htmltools requirements: host: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - r-base >=3.5.1 + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base - r-colourpicker - r-cowplot - r-dplyr @@ -42,12 +44,12 @@ requirements: - r-vipor - r-viridislite run: - - bioconductor-annotationdbi - - bioconductor-biocgenerics - - bioconductor-s4vectors - - bioconductor-singlecellexperiment - - bioconductor-summarizedexperiment - - r-base >=3.5.1 + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base - r-colourpicker - r-cowplot - r-dplyr @@ -69,6 +71,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Provides functions for creating an interactive Shiny-based graphical user interface for exploring data stored in SummarizedExperiment objects, including row- and column-level metadata. Particular attention is given to single-cell data in a SingleCellExperiment object with visualization of dimensionality reduction results.' +extra: + parent_recipe: + name: bioconductor-isee + path: recipes/bioconductor-isee + version: 1.0.1 + diff --git a/recipes/bioconductor-iseq/build.sh b/recipes/bioconductor-iseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iseq/build.sh +++ b/recipes/bioconductor-iseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iseq/meta.yaml b/recipes/bioconductor-iseq/meta.yaml index d8edcfb64aab7..e7d06b9bffc19 100644 --- a/recipes/bioconductor-iseq/meta.yaml +++ b/recipes/bioconductor-iseq/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "iSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c60fc7cc08676ba1d93e82a80973ad6ff93953eb44d235d4d27ee28fe5a8d510 + md5: 2059cc665dc0cd50aa204f216a64d332 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'This package uses Bayesian hidden Ising models to identify IP-enriched genomic regions from ChIP-seq data. It can be used to analyze ChIP-seq data with and without controls and replicates.' + summary: 'Bayesian hidden Ising models are implemented to identify IP-enriched genomic regions from ChIP-seq data. They can be used to analyze ChIP-seq data with and without controls and replicates.' extra: identifiers: - biotools:iseq - doi:10.1111/j.1541-0420.2009.01379.x + parent_recipe: + name: bioconductor-iseq + path: recipes/bioconductor-iseq + version: 1.32.0 + diff --git a/recipes/bioconductor-isobar/build.sh b/recipes/bioconductor-isobar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isobar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isobar/meta.yaml b/recipes/bioconductor-isobar/meta.yaml new file mode 100644 index 0000000000000..4da91515ee213 --- /dev/null +++ b/recipes/bioconductor-isobar/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.28.0" %} +{% set name = "isobar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 68833968f99c12527e9923447b075d79 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MSnbase, OrgMassSpecR, XML, RJSONIO, Hmisc, gplots, RColorBrewer, gridExtra, limma, boot, DBI, MASS +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-distr + - r-ggplot2 + - r-plyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-distr + - r-ggplot2 + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-2 + summary: 'isobar provides methods for preprocessing, normalization, and report generation for the analysis of quantitative mass spectrometry proteomics data labeled with isobaric tags, such as iTRAQ and TMT. Features modules for integrating and validating PTM-centric datasets (isobar-PTM). More information on http://www.ms-isobar.org.' + diff --git a/recipes/bioconductor-isocorrector/build.sh b/recipes/bioconductor-isocorrector/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isocorrector/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isocorrector/meta.yaml b/recipes/bioconductor-isocorrector/meta.yaml new file mode 100644 index 0000000000000..c5ed8771bff40 --- /dev/null +++ b/recipes/bioconductor-isocorrector/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.4" %} +{% set name = "IsoCorrectoR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 87ddda98d204e951ce8063456c77bb86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - r-base + - r-dplyr + - r-magrittr + - r-pracma + - r-quadprog + - r-readr + - r-readxl + - r-stringr + - r-tibble + - r-writexls + run: + - r-base + - r-dplyr + - r-magrittr + - r-pracma + - r-quadprog + - r-readr + - r-readxl + - r-stringr + - r-tibble + - r-writexls +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'IsoCorrectoR performs the correction of mass spectrometry data from stable isotope labeling/tracing metabolomics experiments with regard to natural isotope abundance and tracer impurity. Data from both MS and MS/MS measurements can be corrected (with any tracer isotope: 13C, 15N, 18O...), as well as high resolution MS data from multiple-tracer experiments (e.g. 13C and 15N used simultaneously). See the Bioconductor package IsoCorrectoRGUI for a graphical user interface to IsoCorrectoR.' + diff --git a/recipes/bioconductor-isoformswitchanalyzer/build.sh b/recipes/bioconductor-isoformswitchanalyzer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/build.sh +++ b/recipes/bioconductor-isoformswitchanalyzer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml index 178e2ee8d9510..a6326460b614c 100644 --- a/recipes/bioconductor-isoformswitchanalyzer/meta.yaml +++ b/recipes/bioconductor-isoformswitchanalyzer/meta.yaml @@ -1,61 +1,72 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "IsoformSwitchAnalyzeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 21d5419ad3361793d6b39903f732bfbaffcf5bca7edae1ee2b969e75709d67fc + md5: a4b45dc8dc2a54692d8a27ba67568d16 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, BSgenome.Hsapiens.UCSC.hg19, cummeRbund requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-cummerbund >=2.22.0,<2.24.0' - - 'bioconductor-drimseq >=1.8.0,<1.10.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-tximport >=1.8.0,<1.10.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dexseq >=1.28.0,<1.29.0' + - 'bioconductor-drimseq >=1.10.0,<1.11.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-tximport >=1.10.0,<1.11.0' - r-base - r-dbi + - r-dplyr - r-futile.logger - r-ggplot2 - r-gridextra + - r-magrittr - r-plyr - r-rcolorbrewer + - r-readr - r-reshape2 + - r-stringr - r-venndiagram run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-cummerbund >=2.22.0,<2.24.0' - - 'bioconductor-drimseq >=1.8.0,<1.10.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-tximport >=1.8.0,<1.10.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dexseq >=1.28.0,<1.29.0' + - 'bioconductor-drimseq >=1.10.0,<1.11.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-tximport >=1.10.0,<1.11.0' - r-base - r-dbi + - r-dplyr - r-futile.logger - r-ggplot2 - r-gridextra + - r-magrittr - r-plyr - r-rcolorbrewer + - r-readr - r-reshape2 + - r-stringr - r-venndiagram build: - {{ compiler('c') }} @@ -64,10 +75,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'IsoformSwitchAnalyzeR enables identification and analysis of isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' + summary: 'IsoformSwitchAnalyzeR enables identification and analysis of alternative splicing and isoform switches with predicted functional consequences (such as gain/loss of protein domains etc) from quantification by Kallisto, Salmon, Cufflinks/Cuffdiff, RSEM etc.' extra: identifiers: - biotools:IsoformSwitchAnalyzeR - doi:10.1158/1541-7786.MCR-16-0459 + parent_recipe: + name: bioconductor-isoformswitchanalyzer + path: recipes/bioconductor-isoformswitchanalyzer + version: 1.2.0 + diff --git a/recipes/bioconductor-isogenegui/build.sh b/recipes/bioconductor-isogenegui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-isogenegui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isogenegui/meta.yaml b/recipes/bioconductor-isogenegui/meta.yaml new file mode 100644 index 0000000000000..573310b2a5656 --- /dev/null +++ b/recipes/bioconductor-isogenegui/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "2.18.0" %} +{% set name = "IsoGeneGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 872514812096a9484b45f0c86cd63911 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-ff + - r-goric + - r-iso + - r-isogene + - r-jpeg + - r-orcme + - r-oriclust + - r-orqa + - r-rcolorbrewer + - r-rcpp + - r-relimp + - r-tkrplot + - r-xlsx + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-ff + - r-goric + - r-iso + - r-isogene + - r-jpeg + - r-orcme + - r-oriclust + - r-orqa + - r-rcolorbrewer + - r-rcpp + - r-relimp + - r-tkrplot + - r-xlsx + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The IsoGene Graphical User Interface (IsoGene-GUI) is a user friendly interface of the IsoGene package which is aimed to identify for genes with a monotonic trend in the expression levels with respect to the increasing doses. Additionally, GUI extension of original package contains various tools to perform clustering of dose-response profiles. Testing is addressed through several test statistics: global likelihood ratio test (E2), Bartholomew 1961, Barlow et al. 1972 and Robertson et al. 1988), Williams (1971, 1972), Marcus (1976), the M (Hu et al. 2005) and the modified M (Lin et al. 2007). The p-values of the global likelihood ratio test (E2) are obtained using the exact distribution and permutations. The other four test statistics are obtained using permutations. Several p-values adjustment are provided: Bonferroni, Holm (1979), Hochberg (1988), and Sidak procedures for controlling the family-wise Type I error rate (FWER), and BH (Benjamini and Hochberg 1995) and BY (Benjamini and Yekutieli 2001) procedures are used for controlling the FDR. The inference is based on resampling methods, which control the False Discovery Rate (FDR), for both permutations (Ge et al., 2003) and the Significance Analysis of Microarrays (SAM, Tusher et al., 2001). Clustering methods are outsourced from CRAN packages ORCME, ORIClust. The package ORCME is based on delta-clustering method (Cheng and Church, 2000) and ORIClust on Order Restricted Information Criterion (Liu et al., 2009), both perform same task but from different perspective and their outputs are clusters of genes. Additionally, profile selection for given gene based on Generalized ORIC (Kuiper et al., 2014) from package goric and permutation test for E2 based on package orQA are included in IsoGene-GUI. None of these four packages has GUI.' + diff --git a/recipes/bioconductor-isolde/build.sh b/recipes/bioconductor-isolde/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-isolde/build.sh +++ b/recipes/bioconductor-isolde/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isolde/meta.yaml b/recipes/bioconductor-isolde/meta.yaml index 3ef00057a78db..8605c934a38d1 100644 --- a/recipes/bioconductor-isolde/meta.yaml +++ b/recipes/bioconductor-isolde/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ISoLDE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f8818e5f486f93027a1c25901db3750423508a52a375a1e236d572a79662000e + md5: f88acfd71b44004b7c44811e84869022 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.0)' summary: 'This package provides ISoLDE a new method for identifying imprinted genes. This method is dedicated to data arising from RNA sequencing technologies. The ISoLDE package implements original statistical methodology described in the publication below.' extra: identifiers: - biotools:isolde - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-isolde + path: recipes/bioconductor-isolde + version: 1.8.0 + diff --git a/recipes/bioconductor-isomirs/build.sh b/recipes/bioconductor-isomirs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-isomirs/build.sh +++ b/recipes/bioconductor-isomirs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-isomirs/meta.yaml b/recipes/bioconductor-isomirs/meta.yaml index b8cb59b24e338..178f298c8f366 100644 --- a/recipes/bioconductor-isomirs/meta.yaml +++ b/recipes/bioconductor-isomirs/meta.yaml @@ -1,35 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "isomiRs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a3144607ec7b762f47ffca04c00208ddca725eb5e4bb741ae98cc48da4e6f649 + md5: e7add4edfd77ebeee4faeedb961b8204 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, org.Mm.eg.db, targetscan.Hs.eg.db, pheatmap, BiocStyle, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-targetscan.hs.eg.db >=0.6.1,<0.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-degreport >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-assertive.sets - r-base + - r-cluster + - r-cowplot - r-discriminer - r-dplyr - r-ggally @@ -44,18 +48,20 @@ requirements: - r-tibble - r-tidyr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-targetscan.hs.eg.db >=0.6.1,<0.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-degreport >=1.18.0,<1.19.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-assertive.sets - r-base + - r-cluster + - r-cowplot - r-discriminer - r-dplyr - r-ggally @@ -73,10 +79,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Characterization of miRNAs and isomiRs, clustering and differential expression.' extra: identifiers: - biotools:isomirs - doi:10.1093/bioinformatics/btv632 + parent_recipe: + name: bioconductor-isomirs + path: recipes/bioconductor-isomirs + version: 1.8.0 + diff --git a/recipes/bioconductor-italics/build.sh b/recipes/bioconductor-italics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-italics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-italics/meta.yaml b/recipes/bioconductor-italics/meta.yaml new file mode 100644 index 0000000000000..cab14240d0d3b --- /dev/null +++ b/recipes/bioconductor-italics/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "2.42.0" %} +{% set name = "ITALICS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ff61276d7d7957d1d43f81a3c44c143c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pd.mapping50k.hind240, pd.mapping250k.sty, pd.mapping250k.nsp +requirements: + host: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-italicsdata >=2.20.0,<2.21.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' + - r-base + - r-dbi + run: + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-italicsdata >=2.20.0,<2.21.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-pd.mapping50k.xba240 >=3.12.0,<3.13.0' + - r-base + - r-dbi +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A Method to normalize of Affymetrix GeneChip Human Mapping 100K and 500K set' + diff --git a/recipes/bioconductor-italicsdata/meta.yaml b/recipes/bioconductor-italicsdata/meta.yaml new file mode 100644 index 0000000000000..3b5c427bc0a58 --- /dev/null +++ b/recipes/bioconductor-italicsdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.20.0" %} +{% set name = "ITALICSData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a6efafe837fc28cafd205d8acfc3a94a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Data needed to use the ITALICS package' + diff --git a/recipes/bioconductor-italicsdata/post-link.sh b/recipes/bioconductor-italicsdata/post-link.sh new file mode 100644 index 0000000000000..6d0f84a1977df --- /dev/null +++ b/recipes/bioconductor-italicsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ITALICSData_2.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ITALICSData_2.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ITALICSData_2.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-italicsdata/bioconductor-italicsdata_2.20.0_src_all.tar.gz" +) +MD5="a6efafe837fc28cafd205d8acfc3a94a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-italicsdata/pre-unlink.sh b/recipes/bioconductor-italicsdata/pre-unlink.sh new file mode 100644 index 0000000000000..45b70cdc4aed6 --- /dev/null +++ b/recipes/bioconductor-italicsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ITALICSData diff --git a/recipes/bioconductor-iterativebma/build.sh b/recipes/bioconductor-iterativebma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iterativebma/build.sh +++ b/recipes/bioconductor-iterativebma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iterativebma/meta.yaml b/recipes/bioconductor-iterativebma/meta.yaml index 4600ed96e385b..32a215e673c12 100644 --- a/recipes/bioconductor-iterativebma/meta.yaml +++ b/recipes/bioconductor-iterativebma/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "iterativeBMA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 42abbb1fbde3e556c7cf10f1544fe18093e9b0f6aac88e204eaeb7dff734fd94 + md5: 7ceea6bdeb99f7b8ff5b46f8e938b860 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-bma - r-leaps run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-bma - r-leaps @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The iterative Bayesian Model Averaging (BMA) algorithm is a variable selection and classification algorithm with an application of classifying 2-class microarray samples, as described in Yeung, Bumgarner and Raftery (Bioinformatics 2005, 21: 2394-2402).' extra: identifiers: - biotools:iterativebma - doi:10.1186/gb-2008-9-7-r118 + parent_recipe: + name: bioconductor-iterativebma + path: recipes/bioconductor-iterativebma + version: 1.38.0 + diff --git a/recipes/bioconductor-iterativebmasurv/build.sh b/recipes/bioconductor-iterativebmasurv/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iterativebmasurv/build.sh +++ b/recipes/bioconductor-iterativebmasurv/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iterativebmasurv/meta.yaml b/recipes/bioconductor-iterativebmasurv/meta.yaml index c957b55260e4a..dc2d58d47c8a6 100644 --- a/recipes/bioconductor-iterativebmasurv/meta.yaml +++ b/recipes/bioconductor-iterativebmasurv/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "iterativeBMAsurv" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5fca0142b00cb06024829f018c50822c7014489a15d19ccb6b2b2e6ee3a20cfb + md5: 0260494ff7be19fe0716230c2162fb09 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The iterative Bayesian Model Averaging (BMA) algorithm for survival analysis is a variable selection method for applying survival analysis to microarray data.' extra: identifiers: - biotools:iterativebmasurv - doi:10.1186/1471-2105-10-72 + parent_recipe: + name: bioconductor-iterativebmasurv + path: recipes/bioconductor-iterativebmasurv + version: 1.38.0 + diff --git a/recipes/bioconductor-iterclust/build.sh b/recipes/bioconductor-iterclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iterclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iterclust/meta.yaml b/recipes/bioconductor-iterclust/meta.yaml new file mode 100644 index 0000000000000..2091ef569c571 --- /dev/null +++ b/recipes/bioconductor-iterclust/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.4.0" %} +{% set name = "iterClust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9d834de783d4ec4af9b9ead22236616b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: tsne, bcellViper +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-cluster + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-cluster +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'A framework for performing clustering analysis iteratively.' + diff --git a/recipes/bioconductor-iteremoval/build.sh b/recipes/bioconductor-iteremoval/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-iteremoval/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iteremoval/meta.yaml b/recipes/bioconductor-iteremoval/meta.yaml new file mode 100644 index 0000000000000..a8aa232d20122 --- /dev/null +++ b/recipes/bioconductor-iteremoval/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.2.0" %} +{% set name = "iteremoval" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eb105f0df6dd4e19a8683152705c6348 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - r-magrittr + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - r-magrittr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The package provides a flexible algorithm to screen features of two distinct groups in consideration of overfitting and overall performance. It was originally tailored for methylation locus screening of NGS data, and it can also be used as a generic method for feature selection. Each step of the algorithm provides a default method for simple implemention, and the method can be replaced by a user defined function.' + diff --git a/recipes/bioconductor-ivas/build.sh b/recipes/bioconductor-ivas/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ivas/build.sh +++ b/recipes/bioconductor-ivas/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ivas/meta.yaml b/recipes/bioconductor-ivas/meta.yaml index a654827dc6353..18ce08f05c299 100644 --- a/recipes/bioconductor-ivas/meta.yaml +++ b/recipes/bioconductor-ivas/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "IVAS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c4e24044672745db223dad17fcac1ddbb749d11bcc8cb51995fcfcdea05b5a26 + md5: deffefe8491728061122ab65714e3730 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -35,15 +37,15 @@ requirements: - r-lme4 - r-matrix run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-doparallel - r-foreach @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identification of genetic variants affecting alternative splicing.' extra: identifiers: - biotools:ivas - doi:10.1007/s13258-016-0466-7 + parent_recipe: + name: bioconductor-ivas + path: recipes/bioconductor-ivas + version: 2.0.0 + diff --git a/recipes/bioconductor-ivygapse/build.sh b/recipes/bioconductor-ivygapse/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ivygapse/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ivygapse/meta.yaml b/recipes/bioconductor-ivygapse/meta.yaml new file mode 100644 index 0000000000000..9b6c1637ffa10 --- /dev/null +++ b/recipes/bioconductor-ivygapse/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.0" %} +{% set name = "ivygapSE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e40c121410d8cd59555a1860e69c7e02 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, png, limma, grid, DT, randomForest, digest, testthat +requirements: + host: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-hwriter + - r-plotly + - r-shiny + - r-survival + - r-survminer + - r-upsetr + run: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-hwriter + - r-plotly + - r-shiny + - r-survival + - r-survminer + - r-upsetr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Define a SummarizedExperiment and exploratory app for Ivy-GAP glioblastoma image, expression, and clinical data.' + diff --git a/recipes/bioconductor-iwtomics/build.sh b/recipes/bioconductor-iwtomics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-iwtomics/build.sh +++ b/recipes/bioconductor-iwtomics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-iwtomics/meta.yaml b/recipes/bioconductor-iwtomics/meta.yaml index 755f69893b89c..e83d182ef7467 100644 --- a/recipes/bioconductor-iwtomics/meta.yaml +++ b/recipes/bioconductor-iwtomics/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "IWTomics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 52eaa007db7ad9564f5bc777c623bdfa02139d9e7e0a3388652365d1d94b9342 + md5: 41ae9142f344cc1b42205ffe20758cec build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda - r-gtable - r-kernsmooth run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda - r-gtable @@ -37,8 +39,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Implementation of the Interval-Wise Testing (IWT) for omics data. This inferential procedure tests for differences in "Omics" data between two groups of genomic regions (or between a group of genomic regions and a reference center of symmetry), and does not require fixing location and scale at the outset.' - +extra: + parent_recipe: + name: bioconductor-iwtomics + path: recipes/bioconductor-iwtomics + version: 1.4.0 diff --git a/recipes/bioconductor-iyer517/meta.yaml b/recipes/bioconductor-iyer517/meta.yaml new file mode 100644 index 0000000000000..c4f940a21b5f2 --- /dev/null +++ b/recipes/bioconductor-iyer517/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "Iyer517" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: db3def2128ea25dabad86019961b2126 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'representation of public Iyer data from http://genome-www.stanford.edu/serum/clusters.html' + diff --git a/recipes/bioconductor-iyer517/post-link.sh b/recipes/bioconductor-iyer517/post-link.sh new file mode 100644 index 0000000000000..edffbd7b6b1df --- /dev/null +++ b/recipes/bioconductor-iyer517/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Iyer517_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Iyer517_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/Iyer517_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-iyer517/bioconductor-iyer517_1.24.0_src_all.tar.gz" +) +MD5="db3def2128ea25dabad86019961b2126" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-iyer517/pre-unlink.sh b/recipes/bioconductor-iyer517/pre-unlink.sh new file mode 100644 index 0000000000000..e7b0f51201eaf --- /dev/null +++ b/recipes/bioconductor-iyer517/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Iyer517 diff --git a/recipes/bioconductor-jaspar2014/meta.yaml b/recipes/bioconductor-jaspar2014/meta.yaml index 493d5959f789c..c1cf0bcc3adee 100644 --- a/recipes/bioconductor-jaspar2014/meta.yaml +++ b/recipes/bioconductor-jaspar2014/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "JASPAR2014" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1a216837d63548d9f07526bfdaee36c9f534c4e2268c5fa1672cfcf8a9835e1d + md5: 4b68fc946528a33446e29411731e9097 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2014. To search this databases, please use the package TFBSTools.' - +extra: + parent_recipe: + name: bioconductor-jaspar2014 + path: recipes/bioconductor-jaspar2014 + version: 1.16.0 diff --git a/recipes/bioconductor-jaspar2014/post-link.sh b/recipes/bioconductor-jaspar2014/post-link.sh index dc6c0e6c89a77..7716947c49769 100644 --- a/recipes/bioconductor-jaspar2014/post-link.sh +++ b/recipes/bioconductor-jaspar2014/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="JASPAR2014_1.16.0.tar.gz" +FN="JASPAR2014_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/JASPAR2014_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/JASPAR2014_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JASPAR2014_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2014_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2014/bioconductor-jaspar2014_1.18.0_src_all.tar.gz" ) -MD5="62bc9538b7fb9dc6d8a926aa61bbc42e" +MD5="4b68fc946528a33446e29411731e9097" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-jaspar2016/meta.yaml b/recipes/bioconductor-jaspar2016/meta.yaml index 7b05c2bc2aa62..feb88c584cebc 100644 --- a/recipes/bioconductor-jaspar2016/meta.yaml +++ b/recipes/bioconductor-jaspar2016/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "JASPAR2016" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0c419dd94d66bb02289b5827ab1dfbe7ba739acc82af5bc929f93de85532e9d8 + md5: 3dc95f750e4a98dfb227a4c3de6ce501 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2016. To search this databases, please use the package TFBSTools (>= 1.8.1).' - +extra: + parent_recipe: + name: bioconductor-jaspar2016 + path: recipes/bioconductor-jaspar2016 + version: 1.8.0 diff --git a/recipes/bioconductor-jaspar2016/post-link.sh b/recipes/bioconductor-jaspar2016/post-link.sh index f25e74d11874a..d357124e150ee 100644 --- a/recipes/bioconductor-jaspar2016/post-link.sh +++ b/recipes/bioconductor-jaspar2016/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="JASPAR2016_1.8.0.tar.gz" +FN="JASPAR2016_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/JASPAR2016_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/JASPAR2016_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JASPAR2016_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2016_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2016/bioconductor-jaspar2016_1.10.0_src_all.tar.gz" ) -MD5="19d1e3810b4cda2b16d382b2d646c27d" +MD5="3dc95f750e4a98dfb227a4c3de6ce501" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-jaspar2018/meta.yaml b/recipes/bioconductor-jaspar2018/meta.yaml index 0cd614c48dcf6..afa19f52742e6 100644 --- a/recipes/bioconductor-jaspar2018/meta.yaml +++ b/recipes/bioconductor-jaspar2018/meta.yaml @@ -1,32 +1,39 @@ -{% set version = "1.1.0" %} +{% set version = "1.1.1" %} {% set name = "JASPAR2018" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4439bc1b556eaf66c2b7e30bab28dc9da323b9cba8c53043f587822228473b2b + md5: d91fce6ea0dc9fa6a3be6ebc05c1af5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TFBSTools (>= 1.15.6) requirements: host: - r-base run: - r-base + - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: GPL-2 summary: 'Data package for JASPAR 2018. To search this databases, please use the package TFBSTools (>= 1.15.6).' - +extra: + parent_recipe: + name: bioconductor-jaspar2018 + path: recipes/bioconductor-jaspar2018 + version: 1.1.0 diff --git a/recipes/bioconductor-jaspar2018/post-link.sh b/recipes/bioconductor-jaspar2018/post-link.sh index 63cbb3b91da35..2f4175df6b840 100755 --- a/recipes/bioconductor-jaspar2018/post-link.sh +++ b/recipes/bioconductor-jaspar2018/post-link.sh @@ -1,10 +1,11 @@ #!/bin/bash -FN="JASPAR2018_1.1.0.tar.gz" +FN="JASPAR2018_1.1.1.tar.gz" URLS=( - "https://bioconductor.org/packages/3.7/bioc/src/contrib/JASPAR2018_1.1.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/JASPAR2018_1.1.1.tar.gz" + "https://bioarchive.galaxyproject.org/JASPAR2018_1.1.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jaspar2018/bioconductor-jaspar2018_1.1.1_src_all.tar.gz" ) -MD5="7f6d748701d83294d6138b265657712a" +MD5="d91fce6ea0dc9fa6a3be6ebc05c1af5d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-jazaerimetadata.db/meta.yaml b/recipes/bioconductor-jazaerimetadata.db/meta.yaml new file mode 100644 index 0000000000000..4f1cfc35ffc19 --- /dev/null +++ b/recipes/bioconductor-jazaerimetadata.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "JazaeriMetaData.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3a154a74ac2acebe3471b039c9d9a4dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A data package containing annotation data for JazaeriMetaData assembled using data from public repositories' + diff --git a/recipes/bioconductor-jazaerimetadata.db/post-link.sh b/recipes/bioconductor-jazaerimetadata.db/post-link.sh new file mode 100644 index 0000000000000..b44bbf4a4aff3 --- /dev/null +++ b/recipes/bioconductor-jazaerimetadata.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="JazaeriMetaData.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/JazaeriMetaData.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/JazaeriMetaData.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jazaerimetadata.db/bioconductor-jazaerimetadata.db_3.2.3_src_all.tar.gz" +) +MD5="3a154a74ac2acebe3471b039c9d9a4dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-jazaerimetadata.db/pre-unlink.sh b/recipes/bioconductor-jazaerimetadata.db/pre-unlink.sh new file mode 100644 index 0000000000000..b190ebd14f1ee --- /dev/null +++ b/recipes/bioconductor-jazaerimetadata.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JazaeriMetaData.db diff --git a/recipes/bioconductor-jctseqdata/meta.yaml b/recipes/bioconductor-jctseqdata/meta.yaml new file mode 100644 index 0000000000000..bde4c340cd71e --- /dev/null +++ b/recipes/bioconductor-jctseqdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "JctSeqData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 76da9f6116c1a71cbb2244c7dd5c32a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, DESeq2, DEXSeq, edgeR, JunctionSeq +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Junction count data from an example dataset taken from a subset of the RNA-seq reads from six samples. Data was subsampled and modified to provide edge cases for testing and to reduce file sizes.' + diff --git a/recipes/bioconductor-jctseqdata/post-link.sh b/recipes/bioconductor-jctseqdata/post-link.sh new file mode 100644 index 0000000000000..def3b1fa8c182 --- /dev/null +++ b/recipes/bioconductor-jctseqdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="JctSeqData_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/JctSeqData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/JctSeqData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-jctseqdata/bioconductor-jctseqdata_1.12.0_src_all.tar.gz" +) +MD5="76da9f6116c1a71cbb2244c7dd5c32a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-jctseqdata/pre-unlink.sh b/recipes/bioconductor-jctseqdata/pre-unlink.sh new file mode 100644 index 0000000000000..a4ddca599b6e6 --- /dev/null +++ b/recipes/bioconductor-jctseqdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ JctSeqData diff --git a/recipes/bioconductor-jmosaics/build.sh b/recipes/bioconductor-jmosaics/build.sh index 6c7a1726e3c25..63d60035b254f 100644 --- a/recipes/bioconductor-jmosaics/build.sh +++ b/recipes/bioconductor-jmosaics/build.sh @@ -14,4 +14,4 @@ $R CMD INSTALL --build . # http://docs.continuum.io/conda/build.html # for a list of environment variables that are set during the build # process. -# \ No newline at end of file +# \ No newline at end of file diff --git a/recipes/bioconductor-joda/build.sh b/recipes/bioconductor-joda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-joda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-joda/meta.yaml b/recipes/bioconductor-joda/meta.yaml new file mode 100644 index 0000000000000..250e5e6f240fd --- /dev/null +++ b/recipes/bioconductor-joda/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.30.0" %} +{% set name = "joda" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 40973ebc5b8862fca57737b9a04128a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-bgmm + run: + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-bgmm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Package ''joda'' implements three steps of an algorithm called JODA. The algorithm computes gene deregulation scores. For each gene, its deregulation score reflects how strongly an effect of a certain regulator''s perturbation on this gene differs between two different cell populations. The algorithm utilizes regulator knockdown expression data as well as knowledge about signaling pathways in which the regulators are involved (formalized in a simple matrix model).' + diff --git a/recipes/bioconductor-junctionseq/build.sh b/recipes/bioconductor-junctionseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-junctionseq/build.sh +++ b/recipes/bioconductor-junctionseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-junctionseq/meta.yaml b/recipes/bioconductor-junctionseq/meta.yaml index 632cc15cc95ff..9a78d1311238a 100644 --- a/recipes/bioconductor-junctionseq/meta.yaml +++ b/recipes/bioconductor-junctionseq/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "JunctionSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1a2ef1242f0f2c93559c97c57595f49a18b733c9f1df04add82908d683736aa8 + md5: baea765c524a275d35f74fb752cf0239 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: MASS, knitr, JctSeqData, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-hmisc - r-locfit @@ -37,16 +38,16 @@ requirements: - r-statmod - r-stringr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-hmisc - r-locfit @@ -63,9 +64,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'A Utility for Detection and Visualization of Differential Exon or Splice-Junction Usage in RNA-Seq data.' extra: identifiers: - biotools:junctionseq + parent_recipe: + name: bioconductor-junctionseq + path: recipes/bioconductor-junctionseq + version: 1.10.0 + diff --git a/recipes/bioconductor-karyoploter/build.sh b/recipes/bioconductor-karyoploter/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-karyoploter/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-karyoploter/meta.yaml b/recipes/bioconductor-karyoploter/meta.yaml new file mode 100644 index 0000000000000..9ae6fc9348570 --- /dev/null +++ b/recipes/bioconductor-karyoploter/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.8.4" %} +{% set name = "karyoploteR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de39049638bc426d5275cc5bb8a49ddd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat, magrittr, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, pasillaBamSubset +requirements: + host: + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-bezier + - r-digest + - r-memoise + run: + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-regioner >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-bezier + - r-digest + - r-memoise +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'karyoploteR creates karyotype plots of arbitrary genomes and offers a complete set of functions to plot arbitrary data on them. It mimicks many R base graphics functions coupling them with a coordinate change function automatically mapping the chromosome and data coordinates into the plot coordinates. In addition to the provided data plotting functions, it is easy to add new ones.' + diff --git a/recipes/bioconductor-kcsmart/build.sh b/recipes/bioconductor-kcsmart/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-kcsmart/build.sh +++ b/recipes/bioconductor-kcsmart/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kcsmart/meta.yaml b/recipes/bioconductor-kcsmart/meta.yaml index d134f39436107..a483554d26771 100644 --- a/recipes/bioconductor-kcsmart/meta.yaml +++ b/recipes/bioconductor-kcsmart/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "KCsmart" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f59ff9b95fad22a288befde7d70432ac5f1c6ec6fb48393486a23c8437dcf6eb + md5: 8f57fd4003e5da98c7cd7749ac054e70 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-kernsmooth run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-kernsmooth test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Multi sample aCGH analysis package using kernel convolution' extra: identifiers: - biotools:kcsmart - doi:10.1186/1756-0500-3-298 + parent_recipe: + name: bioconductor-kcsmart + path: recipes/bioconductor-kcsmart + version: 2.38.0 + diff --git a/recipes/bioconductor-kebabs/build.sh b/recipes/bioconductor-kebabs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-kebabs/build.sh +++ b/recipes/bioconductor-kebabs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kebabs/meta.yaml b/recipes/bioconductor-kebabs/meta.yaml index 6034ac82e2fe2..e99f711799d98 100644 --- a/recipes/bioconductor-kebabs/meta.yaml +++ b/recipes/bioconductor-kebabs/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "kebabs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 060e19e97316757ec24008fa9e4d4a370e81dcfceb0e886f15cf78ad2d0104e8 + md5: 219c50a9e26b4adfd9e23c8fb3684bc6 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: SparseM, Biobase, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-apcluster - r-base - r-e1071 @@ -30,10 +31,10 @@ requirements: - r-matrix - 'r-rcpp >=0.11.2' run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-apcluster - r-base - r-e1071 @@ -49,8 +50,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.1)' summary: 'The package provides functionality for kernel-based analysis of DNA, RNA, and amino acid sequences via SVM-based methods. As core functionality, kebabs implements following sequence kernels: spectrum kernel, mismatch kernel, gappy pair kernel, and motif kernel. Apart from an efficient implementation of standard position-independent functionality, the kernels are extended in a novel way to take the position of patterns into account for the similarity measure. Because of the flexibility of the kernel formulation, other kernels like the weighted degree kernel or the shifted weighted degree kernel with constant weighting of positions are included as special cases. An annotation-specific variant of the kernels uses annotation information placed along the sequence together with the patterns in the sequence. The package allows for the generation of a kernel matrix or an explicit feature representation in dense or sparse format for all available kernels which can be used with methods implemented in other R packages. With focus on SVM-based methods, kebabs provides a framework which simplifies the usage of existing SVM implementations in kernlab, e1071, and LiblineaR. Binary and multi-class classification as well as regression tasks can be used in a unified way without having to deal with the different functions, parameters, and formats of the selected SVM. As support for choosing hyperparameters, the package provides cross validation - including grouped cross validation, grid search and model selection functions. For easier biological interpretation of the results, the package computes feature weights for all SVMs and prediction profiles which show the contribution of individual sequence positions to the prediction result and indicate the relevance of sequence sections for the learning result and the underlying biological functions.' - +extra: + parent_recipe: + name: bioconductor-kebabs + path: recipes/bioconductor-kebabs + version: 1.14.0 diff --git a/recipes/bioconductor-kegg.db/meta.yaml b/recipes/bioconductor-kegg.db/meta.yaml index 9301a3edf51dc..660de9b50be92 100644 --- a/recipes/bioconductor-kegg.db/meta.yaml +++ b/recipes/bioconductor-kegg.db/meta.yaml @@ -1,35 +1,41 @@ {% set version = "3.2.3" %} {% set name = "KEGG.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 02ea4630a3ec06a8d9a6151627c96d3f71dfc7e8857800bb5c0cdb6a838d6963 + md5: 023ac22f57063627c2e62d1ae5e011b0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'file LICENSE' summary: 'A set of annotation maps for KEGG assembled using data from KEGG' - +extra: + parent_recipe: + name: bioconductor-kegg.db + path: recipes/bioconductor-kegg.db + version: 3.2.3 diff --git a/recipes/bioconductor-kegg.db/post-link.sh b/recipes/bioconductor-kegg.db/post-link.sh index 709d08d83b1f5..a7620544568ec 100644 --- a/recipes/bioconductor-kegg.db/post-link.sh +++ b/recipes/bioconductor-kegg.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="KEGG.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/KEGG.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/KEGG.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-kegg.db/bioconductor-kegg.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml new file mode 100644 index 0000000000000..19aca1c673133 --- /dev/null +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "KEGGandMetacoreDzPathwaysGEO" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: da545248fec755e65427c118cd8d518d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'This is a collection of 18 data sets for which the phenotype is a disease with a corresponding pathway in either KEGG or metacore database.This collection of datasets were used as gold standard in comparing gene set analysis methods.' + diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh new file mode 100644 index 0000000000000..c89436feb0f6e --- /dev/null +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/KEGGandMetacoreDzPathwaysGEO_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggandmetacoredzpathwaysgeo/bioconductor-keggandmetacoredzpathwaysgeo_1.2.0_src_all.tar.gz" +) +MD5="da545248fec755e65427c118cd8d518d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-keggandmetacoredzpathwaysgeo/pre-unlink.sh b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/pre-unlink.sh new file mode 100644 index 0000000000000..889e7b9591c03 --- /dev/null +++ b/recipes/bioconductor-keggandmetacoredzpathwaysgeo/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ KEGGandMetacoreDzPathwaysGEO diff --git a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml index 04b5db93e41a4..0a158c67ed50d 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml +++ b/recipes/bioconductor-keggdzpathwaysgeo/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "KEGGdzPathwaysGEO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 19696755848b79a7fb9b9e0f225b63d8ea2909cff32198fe22f5e601340283eb + md5: 773a71a68a75a39fc631776efb73e7dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This is a collection of 24 data sets for which the phenotype is a disease with a corresponding pathway in the KEGG database.This collection of datasets were used as gold standard in comparing gene set analysis methods by the PADOG package.' - +extra: + parent_recipe: + name: bioconductor-keggdzpathwaysgeo + path: recipes/bioconductor-keggdzpathwaysgeo + version: 1.18.0 diff --git a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh index bd723f1826f0f..ece2ced785bd9 100644 --- a/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh +++ b/recipes/bioconductor-keggdzpathwaysgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KEGGdzPathwaysGEO_1.18.0.tar.gz" +FN="KEGGdzPathwaysGEO_1.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KEGGdzPathwaysGEO_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/KEGGdzPathwaysGEO_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-keggdzpathwaysgeo/bioconductor-keggdzpathwaysgeo_1.20.0_src_all.tar.gz" ) -MD5="d701ac5a9236c01ea5354080d0142eed" +MD5="773a71a68a75a39fc631776efb73e7dc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-kegggraph/build.sh b/recipes/bioconductor-kegggraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-kegggraph/build.sh +++ b/recipes/bioconductor-kegggraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kegggraph/meta.yaml b/recipes/bioconductor-kegggraph/meta.yaml index e16b787354866..527445dd033ed 100644 --- a/recipes/bioconductor-kegggraph/meta.yaml +++ b/recipes/bioconductor-kegggraph/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "KEGGgraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 326afc5c49c29fd6722641b48e68c89cc01bf892a06499951b61ea43e817ad96 + md5: 6299732316aed3d57a74c3750b1ab43c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz, RBGL, RUnit, RColorBrewer, KEGG.db, org.Hs.eg.db, hgu133plus2.db, SPIA requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - 'r-xml >=2.3-0' run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - 'r-xml >=2.3-0' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'KEGGGraph is an interface between KEGG pathway and graph object as well as a collection of tools to analyze, dissect and visualize these graphs. It parses the regularly updated KGML (KEGG XML) files into graph models maintaining all essential pathway attributes. The package offers functionalities including parsing, graph operation, visualization and etc.' extra: identifiers: - biotools:kegggraph + parent_recipe: + name: bioconductor-kegggraph + path: recipes/bioconductor-kegggraph + version: 1.40.0 + diff --git a/recipes/bioconductor-kegglincs/build.sh b/recipes/bioconductor-kegglincs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-kegglincs/build.sh +++ b/recipes/bioconductor-kegglincs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kegglincs/meta.yaml b/recipes/bioconductor-kegglincs/meta.yaml index 6dc12e5ebfb97..89b0b7415e620 100644 --- a/recipes/bioconductor-kegglincs/meta.yaml +++ b/recipes/bioconductor-kegglincs/meta.yaml @@ -1,29 +1,32 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "KEGGlincs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fa61e9faa467beb8500f68dcce170d8a093bf073798d13e9a58f9d6eea6b0d45 + md5: 563a47dca90ab2a1999f27257ad8a4bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocManager (>= 1.20.3), knitr, graph +# SystemRequirements: Cytoscape (>= 3.3.0), Java (>= 8) requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-kodata >=1.6.0,<1.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-kodata >=1.8.0,<1.9.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-gtools - r-httr @@ -32,12 +35,12 @@ requirements: - r-rjsonio - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-kodata >=1.6.0,<1.8.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-kodata >=1.8.0,<1.9.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-gtools - r-httr @@ -49,10 +52,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'See what is going on ''under the hood'' of KEGG pathways by explicitly re-creating the pathway maps from information obtained from KGML files.' extra: identifiers: - biotools:kegglincs - doi:10.7490/f1000research.1113436.1 + parent_recipe: + name: bioconductor-kegglincs + path: recipes/bioconductor-kegglincs + version: 1.6.2 + diff --git a/recipes/bioconductor-keggorthology/build.sh b/recipes/bioconductor-keggorthology/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-keggorthology/build.sh +++ b/recipes/bioconductor-keggorthology/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-keggorthology/meta.yaml b/recipes/bioconductor-keggorthology/meta.yaml index 0b9653018785f..ce369fb59c205 100644 --- a/recipes/bioconductor-keggorthology/meta.yaml +++ b/recipes/bioconductor-keggorthology/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "keggorthology" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9d57ff72633e6d05b6201f8aaec51de8f0764d00acce8e6724055cbfceb1bc7c + md5: 62ca96db218f39f0168b022ccf63fcce build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RBGL,ALL requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hgu95av2.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hgu95av2.db >=3.2.0,<3.3.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hgu95av2.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hgu95av2.db >=3.2.0,<3.3.0' - r-base - r-dbi test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'graphical representation of the Feb 2010 KEGG Orthology. The KEGG orthology is a set of pathway IDs that are not to be confused with the KEGG ortholog IDs.' extra: identifiers: - biotools:keggorthology - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-keggorthology + path: recipes/bioconductor-keggorthology + version: 2.32.0 + diff --git a/recipes/bioconductor-keggprofile/build.sh b/recipes/bioconductor-keggprofile/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-keggprofile/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-keggprofile/meta.yaml b/recipes/bioconductor-keggprofile/meta.yaml new file mode 100644 index 0000000000000..05cacb898013a --- /dev/null +++ b/recipes/bioconductor-keggprofile/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.24.0" %} +{% set name = "KEGGprofile" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 94f3b5f4687557760207e432fba9c2e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - r-base + - r-png + - r-rcurl + - r-teachingdemos + - r-xml + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - r-base + - r-png + - r-rcurl + - r-teachingdemos + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'KEGGprofile is an annotation and visualization tool which integrated the expression profiles and the function annotation in KEGG pathway maps. The multi-types and multi-groups expression data can be visualized in one pathway map. KEGGprofile facilitated more detailed analysis about the specific function changes inner pathway or temporal correlations in different genes and samples.' + diff --git a/recipes/bioconductor-keggrest/build.sh b/recipes/bioconductor-keggrest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-keggrest/build.sh +++ b/recipes/bioconductor-keggrest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-keggrest/meta.yaml b/recipes/bioconductor-keggrest/meta.yaml index 84160896b11c5..a171fa01c9056 100644 --- a/recipes/bioconductor-keggrest/meta.yaml +++ b/recipes/bioconductor-keggrest/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "KEGGREST" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4a3be78265f680f725bd4a9ea4f35cffc90ea1d98c5020281dac2e84e7aa1572 + md5: a261af7eef51941349a3ff93d4b4e28b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-httr - r-png run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-httr - r-png @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package that provides a client interface to the KEGG REST server. Based on KEGGSOAP by J. Zhang, R. Gentleman, and Marc Carlson, and KEGG (python package) by Aurelien Mazurie.' extra: identifiers: - biotools:keggrest - doi:10.1007/s11845-015-1283-8 + parent_recipe: + name: bioconductor-keggrest + path: recipes/bioconductor-keggrest + version: 1.20.2 + diff --git a/recipes/bioconductor-kidpack/meta.yaml b/recipes/bioconductor-kidpack/meta.yaml new file mode 100644 index 0000000000000..258d489fc8226 --- /dev/null +++ b/recipes/bioconductor-kidpack/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "kidpack" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 322beb70d039afe48c7107df1a498bc4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'kidney microarray data' + diff --git a/recipes/bioconductor-kidpack/post-link.sh b/recipes/bioconductor-kidpack/post-link.sh new file mode 100644 index 0000000000000..f30e762da9b94 --- /dev/null +++ b/recipes/bioconductor-kidpack/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="kidpack_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/kidpack_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/kidpack_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kidpack/bioconductor-kidpack_1.24.0_src_all.tar.gz" +) +MD5="322beb70d039afe48c7107df1a498bc4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-kidpack/pre-unlink.sh b/recipes/bioconductor-kidpack/pre-unlink.sh new file mode 100644 index 0000000000000..79a1288c4bcf6 --- /dev/null +++ b/recipes/bioconductor-kidpack/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ kidpack diff --git a/recipes/bioconductor-kimod/build.sh b/recipes/bioconductor-kimod/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-kimod/build.sh +++ b/recipes/bioconductor-kimod/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kimod/meta.yaml b/recipes/bioconductor-kimod/meta.yaml index 3e06e522220c8..ca073f0952834 100644 --- a/recipes/bioconductor-kimod/meta.yaml +++ b/recipes/bioconductor-kimod/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "kimod" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c91a16dbce166039ff2c3c2848df2a8096ae1c51c77134c3408487c5c445280d + md5: 3320975d680f42063eced2de930fe779 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package allows to work with mixed omics data (transcriptomics, proteomics, microarray-chips, rna-seq data), introducing the following improvements: distance options (for numeric and/or categorical variables) for each of the tables, bootstrap resampling techniques on the residuals matrices for all methods, that enable perform confidence ellipses for the projection of individuals, variables and biplot methodology to project variables (gene expression) on the compromise. Since the main purpose of the package is to use these techniques to omic data analysis, it includes an example data from four different microarray platforms (i.e.,Agilent, Affymetrix HGU 95, Affymetrix HGU 133 and Affymetrix HGU 133plus 2.0) on the NCI-60 cell lines.NCI60_4arrays is a list containing the NCI-60 microarray data with only few hundreds of genes randomly selected in each platform to keep the size of the package small. The data are the same that the package omicade4 used to implement the co-inertia analysis. The references in packages follow the style of the APA-6th norm.' extra: identifiers: - biotools:kimod - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-kimod + path: recipes/bioconductor-kimod + version: 1.8.0 + diff --git a/recipes/bioconductor-kinswingr/build.sh b/recipes/bioconductor-kinswingr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-kinswingr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kinswingr/meta.yaml b/recipes/bioconductor-kinswingr/meta.yaml new file mode 100644 index 0000000000000..daa7cad17dde6 --- /dev/null +++ b/recipes/bioconductor-kinswingr/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.3" %} +{% set name = "KinSwingR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2fdf011f7c6e01a7283be53eadfec809 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-sqldf + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-sqldf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'KinSwingR integrates phosphosite data derived from mass-spectrometry data and kinase-substrate predictions to predict kinase activity. Several functions allow the user to build PWM models of kinase-subtrates, statistically infer PWM:substrate matches, and integrate these data to infer kinase activity.' + diff --git a/recipes/bioconductor-kissde/build.sh b/recipes/bioconductor-kissde/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-kissde/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-kissde/meta.yaml b/recipes/bioconductor-kissde/meta.yaml new file mode 100644 index 0000000000000..bc8a6b7823662 --- /dev/null +++ b/recipes/bioconductor-kissde/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "kissDE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a68a4d0b79ff6681ae24ccd879f5caba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dss >=2.30.0,<2.31.0' + - r-aod + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gplots + - r-matrixstats + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dss >=2.30.0,<2.31.0' + - r-aod + - r-base + - r-doparallel + - r-foreach + - r-ggplot2 + - r-gplots + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Retrieves condition-specific variants in RNA-seq data (SNVs, alternative-splicings, indels). It has been developed as a post-treatment of ''KisSplice'' but can also be used with user''s own data.' + diff --git a/recipes/bioconductor-kodata/meta.yaml b/recipes/bioconductor-kodata/meta.yaml index e2106ffdf8e75..13d6095fa60b0 100644 --- a/recipes/bioconductor-kodata/meta.yaml +++ b/recipes/bioconductor-kodata/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "KOdata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9aa4e4082fadfae9f2b4c97082f47f00b3aeb5b465e3666547261924a2ccf717 + md5: e5ea569cc1a24a77599835327a104962 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Contains consensus genomic signatures (CGS) for experimental cell-line specific gene knock-outs as well as baseline gene expression data for a subset of experimental cell-lines. Intended for use with package KEGGlincs.' - +extra: + parent_recipe: + name: bioconductor-kodata + path: recipes/bioconductor-kodata + version: 1.6.0 diff --git a/recipes/bioconductor-kodata/post-link.sh b/recipes/bioconductor-kodata/post-link.sh index 74bcf8dea98a7..e2585228793e4 100644 --- a/recipes/bioconductor-kodata/post-link.sh +++ b/recipes/bioconductor-kodata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="KOdata_1.6.0.tar.gz" +FN="KOdata_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/KOdata_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/KOdata_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/KOdata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/KOdata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-kodata/bioconductor-kodata_1.8.0_src_all.tar.gz" ) -MD5="dc3b30e0ba2762efc3f80d0b9718e709" +MD5="e5ea569cc1a24a77599835327a104962" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-lapmix/build.sh b/recipes/bioconductor-lapmix/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lapmix/build.sh +++ b/recipes/bioconductor-lapmix/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lapmix/meta.yaml b/recipes/bioconductor-lapmix/meta.yaml index 95aeb71df3d8f..b5993e2c52498 100644 --- a/recipes/bioconductor-lapmix/meta.yaml +++ b/recipes/bioconductor-lapmix/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "lapmix" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 49c79ea0e469b65e65013a1160efa2e94f55f645c45cefe13d2918427f4c30ab + md5: c923e2cecb461a0f5eda9c6c1e79b1f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Laplace mixture modelling of microarray experiments. A hierarchical Bayesian approach is used, and the hyperparameters are estimated using empirical Bayes. The main purpose is to identify differentially expressed genes.' extra: identifiers: - biotools:lapmix - doi:10.1093/biostatistics/kxj032 + parent_recipe: + name: bioconductor-lapmix + path: recipes/bioconductor-lapmix + version: 1.46.0 + diff --git a/recipes/bioconductor-lapointe.db/meta.yaml b/recipes/bioconductor-lapointe.db/meta.yaml new file mode 100644 index 0000000000000..328ef83c33c30 --- /dev/null +++ b/recipes/bioconductor-lapointe.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "LAPOINTE.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 434b25ad7411201d8be6bb1a0463b387 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package containing metadata for LAPOINTE arrays assembled using data from public repositories' + diff --git a/recipes/bioconductor-lapointe.db/post-link.sh b/recipes/bioconductor-lapointe.db/post-link.sh new file mode 100644 index 0000000000000..6e4d4ba91a1d3 --- /dev/null +++ b/recipes/bioconductor-lapointe.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LAPOINTE.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LAPOINTE.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/LAPOINTE.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lapointe.db/bioconductor-lapointe.db_3.2.3_src_all.tar.gz" +) +MD5="434b25ad7411201d8be6bb1a0463b387" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lapointe.db/pre-unlink.sh b/recipes/bioconductor-lapointe.db/pre-unlink.sh new file mode 100644 index 0000000000000..64ace59db4aa4 --- /dev/null +++ b/recipes/bioconductor-lapointe.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LAPOINTE.db diff --git a/recipes/bioconductor-lbe/build.sh b/recipes/bioconductor-lbe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lbe/build.sh +++ b/recipes/bioconductor-lbe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lbe/meta.yaml b/recipes/bioconductor-lbe/meta.yaml index 0502b670e6eed..2c98a80edc9f1 100644 --- a/recipes/bioconductor-lbe/meta.yaml +++ b/recipes/bioconductor-lbe/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "LBE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d0dcc9afb41446a8678ef0462f0338c3ae8c3ae560d014401c591250922fcaba + md5: fe7324956ca41278f4c97e74910242bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: qvalue requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'LBE is an efficient procedure for estimating the proportion of true null hypotheses, the false discovery rate (and so the q-values) in the framework of estimating procedures based on the marginal distribution of the p-values without assumption for the alternative hypothesis.' extra: identifiers: - biotools:lbe - doi:10.1093/bioinformatics/bti063 + parent_recipe: + name: bioconductor-lbe + path: recipes/bioconductor-lbe + version: 1.48.0 + diff --git a/recipes/bioconductor-ldblock/build.sh b/recipes/bioconductor-ldblock/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ldblock/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ldblock/meta.yaml b/recipes/bioconductor-ldblock/meta.yaml new file mode 100644 index 0000000000000..3577e9127f876 --- /dev/null +++ b/recipes/bioconductor-ldblock/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.12.0" %} +{% set name = "ldblock" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d9097bcd8ed27b87d49e01b1e17917c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-erma >=0.14.0,<0.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-matrix + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-erma >=0.14.0,<0.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Define data structures for linkage disequilibrium measures in populations.' + diff --git a/recipes/bioconductor-lea/build.sh b/recipes/bioconductor-lea/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lea/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lea/meta.yaml b/recipes/bioconductor-lea/meta.yaml new file mode 100644 index 0000000000000..78ed685fd0d73 --- /dev/null +++ b/recipes/bioconductor-lea/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.4.0" %} +{% set name = "LEA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 09abcae8ba7f52591c344deec4c62867 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'LEA is an R package dedicated to landscape genomics and ecological association tests. LEA can run analyses of population structure and genomewide tests for local adaptation. The package includes statistical methods for estimating ancestry coefficients from large genotypic matrices and for evaluating the number of ancestral populations (snmf, pca). It performs statistical tests using latent factor mixed models for identifying genetic polymorphisms that exhibit association with environmental gradients or phenotypic traits (lfmm). LEA is mainly based on optimized C programs that can scale with the dimension of large data sets.' + diff --git a/recipes/bioconductor-ledpred/build.sh b/recipes/bioconductor-ledpred/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ledpred/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ledpred/meta.yaml b/recipes/bioconductor-ledpred/meta.yaml new file mode 100644 index 0000000000000..e1c7b71e1c537 --- /dev/null +++ b/recipes/bioconductor-ledpred/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.16.0" %} +{% set name = "LedPred" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 689b1b8c2a3248119bd8f8c4c6f16c77 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-akima + - r-base + - 'r-e1071 >=1.6' + - r-ggplot2 + - r-irr + - r-jsonlite + - r-plot3d + - r-plyr + - r-rcurl + - r-rocr + - r-testthat + run: + - r-akima + - r-base + - 'r-e1071 >=1.6' + - r-ggplot2 + - r-irr + - r-jsonlite + - r-plot3d + - r-plyr + - r-rcurl + - r-rocr + - r-testthat +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT | file LICENSE' + summary: 'This package aims at creating a predictive model of regulatory sequences used to score unknown sequences based on the content of DNA motifs, next-generation sequencing (NGS) peaks and signals and other numerical scores of the sequences using supervised classification. The package contains a workflow based on the support vector machine (SVM) algorithm that maps features to sequences, optimize SVM parameters and feature number and creates a model that can be stored and used to score the regulatory potential of unknown sequences.' + diff --git a/recipes/bioconductor-leebamviews/meta.yaml b/recipes/bioconductor-leebamviews/meta.yaml new file mode 100644 index 0000000000000..8c83e025a0fd5 --- /dev/null +++ b/recipes/bioconductor-leebamviews/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.18.0" %} +{% set name = "leeBamViews" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0ef787cb317db2a29797f2b72a513c60 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomeGraphs, biomaRt, org.Sc.sgd.db, edgeR +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'Artistic 2.0' + summary: 'data from PMID 19096707; prototype for managing multiple NGS samples' + diff --git a/recipes/bioconductor-leebamviews/post-link.sh b/recipes/bioconductor-leebamviews/post-link.sh new file mode 100644 index 0000000000000..ca748e3d760b0 --- /dev/null +++ b/recipes/bioconductor-leebamviews/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="leeBamViews_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/leeBamViews_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/leeBamViews_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-leebamviews/bioconductor-leebamviews_1.18.0_src_all.tar.gz" +) +MD5="0ef787cb317db2a29797f2b72a513c60" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-leebamviews/pre-unlink.sh b/recipes/bioconductor-leebamviews/pre-unlink.sh new file mode 100644 index 0000000000000..c94dea5bb2c68 --- /dev/null +++ b/recipes/bioconductor-leebamviews/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ leeBamViews diff --git a/recipes/bioconductor-les/build.sh b/recipes/bioconductor-les/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-les/build.sh +++ b/recipes/bioconductor-les/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-les/meta.yaml b/recipes/bioconductor-les/meta.yaml index 2bb2ed3d1f005..faa82b0edb9a1 100644 --- a/recipes/bioconductor-les/meta.yaml +++ b/recipes/bioconductor-les/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "les" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4e7b1092231c92a8a999c9305d0b42cdf2ba15ad7e1931c5fdf85afd39847788 + md5: d1f865bfb6b23e1d6dc272b84ca3c8d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, limma requirements: host: - r-base @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ''les'' package estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.' extra: identifiers: - biotools:les - doi:10.1089/cmb.2008.0226 + parent_recipe: + name: bioconductor-les + path: recipes/bioconductor-les + version: 1.30.0 + diff --git a/recipes/bioconductor-leukemiaseset/meta.yaml b/recipes/bioconductor-leukemiaseset/meta.yaml new file mode 100644 index 0000000000000..05198a36074d9 --- /dev/null +++ b/recipes/bioconductor-leukemiaseset/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "leukemiasEset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 266d9f40a851b36ce15025356ed08a72 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Expressionset containing gene expresion data from 60 bone marrow samples of patients with one of the four main types of leukemia (ALL, AML, CLL, CML) or non-leukemia.' + diff --git a/recipes/bioconductor-leukemiaseset/post-link.sh b/recipes/bioconductor-leukemiaseset/post-link.sh new file mode 100644 index 0000000000000..ed7ad9f0a000f --- /dev/null +++ b/recipes/bioconductor-leukemiaseset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="leukemiasEset_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/leukemiasEset_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/leukemiasEset_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-leukemiaseset/bioconductor-leukemiaseset_1.18.0_src_all.tar.gz" +) +MD5="266d9f40a851b36ce15025356ed08a72" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-leukemiaseset/pre-unlink.sh b/recipes/bioconductor-leukemiaseset/pre-unlink.sh new file mode 100644 index 0000000000000..a0e65ad38d47b --- /dev/null +++ b/recipes/bioconductor-leukemiaseset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ leukemiasEset diff --git a/recipes/bioconductor-levi/build.sh b/recipes/bioconductor-levi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-levi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-levi/meta.yaml b/recipes/bioconductor-levi/meta.yaml new file mode 100644 index 0000000000000..4ff914801dff0 --- /dev/null +++ b/recipes/bioconductor-levi/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "levi" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 816a51b096ed10aa182443879db1c581 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + - 'r-colorspace >=1.3-2' + - 'r-dplyr >=0.7.4' + - 'r-dt >=0.4' + - 'r-ggplot2 >=2.2.1' + - 'r-httr >=1.3.1' + - 'r-igraph >=1.2.1' + - r-knitr + - 'r-rcolorbrewer >=1.1-2' + - 'r-rcpp >=0.12.18' + - 'r-reshape2 >=1.4.3' + - 'r-shiny >=1.0.5' + - 'r-shinydashboard >=0.7.0' + - 'r-shinyjs >=1.0' + - r-testthat + - 'r-xml2 >=1.2.0' + run: + - r-base + - 'r-colorspace >=1.3-2' + - 'r-dplyr >=0.7.4' + - 'r-dt >=0.4' + - 'r-ggplot2 >=2.2.1' + - 'r-httr >=1.3.1' + - 'r-igraph >=1.2.1' + - r-knitr + - 'r-rcolorbrewer >=1.1-2' + - 'r-rcpp >=0.12.18' + - 'r-reshape2 >=1.4.3' + - 'r-shiny >=1.0.5' + - 'r-shinydashboard >=0.7.0' + - 'r-shinyjs >=1.0' + - r-testthat + - 'r-xml2 >=1.2.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The tool integrates data from biological networks with transcriptomes, displaying a heatmap with surface curves to evidence the altered regions.' + diff --git a/recipes/bioconductor-lfa/build.sh b/recipes/bioconductor-lfa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lfa/build.sh +++ b/recipes/bioconductor-lfa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lfa/meta.yaml b/recipes/bioconductor-lfa/meta.yaml index 1d06b4c260a42..318bf315e2880 100644 --- a/recipes/bioconductor-lfa/meta.yaml +++ b/recipes/bioconductor-lfa/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "lfa" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 811f74e732d71c8587289fa21542859343a5f2acedbe4e49deca34d13fed3db4 + md5: 0d6d80f6ebb2ff5c3fc03d7255c2d4e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, ggplot2 requirements: host: - r-base @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'LFA is a method for a PCA analogue on Binomial data via estimation of latent structure in the natural parameter.' extra: identifiers: - biotools:lfa - doi:10.1093/bioinformatics/btv641 + parent_recipe: + name: bioconductor-lfa + path: recipes/bioconductor-lfa + version: 1.10.0 + diff --git a/recipes/bioconductor-liebermanaidenhic2009/meta.yaml b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml new file mode 100644 index 0000000000000..94d0a649062e9 --- /dev/null +++ b/recipes/bioconductor-liebermanaidenhic2009/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.20.0" %} +{% set name = "LiebermanAidenHiC2009" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 94eef9564f0209911a15142129efd9d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-kernsmooth + run: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-kernsmooth + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package provides data that were presented in the article "Comprehensive mapping of long-range interactions reveals folding principles of the human genome", Science 2009 Oct 9;326(5950):289-93. PMID: 19815776' + diff --git a/recipes/bioconductor-liebermanaidenhic2009/post-link.sh b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh new file mode 100644 index 0000000000000..b6eb699daaca8 --- /dev/null +++ b/recipes/bioconductor-liebermanaidenhic2009/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LiebermanAidenHiC2009_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LiebermanAidenHiC2009_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/LiebermanAidenHiC2009_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-liebermanaidenhic2009/bioconductor-liebermanaidenhic2009_0.20.0_src_all.tar.gz" +) +MD5="94eef9564f0209911a15142129efd9d0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-liebermanaidenhic2009/pre-unlink.sh b/recipes/bioconductor-liebermanaidenhic2009/pre-unlink.sh new file mode 100644 index 0000000000000..f77c5aefd7079 --- /dev/null +++ b/recipes/bioconductor-liebermanaidenhic2009/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LiebermanAidenHiC2009 diff --git a/recipes/bioconductor-limma/build.sh b/recipes/bioconductor-limma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-limma/build.sh +++ b/recipes/bioconductor-limma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-limma/meta.yaml b/recipes/bioconductor-limma/meta.yaml index cd63ac25ce235..7afab488223ff 100644 --- a/recipes/bioconductor-limma/meta.yaml +++ b/recipes/bioconductor-limma/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "3.36.5" %} +{% set version = "3.38.3" %} {% set name = "limma" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dd387189502b1ab1496abb1ab51d84e3144a3628d3b8a61d76869ea84be22334 + md5: 71d46ed99a9c5267645c6ad5c6bec64b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affy, AnnotationDbi, BiasedUrn, Biobase, ellipse, GO.db, gplots, illuminaio, locfit, MASS, org.Hs.eg.db, splines, statmod (>= 1.2.2), vsn requirements: host: - r-base @@ -28,9 +29,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Data analysis, linear models and differential expression for microarray data.' extra: identifiers: - biotools:limma + parent_recipe: + name: bioconductor-limma + path: recipes/bioconductor-limma + version: 3.36.5 + diff --git a/recipes/bioconductor-limmagui/build.sh b/recipes/bioconductor-limmagui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-limmagui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-limmagui/meta.yaml b/recipes/bioconductor-limmagui/meta.yaml new file mode 100644 index 0000000000000..e64331cb628f4 --- /dev/null +++ b/recipes/bioconductor-limmagui/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.58.0" %} +{% set name = "limmaGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 294967acdf8df9dfe9242d09ba53b527 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-r2html + - r-tkrplot + - r-xtable + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-r2html + - r-tkrplot + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'A Graphical User Interface for differential expression analysis of two-color microarray data using the limma package.' + diff --git a/recipes/bioconductor-linc/build.sh b/recipes/bioconductor-linc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-linc/build.sh +++ b/recipes/bioconductor-linc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-linc/meta.yaml b/recipes/bioconductor-linc/meta.yaml index cfc99e0181c48..de436585ff083 100644 --- a/recipes/bioconductor-linc/meta.yaml +++ b/recipes/bioconductor-linc/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "LINC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fa99f4972967990f8a5517a948573fcd50df811c86affbbf1349e8144f37c855 + md5: 29086a9caad42adcd346b9efa078457e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, knitr, biomaRt requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-clusterprofiler >=3.8.1,<3.10.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-ggtree >=1.12.7,<1.14.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-reactomepa >=1.24.0,<1.26.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-ape - r-base - r-ggplot2 @@ -33,13 +34,13 @@ requirements: - 'r-rcpp >=0.11.0' - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-clusterprofiler >=3.8.1,<3.10.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-ggtree >=1.12.7,<1.14.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-reactomepa >=1.24.0,<1.26.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-ape - r-base - r-ggplot2 @@ -55,10 +56,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides methods to compute co-expression networks of lincRNAs and protein-coding genes. Biological terms associated with the sets of protein-coding genes predict the biological contexts of lincRNAs according to the ''Guilty by Association'' approach.' extra: identifiers: - biotools:linc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-linc + path: recipes/bioconductor-linc + version: 1.8.0 + diff --git a/recipes/bioconductor-lineagepulse/build.sh b/recipes/bioconductor-lineagepulse/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lineagepulse/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lineagepulse/meta.yaml b/recipes/bioconductor-lineagepulse/meta.yaml new file mode 100644 index 0000000000000..94053c8cc5638 --- /dev/null +++ b/recipes/bioconductor-lineagepulse/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.2.0" %} +{% set name = "LineagePulse" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9271369de31f071054199e8dd0781c57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-ggplot2 + - r-gplots + - r-knitr + - r-matrix + - r-rcolorbrewer + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-circlize + - r-ggplot2 + - r-gplots + - r-knitr + - r-matrix + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'LineagePulse is a differential expression and expression model fitting package tailored to single-cell RNA-seq data (scRNA-seq). LineagePulse accounts for batch effects, drop-out and variable sequencing depth. One can use LineagePulse to perform longitudinal differential expression analysis across pseudotime as a continuous coordinate or between discrete groups of cells (e.g. pre-defined clusters or experimental conditions). Expression model fits can be directly extracted from LineagePulse.' + diff --git a/recipes/bioconductor-linnorm/build.sh b/recipes/bioconductor-linnorm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-linnorm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-linnorm/meta.yaml b/recipes/bioconductor-linnorm/meta.yaml new file mode 100644 index 0000000000000..622275bb2c958 --- /dev/null +++ b/recipes/bioconductor-linnorm/meta.yaml @@ -0,0 +1,72 @@ +{% set version = "2.6.0" %} +{% set name = "Linnorm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 22fa271b9fca728cf1fe1544e536e3b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, gplots, RColorBrewer, moments, testthat +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-amap + - r-apcluster + - r-base + - r-ellipse + - r-fastcluster + - r-fpc + - r-ggdendro + - r-ggplot2 + - r-gmodels + - r-igraph + - r-mass + - r-mclust + - 'r-rcpp >=0.12.2' + - 'r-rcpparmadillo >=0.8.100.1.0' + - r-rtsne + - r-statmod + - r-vegan + - r-zoo + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-amap + - r-apcluster + - r-base + - r-ellipse + - r-fastcluster + - r-fpc + - r-ggdendro + - r-ggplot2 + - r-gmodels + - r-igraph + - r-mass + - r-mclust + - 'r-rcpp >=0.12.2' + - 'r-rcpparmadillo >=0.8.100.1.0' + - r-rtsne + - r-statmod + - r-vegan + - r-zoo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Linnorm is an R package for the analysis of RNA-seq, scRNA-seq, ChIP-seq count data or any large scale count data. It transforms such datasets for parametric tests. In addition to the transformtion function (Linnorm), the following pipelines are implemented: 1. Library size/Batch effect normalization (Linnorm.Norm), 2. Cell subpopluation analysis and visualization using t-SNE or PCA K-means clustering or Hierarchical clustering (Linnorm.tSNE, Linnorm.PCA, Linnorm.HClust), 3. Differential expression analysis or differential peak detection using limma (Linnorm.limma), 4. Highly variable gene discovery and visualization (Linnorm.HVar), 5. Gene correlation network analysis and visualization (Linnorm.Cor), 6. Stable gene selection for scRNA-seq data; for users without or do not want to rely on spike-in genes (Linnorm.SGenes). 7. Data imputation. (under development) (Linnorm.DataImput). Linnorm can work with raw count, CPM, RPKM, FPKM and TPM. Additionally, the RnaXSim function is included for simulating RNA-seq data for the evaluation of DEG analysis methods.' + diff --git a/recipes/bioconductor-liquidassociation/build.sh b/recipes/bioconductor-liquidassociation/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-liquidassociation/build.sh +++ b/recipes/bioconductor-liquidassociation/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-liquidassociation/meta.yaml b/recipes/bioconductor-liquidassociation/meta.yaml index 19a46e1079e14..8479f03eb2248 100644 --- a/recipes/bioconductor-liquidassociation/meta.yaml +++ b/recipes/bioconductor-liquidassociation/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "LiquidAssociation" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4ced300a886d072525ba67663e38b61546cd4dda9d650df0c1109b29977fe26e + md5: 0c5372f29db62136b3797b29b3debe18 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-yeastcc >=1.20.0,<1.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-yeastcc >=1.22.0,<1.23.0' - r-base - r-geepack run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-yeastcc >=1.20.0,<1.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-yeastcc >=1.22.0,<1.23.0' - r-base - r-geepack test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'The package contains functions for calculate direct and model-based estimators for liquid association. It also provides functions for testing the existence of liquid association given a gene triplet data.' extra: identifiers: - biotools:liquidassociation - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-liquidassociation + path: recipes/bioconductor-liquidassociation + version: 1.34.0 + diff --git a/recipes/bioconductor-listeretalbsseq/meta.yaml b/recipes/bioconductor-listeretalbsseq/meta.yaml new file mode 100644 index 0000000000000..2ece8e57c6058 --- /dev/null +++ b/recipes/bioconductor-listeretalbsseq/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.14.0" %} +{% set name = "ListerEtAlBSseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c36fbf6d20c087f6591c9c39174878cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg18 +requirements: + host: + - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-methylpipe >=1.16.0,<1.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'Artistic 2.0' + summary: 'Base resolution bisulfite sequencing data of Human DNA methylomes' + diff --git a/recipes/bioconductor-listeretalbsseq/post-link.sh b/recipes/bioconductor-listeretalbsseq/post-link.sh new file mode 100644 index 0000000000000..e4d791ab0e81e --- /dev/null +++ b/recipes/bioconductor-listeretalbsseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ListerEtAlBSseq_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ListerEtAlBSseq_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/ListerEtAlBSseq_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-listeretalbsseq/bioconductor-listeretalbsseq_1.14.0_src_all.tar.gz" +) +MD5="c36fbf6d20c087f6591c9c39174878cb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-listeretalbsseq/pre-unlink.sh b/recipes/bioconductor-listeretalbsseq/pre-unlink.sh new file mode 100644 index 0000000000000..42c55cb06feef --- /dev/null +++ b/recipes/bioconductor-listeretalbsseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ListerEtAlBSseq diff --git a/recipes/bioconductor-lmdme/build.sh b/recipes/bioconductor-lmdme/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lmdme/build.sh +++ b/recipes/bioconductor-lmdme/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lmdme/meta.yaml b/recipes/bioconductor-lmdme/meta.yaml index c2d8b9063b5bb..72aa95c4b4eeb 100644 --- a/recipes/bioconductor-lmdme/meta.yaml +++ b/recipes/bioconductor-lmdme/meta.yaml @@ -1,39 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "lmdme" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2f9ffe3b00ec3647ce97a97a2d1295cc1aafd8cf8cfd8733a428af7db210ec32 + md5: d84c1a13e28adbb587d9006cff7938db build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-stemhypoxia >=1.16.0,<1.18.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-stemhypoxia >=1.18.0,<1.19.0' - r-base - r-pls run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-stemhypoxia >=1.16.0,<1.18.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-stemhypoxia >=1.18.0,<1.19.0' - r-base - r-pls test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'linear ANOVA decomposition of Multivariate Designed Experiments implementation based on limma lmFit. Features: i)Flexible formula type interface, ii) Fast limma based implementation, iii) p-values for each estimated coefficient levels in each factor, iv) F values for factor effects and v) plotting functions for PCA and PLS.' extra: identifiers: - biotools:lmdme + parent_recipe: + name: bioconductor-lmdme + path: recipes/bioconductor-lmdme + version: 1.22.0 + diff --git a/recipes/bioconductor-lmgene/build.sh b/recipes/bioconductor-lmgene/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lmgene/build.sh +++ b/recipes/bioconductor-lmgene/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lmgene/conda_build_config.yaml b/recipes/bioconductor-lmgene/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-lmgene/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-lmgene/meta.yaml b/recipes/bioconductor-lmgene/meta.yaml index d96dfdcd880d5..acf41d8512f16 100644 --- a/recipes/bioconductor-lmgene/meta.yaml +++ b/recipes/bioconductor-lmgene/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "LMGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9a602a29c969ca5ba6f93c3e6014f40242e5e841cf19a3fa2d1a6617efb2a49e + md5: 1d5e6672bd23b4c523568b712545643c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-survival run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-survival test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'LMGene package for analysis of microarray data using a linear model and glog data transformation' extra: identifiers: - biotools:lmgene - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-lmgene + path: recipes/bioconductor-lmgene + version: 2.36.0 + diff --git a/recipes/bioconductor-lobstahs/build.sh b/recipes/bioconductor-lobstahs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lobstahs/build.sh +++ b/recipes/bioconductor-lobstahs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lobstahs/meta.yaml b/recipes/bioconductor-lobstahs/meta.yaml index 728828b5a2b71..fa33223778e96 100644 --- a/recipes/bioconductor-lobstahs/meta.yaml +++ b/recipes/bioconductor-lobstahs/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "LOBSTAHS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4bcf09ab10499f0c40ef9bcdcfb447a5ae0224a6b60f8f1e33b31c389081f9f8 + md5: 57f2cb3489b676d6e0e976df889911a7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: PtH2O2lipids, knitr, rmarkdown requirements: host: - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base run: - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3) + file LICENSE' summary: 'LOBSTAHS is a multifunction package for screening, annotation, and putative identification of mass spectral features in large, HPLC-MS lipid datasets. In silico data for a wide range of lipids, oxidized lipids, and oxylipins can be generated from user-supplied structural criteria with a database generation function. LOBSTAHS then applies these databases to assign putative compound identities to features in any high-mass accuracy dataset that has been processed using xcms and CAMERA. Users can then apply a series of orthogonal screening criteria based on adduct ion formation patterns, chromatographic retention time, and other properties, to evaluate and assign confidence scores to this list of preliminary assignments. During the screening routine, LOBSTAHS rejects assignments that do not meet the specified criteria, identifies potential isomers and isobars, and assigns a variety of annotation codes to assist the user in evaluating the accuracy of each assignment.' extra: identifiers: - biotools:lobstahs + parent_recipe: + name: bioconductor-lobstahs + path: recipes/bioconductor-lobstahs + version: 1.6.0 + diff --git a/recipes/bioconductor-loci2path/build.sh b/recipes/bioconductor-loci2path/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-loci2path/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-loci2path/meta.yaml b/recipes/bioconductor-loci2path/meta.yaml new file mode 100644 index 0000000000000..15928a2b4bd32 --- /dev/null +++ b/recipes/bioconductor-loci2path/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.2.0" %} +{% set name = "loci2path" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 90e463d21339295ec91413e52911e733 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-pheatmap + - r-rcolorbrewer + - r-wordcloud + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-pheatmap + - r-rcolorbrewer + - r-wordcloud +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'loci2path performs statistics-rigorous enrichment analysis of eQTLs in genomic regions of interest. Using eQTL collections provided by the Genotype-Tissue Expression (GTEx) project and pathway collections from MSigDB.' + diff --git a/recipes/bioconductor-logicfs/build.sh b/recipes/bioconductor-logicfs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-logicfs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-logicfs/meta.yaml b/recipes/bioconductor-logicfs/meta.yaml new file mode 100644 index 0000000000000..8a923b36e1af9 --- /dev/null +++ b/recipes/bioconductor-logicfs/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.2.0" %} +{% set name = "logicFS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c938e0a3bb72e81baeb62791e8cbd6d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: genefilter, siggenes +requirements: + host: + - r-base + - r-logicreg + - r-mcbiopi + - r-survival + run: + - r-base + - r-logicreg + - r-mcbiopi + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'Identification of interactions between binary variables using Logic Regression. Can, e.g., be used to find interesting SNP interactions. Contains also a bagging version of logic regression for classification.' + diff --git a/recipes/bioconductor-logitt/build.sh b/recipes/bioconductor-logitt/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-logitt/build.sh +++ b/recipes/bioconductor-logitt/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-logitt/conda_build_config.yaml b/recipes/bioconductor-logitt/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-logitt/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-logitt/meta.yaml b/recipes/bioconductor-logitt/meta.yaml index ec69b83e50f09..6032b4f052366 100644 --- a/recipes/bioconductor-logitt/meta.yaml +++ b/recipes/bioconductor-logitt/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "logitT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e788db17ee40993ffb464460e63d2a790d203135cfbcf176d60ddea9b2092e7a + md5: b84aee3b9e43a884c6119562b543a9f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: SpikeInSubset requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The logitT library implements the Logit-t algorithm introduced in --A high performance test of differential gene expression for oligonucleotide arrays-- by William J Lemon, Sandya Liyanarachchi and Ming You for use with Affymetrix data stored in an AffyBatch object in R.' extra: identifiers: - biotools:logitt - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-logitt + path: recipes/bioconductor-logitt + version: 1.38.0 + diff --git a/recipes/bioconductor-logolas/build.sh b/recipes/bioconductor-logolas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-logolas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-logolas/meta.yaml b/recipes/bioconductor-logolas/meta.yaml new file mode 100644 index 0000000000000..0505ab4e0bd5e --- /dev/null +++ b/recipes/bioconductor-logolas/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.6.0" %} +{% set name = "Logolas" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3aacdce238af176577fbf05161b54325 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, Biobase, devtools, xtable, gridExtra, RColorBrewer, seqLogo, ggseqlogo +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-ggplot2 + - r-gridbase + - r-laplacesdemon + - r-squarem + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-ggplot2 + - r-gridbase + - r-laplacesdemon + - r-squarem +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Produces logo plots highlighting both enrichment and depletion of characters, allows for plotting of string symbols, and performs scaling of position-weights adaptively, along with several fun stylizations.' + diff --git a/recipes/bioconductor-lol/build.sh b/recipes/bioconductor-lol/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lol/build.sh +++ b/recipes/bioconductor-lol/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lol/meta.yaml b/recipes/bioconductor-lol/meta.yaml index c387b9ac2441d..0d0957a4ef61b 100644 --- a/recipes/bioconductor-lol/meta.yaml +++ b/recipes/bioconductor-lol/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "lol" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 147983f5f1a7dd599d0c363e26c7336d185324a204f6fa807ba24b6490cfc0cf + md5: 9339f2a964b2d4470286d87eaaba88cb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Various optimization methods for Lasso inference with matrix warpper' extra: identifiers: - biotools:lol - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-lol + path: recipes/bioconductor-lol + version: 1.28.0 + diff --git a/recipes/bioconductor-lola/build.sh b/recipes/bioconductor-lola/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lola/build.sh +++ b/recipes/bioconductor-lola/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lola/meta.yaml b/recipes/bioconductor-lola/meta.yaml index d4a67400e5784..3e18406faecd2 100644 --- a/recipes/bioconductor-lola/meta.yaml +++ b/recipes/bioconductor-lola/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "LOLA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fe640761901f36c325ca8a577ed80b9eb72e71151fee9d01b40abfee37b3075e + md5: e57b955b1d44900a375fce04c3217d1f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: parallel, testthat, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-reshape2 @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides functions for testing overlap of sets of genomic regions with public and custom region set (genomic ranges) databases. This makes it possible to do automated enrichment analysis for genomic region sets, thus facilitating interpretation of functional genomics and epigenomics data.' extra: identifiers: - biotools:lola - doi:10.1093/bioinformatics/btv612 + parent_recipe: + name: bioconductor-lola + path: recipes/bioconductor-lola + version: 1.10.0 + diff --git a/recipes/bioconductor-loomexperiment/build.sh b/recipes/bioconductor-loomexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-loomexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-loomexperiment/meta.yaml b/recipes/bioconductor-loomexperiment/meta.yaml new file mode 100644 index 0000000000000..8396a235ce8cf --- /dev/null +++ b/recipes/bioconductor-loomexperiment/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.1" %} +{% set name = "LoomExperiment" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 332c0891e383c84ae4a4c7cf92cd9727 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr +requirements: + host: + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The LoomExperiment class provide a means to easily convert Bioconductor''s "Experiment" classes to loom files and vice versa.' + diff --git a/recipes/bioconductor-lowmaca/build.sh b/recipes/bioconductor-lowmaca/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lowmaca/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lowmaca/meta.yaml b/recipes/bioconductor-lowmaca/meta.yaml new file mode 100644 index 0000000000000..30fb94fe94e7f --- /dev/null +++ b/recipes/bioconductor-lowmaca/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.12.0" %} +{% set name = "LowMACA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 08f3aa079582ae9129e9e5b82ba1687a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: clustalo, gs, perl +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-lowmacaannotation >=0.99.0,<0.100.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - r-base + - r-cgdsr + - r-data.table + - r-httr + - r-rcolorbrewer + - r-reshape2 + - r-stringr + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-lowmacaannotation >=0.99.0,<0.100.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - r-base + - r-cgdsr + - r-data.table + - r-httr + - r-rcolorbrewer + - r-reshape2 + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The LowMACA package is a simple suite of tools to investigate and analyze the mutation profile of several proteins or pfam domains via consensus alignment. You can conduct an hypothesis driven exploratory analysis using our package simply providing a set of genes or pfam domains of your interest.' + diff --git a/recipes/bioconductor-lowmacaannotation/meta.yaml b/recipes/bioconductor-lowmacaannotation/meta.yaml new file mode 100644 index 0000000000000..affdac27630a2 --- /dev/null +++ b/recipes/bioconductor-lowmacaannotation/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.99.3" %} +{% set name = "LowMACAAnnotation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9e0d3fe7f30fe48aef9c4387eb5bacfa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: GPL-3 + summary: 'A package containing the data to run LowMACA package.' + diff --git a/recipes/bioconductor-lowmacaannotation/post-link.sh b/recipes/bioconductor-lowmacaannotation/post-link.sh new file mode 100644 index 0000000000000..619f1e4ca11de --- /dev/null +++ b/recipes/bioconductor-lowmacaannotation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LowMACAAnnotation_0.99.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LowMACAAnnotation_0.99.3.tar.gz" + "https://bioarchive.galaxyproject.org/LowMACAAnnotation_0.99.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lowmacaannotation/bioconductor-lowmacaannotation_0.99.3_src_all.tar.gz" +) +MD5="9e0d3fe7f30fe48aef9c4387eb5bacfa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lowmacaannotation/pre-unlink.sh b/recipes/bioconductor-lowmacaannotation/pre-unlink.sh new file mode 100644 index 0000000000000..04aa6180cff99 --- /dev/null +++ b/recipes/bioconductor-lowmacaannotation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LowMACAAnnotation diff --git a/recipes/bioconductor-lpe/build.sh b/recipes/bioconductor-lpe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lpe/build.sh +++ b/recipes/bioconductor-lpe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpe/meta.yaml b/recipes/bioconductor-lpe/meta.yaml index 346677eb88ace..e87219cd01e1e 100644 --- a/recipes/bioconductor-lpe/meta.yaml +++ b/recipes/bioconductor-lpe/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "LPE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aca45e60269876d9490d4eb66b66a9fcf6f2c9b0f144b404f7ae03159cd04716 + md5: 7ddf8da425759856e5c6071ec4762b6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This LPE library is used to do significance analysis of microarray data with small number of replicates. It uses resampling based FDR adjustment, and gives less conservative results than traditional ''BH'' or ''BY'' procedures. Data accepted is raw data in txt format from MAS4, MAS5 or dChip. Data can also be supplied after normalization. LPE library is primarily used for analyzing data between two conditions. To use it for paired data, see LPEP library. For using LPE in multiple conditions, use HEM library.' extra: identifiers: - biotools:lpe - doi:10.1093/bioinformatics/btg264 + parent_recipe: + name: bioconductor-lpe + path: recipes/bioconductor-lpe + version: 1.54.0 + diff --git a/recipes/bioconductor-lpeadj/build.sh b/recipes/bioconductor-lpeadj/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lpeadj/build.sh +++ b/recipes/bioconductor-lpeadj/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpeadj/meta.yaml b/recipes/bioconductor-lpeadj/meta.yaml index 2f36df11d812d..3099fb43c137a 100644 --- a/recipes/bioconductor-lpeadj/meta.yaml +++ b/recipes/bioconductor-lpeadj/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "LPEadj" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fc320f61faefa13016d0b2a0a447f167f60951b747d8463f75af51364c64eadf + md5: a50c028087f227ddee20391e296bc199 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-lpe >=1.54.0,<1.56.0' + - 'bioconductor-lpe >=1.56.0,<1.57.0' - r-base run: - - 'bioconductor-lpe >=1.54.0,<1.56.0' + - 'bioconductor-lpe >=1.56.0,<1.57.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Two options are added to the LPE algorithm. The original LPE method sets all variances below the max variance in the ordered distribution of variances to the maximum variance. in LPEadj this option is turned off by default. The second option is to use a variance adjustment based on sample size rather than pi/2. By default the LPEadj uses the sample size based variance adjustment.' extra: identifiers: - biotools:lpeadj - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-lpeadj + path: recipes/bioconductor-lpeadj + version: 1.40.0 + diff --git a/recipes/bioconductor-lpnet/build.sh b/recipes/bioconductor-lpnet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lpnet/build.sh +++ b/recipes/bioconductor-lpnet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpnet/meta.yaml b/recipes/bioconductor-lpnet/meta.yaml index 22162263f6216..5c573da5724c9 100644 --- a/recipes/bioconductor-lpnet/meta.yaml +++ b/recipes/bioconductor-lpnet/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "lpNet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a93576d46ff8d549c86f2fc4a03fa66dfe2320f57928693121446990454d4ab2 + md5: 80548ee68471e1474411ea5d691d205b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' - r-base - r-lpsolve run: - - 'bioconductor-nem >=2.54.0,<2.56.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' - r-base - r-lpsolve test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'lpNet aims at infering biological networks, in particular signaling and gene networks. For that it takes perturbation data, either steady-state or time-series, as input and generates an LP model which allows the inference of signaling networks. For parameter identification either leave-one-out cross-validation or stratified n-fold cross-validation can be used.' extra: identifiers: - biotools:lpnet - doi:10.1093/bioinformatics/btv327 + parent_recipe: + name: bioconductor-lpnet + path: recipes/bioconductor-lpnet + version: 2.12.0 + diff --git a/recipes/bioconductor-lpsymphony/build.sh b/recipes/bioconductor-lpsymphony/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lpsymphony/build.sh +++ b/recipes/bioconductor-lpsymphony/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lpsymphony/meta.yaml b/recipes/bioconductor-lpsymphony/meta.yaml index 0e9cdfc30a501..f7045da8d94da 100644 --- a/recipes/bioconductor-lpsymphony/meta.yaml +++ b/recipes/bioconductor-lpsymphony/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "lpsymphony" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d94a93d4365f2e5e2cbd8e078c4deec2592e96122105a577cc8122db0ec518c0 + md5: ef6e41c4c16fa4ba123f2095618eff4b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr requirements: host: - r-base @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: EPL summary: 'This package was derived from Rsymphony_0.1-17 from CRAN. These packages provide an R interface to SYMPHONY, an open-source linear programming solver written in C++. The main difference between this package and Rsymphony is that it includes the solver source code (SYMPHONY version 5.6), while Rsymphony expects to find header and library files on the users'' system. Thus the intention of lpsymphony is to provide an easy to install interface to SYMPHONY. For Windows, precompiled DLLs are included in this package.' extra: identifiers: - biotools:lpsymphony - doi:10.1007/0-387-23529-9_5 + parent_recipe: + name: bioconductor-lpsymphony + path: recipes/bioconductor-lpsymphony + version: 1.8.0 + diff --git a/recipes/bioconductor-lrbase.ath.eg.db/meta.yaml b/recipes/bioconductor-lrbase.ath.eg.db/meta.yaml new file mode 100644 index 0000000000000..ca67a7d1095b4 --- /dev/null +++ b/recipes/bioconductor-lrbase.ath.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Ath.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6e0a90bea4464b7240e9232181f52dfe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.ath.eg.db/post-link.sh b/recipes/bioconductor-lrbase.ath.eg.db/post-link.sh new file mode 100644 index 0000000000000..5eb0651a81207 --- /dev/null +++ b/recipes/bioconductor-lrbase.ath.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Ath.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Ath.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Ath.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.ath.eg.db/bioconductor-lrbase.ath.eg.db_0.99.1_src_all.tar.gz" +) +MD5="6e0a90bea4464b7240e9232181f52dfe" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.ath.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.ath.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..7eaf634a2eeb5 --- /dev/null +++ b/recipes/bioconductor-lrbase.ath.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Ath.eg.db diff --git a/recipes/bioconductor-lrbase.bta.eg.db/meta.yaml b/recipes/bioconductor-lrbase.bta.eg.db/meta.yaml new file mode 100644 index 0000000000000..2b11c4b6f3844 --- /dev/null +++ b/recipes/bioconductor-lrbase.bta.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Bta.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 86857900bc1930ba591657acf645da0c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.bta.eg.db/post-link.sh b/recipes/bioconductor-lrbase.bta.eg.db/post-link.sh new file mode 100644 index 0000000000000..aceeebac86b9b --- /dev/null +++ b/recipes/bioconductor-lrbase.bta.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Bta.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Bta.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Bta.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.bta.eg.db/bioconductor-lrbase.bta.eg.db_0.99.1_src_all.tar.gz" +) +MD5="86857900bc1930ba591657acf645da0c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.bta.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.bta.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..332fe91f877de --- /dev/null +++ b/recipes/bioconductor-lrbase.bta.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Bta.eg.db diff --git a/recipes/bioconductor-lrbase.cel.eg.db/meta.yaml b/recipes/bioconductor-lrbase.cel.eg.db/meta.yaml new file mode 100644 index 0000000000000..cae1f981fd8e9 --- /dev/null +++ b/recipes/bioconductor-lrbase.cel.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Cel.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5dab8f6ffaaa906809ac88f08a19c1a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.cel.eg.db/post-link.sh b/recipes/bioconductor-lrbase.cel.eg.db/post-link.sh new file mode 100644 index 0000000000000..347f71f388924 --- /dev/null +++ b/recipes/bioconductor-lrbase.cel.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Cel.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Cel.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Cel.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.cel.eg.db/bioconductor-lrbase.cel.eg.db_0.99.1_src_all.tar.gz" +) +MD5="5dab8f6ffaaa906809ac88f08a19c1a8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.cel.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.cel.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..f6a04e48f27b3 --- /dev/null +++ b/recipes/bioconductor-lrbase.cel.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Cel.eg.db diff --git a/recipes/bioconductor-lrbase.dme.eg.db/meta.yaml b/recipes/bioconductor-lrbase.dme.eg.db/meta.yaml new file mode 100644 index 0000000000000..a8992bae84fad --- /dev/null +++ b/recipes/bioconductor-lrbase.dme.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Dme.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7b6f9855980744f690dab1eb844b064c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.dme.eg.db/post-link.sh b/recipes/bioconductor-lrbase.dme.eg.db/post-link.sh new file mode 100644 index 0000000000000..0ec4733f44b3f --- /dev/null +++ b/recipes/bioconductor-lrbase.dme.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Dme.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Dme.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Dme.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.dme.eg.db/bioconductor-lrbase.dme.eg.db_0.99.1_src_all.tar.gz" +) +MD5="7b6f9855980744f690dab1eb844b064c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.dme.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.dme.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..3d4d2c5bb8bb4 --- /dev/null +++ b/recipes/bioconductor-lrbase.dme.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Dme.eg.db diff --git a/recipes/bioconductor-lrbase.dre.eg.db/meta.yaml b/recipes/bioconductor-lrbase.dre.eg.db/meta.yaml new file mode 100644 index 0000000000000..9404277bd0145 --- /dev/null +++ b/recipes/bioconductor-lrbase.dre.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Dre.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c42713ece3330b6905a5d7bca909e560 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.dre.eg.db/post-link.sh b/recipes/bioconductor-lrbase.dre.eg.db/post-link.sh new file mode 100644 index 0000000000000..671abaea9fa3d --- /dev/null +++ b/recipes/bioconductor-lrbase.dre.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Dre.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Dre.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Dre.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.dre.eg.db/bioconductor-lrbase.dre.eg.db_0.99.1_src_all.tar.gz" +) +MD5="c42713ece3330b6905a5d7bca909e560" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.dre.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.dre.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..9ae3b56bbb427 --- /dev/null +++ b/recipes/bioconductor-lrbase.dre.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Dre.eg.db diff --git a/recipes/bioconductor-lrbase.gga.eg.db/meta.yaml b/recipes/bioconductor-lrbase.gga.eg.db/meta.yaml new file mode 100644 index 0000000000000..539c2db8230b1 --- /dev/null +++ b/recipes/bioconductor-lrbase.gga.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Gga.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 373e0e029475e91e3eacf59e600b375f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.gga.eg.db/post-link.sh b/recipes/bioconductor-lrbase.gga.eg.db/post-link.sh new file mode 100644 index 0000000000000..96480ed6e5cf3 --- /dev/null +++ b/recipes/bioconductor-lrbase.gga.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Gga.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Gga.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Gga.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.gga.eg.db/bioconductor-lrbase.gga.eg.db_0.99.1_src_all.tar.gz" +) +MD5="373e0e029475e91e3eacf59e600b375f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.gga.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.gga.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..aab133d61ac5a --- /dev/null +++ b/recipes/bioconductor-lrbase.gga.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Gga.eg.db diff --git a/recipes/bioconductor-lrbase.hsa.eg.db/meta.yaml b/recipes/bioconductor-lrbase.hsa.eg.db/meta.yaml new file mode 100644 index 0000000000000..50d84899b22f0 --- /dev/null +++ b/recipes/bioconductor-lrbase.hsa.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Hsa.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e9efba6f9b13b7a82e1c33ce1f09ea70 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.hsa.eg.db/post-link.sh b/recipes/bioconductor-lrbase.hsa.eg.db/post-link.sh new file mode 100644 index 0000000000000..c10c513ff0574 --- /dev/null +++ b/recipes/bioconductor-lrbase.hsa.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Hsa.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Hsa.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Hsa.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.hsa.eg.db/bioconductor-lrbase.hsa.eg.db_0.99.1_src_all.tar.gz" +) +MD5="e9efba6f9b13b7a82e1c33ce1f09ea70" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.hsa.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.hsa.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..6386667ecbd3d --- /dev/null +++ b/recipes/bioconductor-lrbase.hsa.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Hsa.eg.db diff --git a/recipes/bioconductor-lrbase.mmu.eg.db/meta.yaml b/recipes/bioconductor-lrbase.mmu.eg.db/meta.yaml new file mode 100644 index 0000000000000..5177cb384ae50 --- /dev/null +++ b/recipes/bioconductor-lrbase.mmu.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Mmu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 53e34f533656c1fd9a883d8ba3524351 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.mmu.eg.db/post-link.sh b/recipes/bioconductor-lrbase.mmu.eg.db/post-link.sh new file mode 100644 index 0000000000000..12e195e5f095a --- /dev/null +++ b/recipes/bioconductor-lrbase.mmu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Mmu.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Mmu.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Mmu.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.mmu.eg.db/bioconductor-lrbase.mmu.eg.db_0.99.1_src_all.tar.gz" +) +MD5="53e34f533656c1fd9a883d8ba3524351" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.mmu.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.mmu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..226e786f41455 --- /dev/null +++ b/recipes/bioconductor-lrbase.mmu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Mmu.eg.db diff --git a/recipes/bioconductor-lrbase.pab.eg.db/meta.yaml b/recipes/bioconductor-lrbase.pab.eg.db/meta.yaml new file mode 100644 index 0000000000000..726aa61bd1e65 --- /dev/null +++ b/recipes/bioconductor-lrbase.pab.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Pab.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7492982789b07131beb6f0f9d9ad6743 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.pab.eg.db/post-link.sh b/recipes/bioconductor-lrbase.pab.eg.db/post-link.sh new file mode 100644 index 0000000000000..66c7eb83fc0cb --- /dev/null +++ b/recipes/bioconductor-lrbase.pab.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Pab.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Pab.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Pab.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.pab.eg.db/bioconductor-lrbase.pab.eg.db_0.99.1_src_all.tar.gz" +) +MD5="7492982789b07131beb6f0f9d9ad6743" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.pab.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.pab.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..5dd22b6184635 --- /dev/null +++ b/recipes/bioconductor-lrbase.pab.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Pab.eg.db diff --git a/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml b/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml new file mode 100644 index 0000000000000..d840fdd049d22 --- /dev/null +++ b/recipes/bioconductor-lrbase.rno.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Rno.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a1c517df2d7c1d00aa51db7a9dec29f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh b/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh new file mode 100644 index 0000000000000..e26092454d577 --- /dev/null +++ b/recipes/bioconductor-lrbase.rno.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Rno.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Rno.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Rno.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.rno.eg.db/bioconductor-lrbase.rno.eg.db_0.99.1_src_all.tar.gz" +) +MD5="a1c517df2d7c1d00aa51db7a9dec29f1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.rno.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.rno.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b2f96310f5818 --- /dev/null +++ b/recipes/bioconductor-lrbase.rno.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Rno.eg.db diff --git a/recipes/bioconductor-lrbase.ssc.eg.db/meta.yaml b/recipes/bioconductor-lrbase.ssc.eg.db/meta.yaml new file mode 100644 index 0000000000000..8b8a9c3e5f6fd --- /dev/null +++ b/recipes/bioconductor-lrbase.ssc.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Ssc.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9d3d86ae876cccc7dd930ae11dfa9c65 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.ssc.eg.db/post-link.sh b/recipes/bioconductor-lrbase.ssc.eg.db/post-link.sh new file mode 100644 index 0000000000000..62442c56caf92 --- /dev/null +++ b/recipes/bioconductor-lrbase.ssc.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Ssc.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Ssc.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Ssc.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.ssc.eg.db/bioconductor-lrbase.ssc.eg.db_0.99.1_src_all.tar.gz" +) +MD5="9d3d86ae876cccc7dd930ae11dfa9c65" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.ssc.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.ssc.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..f993974dae0a3 --- /dev/null +++ b/recipes/bioconductor-lrbase.ssc.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Ssc.eg.db diff --git a/recipes/bioconductor-lrbase.xtr.eg.db/meta.yaml b/recipes/bioconductor-lrbase.xtr.eg.db/meta.yaml new file mode 100644 index 0000000000000..24d2a6f8caeb7 --- /dev/null +++ b/recipes/bioconductor-lrbase.xtr.eg.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "0.99.1" %} +{% set name = "LRBase.Xtr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 15a623c432ff779fd062087b836eabbb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + run: + - 'bioconductor-lrbasedbi >=1.0.0,<1.1.0' + - r-base + - r-rsqlite + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the LRBaseDb object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-lrbase.xtr.eg.db/post-link.sh b/recipes/bioconductor-lrbase.xtr.eg.db/post-link.sh new file mode 100644 index 0000000000000..38f89c9e3c066 --- /dev/null +++ b/recipes/bioconductor-lrbase.xtr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LRBase.Xtr.eg.db_0.99.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LRBase.Xtr.eg.db_0.99.1.tar.gz" + "https://bioarchive.galaxyproject.org/LRBase.Xtr.eg.db_0.99.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lrbase.xtr.eg.db/bioconductor-lrbase.xtr.eg.db_0.99.1_src_all.tar.gz" +) +MD5="15a623c432ff779fd062087b836eabbb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lrbase.xtr.eg.db/pre-unlink.sh b/recipes/bioconductor-lrbase.xtr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..74a9c95c82416 --- /dev/null +++ b/recipes/bioconductor-lrbase.xtr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LRBase.Xtr.eg.db diff --git a/recipes/bioconductor-lrbasedbi/build.sh b/recipes/bioconductor-lrbasedbi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lrbasedbi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lrbasedbi/meta.yaml b/recipes/bioconductor-lrbasedbi/meta.yaml new file mode 100644 index 0000000000000..c84d8aeba59e0 --- /dev/null +++ b/recipes/bioconductor-lrbasedbi/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "LRBaseDbi" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f983eacbbe7593cfae1996944d5f4710 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-dbi + - r-rsqlite + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-dbi + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Interface to construct LRBase package (LRBase.XXX.eg.db).' + diff --git a/recipes/bioconductor-lumi/build.sh b/recipes/bioconductor-lumi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lumi/build.sh +++ b/recipes/bioconductor-lumi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lumi/conda_build_config.yaml b/recipes/bioconductor-lumi/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-lumi/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-lumi/meta.yaml b/recipes/bioconductor-lumi/meta.yaml index f1a59c3d96245..8b3e33a4ad4d5 100644 --- a/recipes/bioconductor-lumi/meta.yaml +++ b/recipes/bioconductor-lumi/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "lumi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d272815d5c876f5254f5388da3fd6fcff47d3467be2e0d881f41ad8a4769b419 + md5: 8d2ae23d6b7c8021a10020c0f42baa71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: beadarray, limma, vsn, lumiBarnes, lumiHumanAll.db, lumiHumanIDMapping, genefilter, RColorBrewer requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-kernsmooth @@ -35,14 +37,14 @@ requirements: - r-nleqslv - r-rsqlite run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-dbi - r-kernsmooth @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'The lumi package provides an integrated solution for the Illumina microarray data analysis. It includes functions of Illumina BeadStudio (GenomeStudio) data input, quality control, BeadArray-specific variance stabilization, normalization and gene annotation at the probe level. It also includes the functions of processing Illumina methylation microarrays, especially Illumina Infinium methylation microarrays.' extra: identifiers: - biotools:lumi + parent_recipe: + name: bioconductor-lumi + path: recipes/bioconductor-lumi + version: 2.32.0 + diff --git a/recipes/bioconductor-lumibarnes/meta.yaml b/recipes/bioconductor-lumibarnes/meta.yaml new file mode 100644 index 0000000000000..71467219403d9 --- /dev/null +++ b/recipes/bioconductor-lumibarnes/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "lumiBarnes" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1bd89b6adf74489e3e5a23434809ebac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'The Barnes benchmark dataset can be used to evaluate the algorithms for Illumina microarrays. It measured a titration series of two human tissues, blood and placenta, and includes six samples with the titration ratio of blood and placenta as 100:0, 95:5, 75:25, 50:50, 25:75 and 0:100. The samples were hybridized on HumanRef-8 BeadChip (Illumina, Inc) in duplicate. The data is loaded as an LumiBatch Object (see documents in the lumi package).' + diff --git a/recipes/bioconductor-lumibarnes/post-link.sh b/recipes/bioconductor-lumibarnes/post-link.sh new file mode 100644 index 0000000000000..62c77e5d0dc5c --- /dev/null +++ b/recipes/bioconductor-lumibarnes/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiBarnes_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lumiBarnes_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiBarnes_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumibarnes/bioconductor-lumibarnes_1.22.0_src_all.tar.gz" +) +MD5="1bd89b6adf74489e3e5a23434809ebac" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumibarnes/pre-unlink.sh b/recipes/bioconductor-lumibarnes/pre-unlink.sh new file mode 100644 index 0000000000000..12046732bb9f0 --- /dev/null +++ b/recipes/bioconductor-lumibarnes/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiBarnes diff --git a/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml b/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-lumihumanall.db/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-lumihumanall.db/meta.yaml b/recipes/bioconductor-lumihumanall.db/meta.yaml index 6423c2f1e8d64..9ac4d4ca75ecb 100644 --- a/recipes/bioconductor-lumihumanall.db/meta.yaml +++ b/recipes/bioconductor-lumihumanall.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "1.22.0" %} {% set name = "lumiHumanAll.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2c1bd766e756eb7e01cf196c1809c8a282a4c4caaf1482a0d1961b2c2a8c24e + md5: ce7e219b50833ceab203f0bbfb11d917 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Illumina Human Illumina expression annotation data (chip lumiHumanAll) assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-lumihumanall.db + path: recipes/bioconductor-lumihumanall.db + version: 1.22.0 diff --git a/recipes/bioconductor-lumihumanall.db/post-link.sh b/recipes/bioconductor-lumihumanall.db/post-link.sh index 362182f027941..5fbab6559da22 100644 --- a/recipes/bioconductor-lumihumanall.db/post-link.sh +++ b/recipes/bioconductor-lumihumanall.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="lumiHumanAll.db_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiHumanAll.db_1.22.0.tar.gz" "https://bioarchive.galaxyproject.org/lumiHumanAll.db_1.22.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-lumihumanall.db/bioconductor-lumihumanall.db_1.22.0_src_all.tar.gz" diff --git a/recipes/bioconductor-lumihumanidmapping/meta.yaml b/recipes/bioconductor-lumihumanidmapping/meta.yaml new file mode 100644 index 0000000000000..5ad3b9e521868 --- /dev/null +++ b/recipes/bioconductor-lumihumanidmapping/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.10.1" %} +{% set name = "lumiHumanIDMapping" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 007e5aa2f1596cc08d888ba6dce7148a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - r-dbi + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - r-dbi + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'This package includes mappings information between different types of Illumina IDs of Illumina Human chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Human chips to RefSeq IDs with mapping qualities information.' + diff --git a/recipes/bioconductor-lumihumanidmapping/post-link.sh b/recipes/bioconductor-lumihumanidmapping/post-link.sh new file mode 100644 index 0000000000000..c6673542f4497 --- /dev/null +++ b/recipes/bioconductor-lumihumanidmapping/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiHumanIDMapping_1.10.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiHumanIDMapping_1.10.1.tar.gz" + "https://bioarchive.galaxyproject.org/lumiHumanIDMapping_1.10.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumihumanidmapping/bioconductor-lumihumanidmapping_1.10.1_src_all.tar.gz" +) +MD5="007e5aa2f1596cc08d888ba6dce7148a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumihumanidmapping/pre-unlink.sh b/recipes/bioconductor-lumihumanidmapping/pre-unlink.sh new file mode 100644 index 0000000000000..1295a3cffa1d1 --- /dev/null +++ b/recipes/bioconductor-lumihumanidmapping/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiHumanIDMapping diff --git a/recipes/bioconductor-lumimouseall.db/meta.yaml b/recipes/bioconductor-lumimouseall.db/meta.yaml new file mode 100644 index 0000000000000..8fca36d5e5926 --- /dev/null +++ b/recipes/bioconductor-lumimouseall.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.22.0" %} +{% set name = "lumiMouseAll.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f12330377aaddc83bfa9c37477b999e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Mouse Illumina expression annotation data (chip lumiMouseAll) assembled using data from public repositories' + diff --git a/recipes/bioconductor-lumimouseall.db/post-link.sh b/recipes/bioconductor-lumimouseall.db/post-link.sh new file mode 100644 index 0000000000000..bfb76a9c44502 --- /dev/null +++ b/recipes/bioconductor-lumimouseall.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiMouseAll.db_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiMouseAll.db_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiMouseAll.db_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumimouseall.db/bioconductor-lumimouseall.db_1.22.0_src_all.tar.gz" +) +MD5="6f12330377aaddc83bfa9c37477b999e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumimouseall.db/pre-unlink.sh b/recipes/bioconductor-lumimouseall.db/pre-unlink.sh new file mode 100644 index 0000000000000..fd88423151dda --- /dev/null +++ b/recipes/bioconductor-lumimouseall.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiMouseAll.db diff --git a/recipes/bioconductor-lumimouseidmapping/meta.yaml b/recipes/bioconductor-lumimouseidmapping/meta.yaml new file mode 100644 index 0000000000000..36d5353e288b7 --- /dev/null +++ b/recipes/bioconductor-lumimouseidmapping/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.10.0" %} +{% set name = "lumiMouseIDMapping" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 305aba80ebf6ef4c26899302ea9e50e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'This package includes mappings information between different types of Illumina IDs of Illumina Mouse chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Mouse chips to RefSeq IDs with mapping qualities information.' + diff --git a/recipes/bioconductor-lumimouseidmapping/post-link.sh b/recipes/bioconductor-lumimouseidmapping/post-link.sh new file mode 100644 index 0000000000000..514f72be8bfe8 --- /dev/null +++ b/recipes/bioconductor-lumimouseidmapping/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiMouseIDMapping_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiMouseIDMapping_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiMouseIDMapping_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumimouseidmapping/bioconductor-lumimouseidmapping_1.10.0_src_all.tar.gz" +) +MD5="305aba80ebf6ef4c26899302ea9e50e8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumimouseidmapping/pre-unlink.sh b/recipes/bioconductor-lumimouseidmapping/pre-unlink.sh new file mode 100644 index 0000000000000..3ec37d6fe50dc --- /dev/null +++ b/recipes/bioconductor-lumimouseidmapping/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiMouseIDMapping diff --git a/recipes/bioconductor-lumiratall.db/meta.yaml b/recipes/bioconductor-lumiratall.db/meta.yaml new file mode 100644 index 0000000000000..47dd0c3e3e389 --- /dev/null +++ b/recipes/bioconductor-lumiratall.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.22.0" %} +{% set name = "lumiRatAll.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 65027624574d5e33f18b0a54a54f4be9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Illumina Rat Illumina expression annotation data (chip lumiRatAll) assembled using data from public repositories' + diff --git a/recipes/bioconductor-lumiratall.db/post-link.sh b/recipes/bioconductor-lumiratall.db/post-link.sh new file mode 100644 index 0000000000000..f9151c2b88b09 --- /dev/null +++ b/recipes/bioconductor-lumiratall.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiRatAll.db_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiRatAll.db_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiRatAll.db_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumiratall.db/bioconductor-lumiratall.db_1.22.0_src_all.tar.gz" +) +MD5="65027624574d5e33f18b0a54a54f4be9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumiratall.db/pre-unlink.sh b/recipes/bioconductor-lumiratall.db/pre-unlink.sh new file mode 100644 index 0000000000000..b62cbd8b80b73 --- /dev/null +++ b/recipes/bioconductor-lumiratall.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiRatAll.db diff --git a/recipes/bioconductor-lumiratidmapping/meta.yaml b/recipes/bioconductor-lumiratidmapping/meta.yaml new file mode 100644 index 0000000000000..d45ec08fef71a --- /dev/null +++ b/recipes/bioconductor-lumiratidmapping/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.10.0" %} +{% set name = "lumiRatIDMapping" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1122fc25e3fff62678bed36f9d7b5709 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'This package includes mappings information between different types of Illumina IDs of Illumina Rat chips and nuIDs. It also includes mappings of all nuIDs included in Illumina Rat chips to RefSeq IDs with mapping qualities information.' + diff --git a/recipes/bioconductor-lumiratidmapping/post-link.sh b/recipes/bioconductor-lumiratidmapping/post-link.sh new file mode 100644 index 0000000000000..2f7df5f1431e2 --- /dev/null +++ b/recipes/bioconductor-lumiratidmapping/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lumiRatIDMapping_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/lumiRatIDMapping_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/lumiRatIDMapping_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lumiratidmapping/bioconductor-lumiratidmapping_1.10.0_src_all.tar.gz" +) +MD5="1122fc25e3fff62678bed36f9d7b5709" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lumiratidmapping/pre-unlink.sh b/recipes/bioconductor-lumiratidmapping/pre-unlink.sh new file mode 100644 index 0000000000000..c9c1d8b53f9c9 --- /dev/null +++ b/recipes/bioconductor-lumiratidmapping/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lumiRatIDMapping diff --git a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml index 9f9350ea444ec..efac6d3a93f0e 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml +++ b/recipes/bioconductor-lungcanceracvssccgeo/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "LungCancerACvsSCCGEO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c3b9d6199eb489716b62e1109a056248d6a94f97078782bd738b9ba3c5af8d1f + md5: de4f81552f2a5f3484bd43cb1e089c76 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'This package contains 30 Affymetrix CEL files for 7 Adenocarcinoma (AC) and 8 Squamous cell carcinoma (SCC) lung cancer samples taken at random from 3 GEO datasets (GSE10245, GSE18842 and GSE2109) and other 15 samples from a dataset produced by the organizers of the IMPROVER Diagnostic Signature Challenge available from GEO (GSE43580).' - +extra: + parent_recipe: + name: bioconductor-lungcanceracvssccgeo + path: recipes/bioconductor-lungcanceracvssccgeo + version: 1.16.0 diff --git a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh index 10fdf4fef21c0..a9883af6679a5 100644 --- a/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh +++ b/recipes/bioconductor-lungcanceracvssccgeo/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="LungCancerACvsSCCGEO_1.16.0.tar.gz" +FN="LungCancerACvsSCCGEO_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LungCancerACvsSCCGEO_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerACvsSCCGEO_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcanceracvssccgeo/bioconductor-lungcanceracvssccgeo_1.18.0_src_all.tar.gz" ) -MD5="bad0119977d894701fb20976d5ed8482" +MD5="de4f81552f2a5f3484bd43cb1e089c76" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-lungcancerlines/meta.yaml b/recipes/bioconductor-lungcancerlines/meta.yaml new file mode 100644 index 0000000000000..d2ce005293402 --- /dev/null +++ b/recipes/bioconductor-lungcancerlines/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.20.0" %} +{% set name = "LungCancerLines" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 05943d693a693d21d910d70e7fa2e6b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Reads from an RNA-seq experiment between two lung cancer cell lines: H1993 (met) and H2073 (primary). The reads are stored as Fastq files and are meant for use with the TP53Genome object in the gmapR package.' + diff --git a/recipes/bioconductor-lungcancerlines/post-link.sh b/recipes/bioconductor-lungcancerlines/post-link.sh new file mode 100644 index 0000000000000..ef19b1715bdf3 --- /dev/null +++ b/recipes/bioconductor-lungcancerlines/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LungCancerLines_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/LungCancerLines_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/LungCancerLines_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungcancerlines/bioconductor-lungcancerlines_0.20.0_src_all.tar.gz" +) +MD5="05943d693a693d21d910d70e7fa2e6b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lungcancerlines/pre-unlink.sh b/recipes/bioconductor-lungcancerlines/pre-unlink.sh new file mode 100644 index 0000000000000..f00e91fe2b1c2 --- /dev/null +++ b/recipes/bioconductor-lungcancerlines/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LungCancerLines diff --git a/recipes/bioconductor-lungexpression/meta.yaml b/recipes/bioconductor-lungexpression/meta.yaml new file mode 100644 index 0000000000000..8f9e05bc6eef6 --- /dev/null +++ b/recipes/bioconductor-lungexpression/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.20.0" %} +{% set name = "lungExpression" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ddf0673ccf961ceb1875ac92d104f512 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data from three large lung cancer studies provided as ExpressionSets' + diff --git a/recipes/bioconductor-lungexpression/post-link.sh b/recipes/bioconductor-lungexpression/post-link.sh new file mode 100644 index 0000000000000..719a362508c77 --- /dev/null +++ b/recipes/bioconductor-lungexpression/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lungExpression_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lungExpression_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/lungExpression_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lungexpression/bioconductor-lungexpression_0.20.0_src_all.tar.gz" +) +MD5="ddf0673ccf961ceb1875ac92d104f512" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lungexpression/pre-unlink.sh b/recipes/bioconductor-lungexpression/pre-unlink.sh new file mode 100644 index 0000000000000..77a82d43f373b --- /dev/null +++ b/recipes/bioconductor-lungexpression/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lungExpression diff --git a/recipes/bioconductor-lvsmirna/build.sh b/recipes/bioconductor-lvsmirna/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-lvsmirna/build.sh +++ b/recipes/bioconductor-lvsmirna/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lvsmirna/conda_build_config.yaml b/recipes/bioconductor-lvsmirna/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-lvsmirna/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-lvsmirna/meta.yaml b/recipes/bioconductor-lvsmirna/meta.yaml index a5d9e847037f6..c9cfce638a078 100644 --- a/recipes/bioconductor-lvsmirna/meta.yaml +++ b/recipes/bioconductor-lvsmirna/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "LVSmiRNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 605280d9b3dd048e41f7bf3d5c225b642b199b1b3ab35c361122ce239f5018f9 + md5: 970f3c4e6fb62c5d9dcf870a700288ae build: number: 0 rpaths: @@ -18,23 +18,23 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-mass - r-quantreg - r-sparsem run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-mass - r-quantreg @@ -46,10 +46,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Normalization of Agilent miRNA arrays.' extra: identifiers: - biotools:lvsmirna - doi:10.1261/rna.2345710 + parent_recipe: + name: bioconductor-lvsmirna + path: recipes/bioconductor-lvsmirna + version: 1.30.0 + diff --git a/recipes/bioconductor-lydata/meta.yaml b/recipes/bioconductor-lydata/meta.yaml new file mode 100644 index 0000000000000..be2209bf45d84 --- /dev/null +++ b/recipes/bioconductor-lydata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.8.0" %} +{% set name = "lydata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d64eba72812c41d245f9972c33d71226 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Raw data downloaded from GEO for the compound LY294002. Raw data is from multiple platforms from Affymetrix and Illumina. This data is used to illustrate the cross-platform meta-analysis of microarray data using the crossmeta package.' + diff --git a/recipes/bioconductor-lydata/post-link.sh b/recipes/bioconductor-lydata/post-link.sh new file mode 100644 index 0000000000000..c210ac6e66a05 --- /dev/null +++ b/recipes/bioconductor-lydata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="lydata_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/lydata_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/lydata_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lydata/bioconductor-lydata_1.8.0_src_all.tar.gz" +) +MD5="d64eba72812c41d245f9972c33d71226" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lydata/pre-unlink.sh b/recipes/bioconductor-lydata/pre-unlink.sh new file mode 100644 index 0000000000000..d04f6ae757f78 --- /dev/null +++ b/recipes/bioconductor-lydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ lydata diff --git a/recipes/bioconductor-lymphoseq/build.sh b/recipes/bioconductor-lymphoseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-lymphoseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-lymphoseq/meta.yaml b/recipes/bioconductor-lymphoseq/meta.yaml new file mode 100644 index 0000000000000..96457d24d5916 --- /dev/null +++ b/recipes/bioconductor-lymphoseq/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.10.0" %} +{% set name = "LymphoSeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b5c24b3df8523d37d12cae3fdfe4a33 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, pheatmap, wordcloud, rmarkdown +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' + - 'bioconductor-msa >=1.14.0,<1.15.0' + - r-base + - r-circlize + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ineq + - r-phangorn + - r-plyr + - r-rcolorbrewer + - r-reshape + - r-stringdist + - r-upsetr + - r-venndiagram + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-lymphoseqdb >=0.99.0,<0.100.0' + - 'bioconductor-msa >=1.14.0,<1.15.0' + - r-base + - r-circlize + - r-data.table + - r-dplyr + - r-ggplot2 + - r-ineq + - r-phangorn + - r-plyr + - r-rcolorbrewer + - r-reshape + - r-stringdist + - r-upsetr + - r-venndiagram +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This R package analyzes high-throughput sequencing of T and B cell receptor complementarity determining region 3 (CDR3) sequences generated by Adaptive Biotechnologies'' ImmunoSEQ assay. Its input comes from tab-separated value (.tsv) files exported from the ImmunoSEQ analyzer.' + diff --git a/recipes/bioconductor-lymphoseqdb/meta.yaml b/recipes/bioconductor-lymphoseqdb/meta.yaml new file mode 100644 index 0000000000000..ea2c11b74fdbf --- /dev/null +++ b/recipes/bioconductor-lymphoseqdb/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.99.2" %} +{% set name = "LymphoSeqDB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 22fc0dc2439ef497982a5ffddda1e418 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides annotation databases that support the package LymphoSeq.' + diff --git a/recipes/bioconductor-lymphoseqdb/post-link.sh b/recipes/bioconductor-lymphoseqdb/post-link.sh new file mode 100644 index 0000000000000..17d02fe94bf9c --- /dev/null +++ b/recipes/bioconductor-lymphoseqdb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="LymphoSeqDB_0.99.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/LymphoSeqDB_0.99.2.tar.gz" + "https://bioarchive.galaxyproject.org/LymphoSeqDB_0.99.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-lymphoseqdb/bioconductor-lymphoseqdb_0.99.2_src_all.tar.gz" +) +MD5="22fc0dc2439ef497982a5ffddda1e418" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-lymphoseqdb/pre-unlink.sh b/recipes/bioconductor-lymphoseqdb/pre-unlink.sh new file mode 100644 index 0000000000000..4554a9230e3e3 --- /dev/null +++ b/recipes/bioconductor-lymphoseqdb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ LymphoSeqDB diff --git a/recipes/bioconductor-m10kcod.db/meta.yaml b/recipes/bioconductor-m10kcod.db/meta.yaml new file mode 100644 index 0000000000000..497ac5dba9bb0 --- /dev/null +++ b/recipes/bioconductor-m10kcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "m10kcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 04811628e4b37cd6d24e0b2a17d79ab8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink UniSet Mouse I Bioarray (~10 000 mouse gene targets) annotation data (chip m10kcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-m10kcod.db/post-link.sh b/recipes/bioconductor-m10kcod.db/post-link.sh new file mode 100644 index 0000000000000..b1f800c37f600 --- /dev/null +++ b/recipes/bioconductor-m10kcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="m10kcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/m10kcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/m10kcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m10kcod.db/bioconductor-m10kcod.db_3.4.0_src_all.tar.gz" +) +MD5="04811628e4b37cd6d24e0b2a17d79ab8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-m10kcod.db/pre-unlink.sh b/recipes/bioconductor-m10kcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..146fda839b2dd --- /dev/null +++ b/recipes/bioconductor-m10kcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ m10kcod.db diff --git a/recipes/bioconductor-m20kcod.db/meta.yaml b/recipes/bioconductor-m20kcod.db/meta.yaml new file mode 100644 index 0000000000000..ec8aa27e87561 --- /dev/null +++ b/recipes/bioconductor-m20kcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "m20kcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f2f734fb41e1ae4e949abf09687733bf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink UniSet Mouse 20k I Bioarray annotation data (chip m20kcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-m20kcod.db/post-link.sh b/recipes/bioconductor-m20kcod.db/post-link.sh new file mode 100644 index 0000000000000..1d8b00641ee4a --- /dev/null +++ b/recipes/bioconductor-m20kcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="m20kcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/m20kcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/m20kcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m20kcod.db/bioconductor-m20kcod.db_3.4.0_src_all.tar.gz" +) +MD5="f2f734fb41e1ae4e949abf09687733bf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-m20kcod.db/pre-unlink.sh b/recipes/bioconductor-m20kcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..8e5cf1d5e8072 --- /dev/null +++ b/recipes/bioconductor-m20kcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ m20kcod.db diff --git a/recipes/bioconductor-m3c/build.sh b/recipes/bioconductor-m3c/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-m3c/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-m3c/meta.yaml b/recipes/bioconductor-m3c/meta.yaml new file mode 100644 index 0000000000000..6318ad45d9148 --- /dev/null +++ b/recipes/bioconductor-m3c/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.4.0" %} +{% set name = "M3C" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f6491da354de5d2795f452c1ec61252 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - r-cluster + - r-dendextend + - r-doparallel + - r-dosnow + - r-foreach + - r-ggplot2 + - r-matrix + - r-matrixcalc + - r-nmf + - r-rcolorbrewer + - r-rtsne + - r-sigclust + - r-survival + run: + - r-base + - r-cluster + - r-dendextend + - r-doparallel + - r-dosnow + - r-foreach + - r-ggplot2 + - r-matrix + - r-matrixcalc + - r-nmf + - r-rcolorbrewer + - r-rtsne + - r-sigclust + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Genome-wide data is used to stratify large complex datasets into classes using class discovery algorithms. A widely applied technique is consensus clustering, however; the approach is prone to overfitting and false positives. These issues arise from not considering reference distributions while selecting the number of classes (K). As a solution, we developed Monte Carlo reference-based consensus clustering (M3C). M3C uses a multi-core enabled Monte Carlo simulation to generate null distributions along the range of K which are used to select its value. Using a reference, that maintains the correlation structure of the input features, eliminates the limitations of consensus clustering. M3C uses the Relative Cluster Stability Index (RCSI) and p values to decide on the value of K and reject the null hypothesis, K=1. M3C can also quantify structural relationships between clusters, and uses spectral clustering to deal with non-Gaussian and complex structures. M3C can automatically analyse biological or clinical data with respect to the discovered classes.' + diff --git a/recipes/bioconductor-m3d/build.sh b/recipes/bioconductor-m3d/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-m3d/build.sh +++ b/recipes/bioconductor-m3d/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-m3d/meta.yaml b/recipes/bioconductor-m3d/meta.yaml index 352fe0a8f2251..ae50696f110a2 100644 --- a/recipes/bioconductor-m3d/meta.yaml +++ b/recipes/bioconductor-m3d/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "M3D" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 306c0dc66599465d9799e2c3dbdf5cd94af4dda040ffeb14df29ac0edd432942 + md5: 77b8592c2b95342c0d27f10277002627 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biseq >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biseq >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-rcpp run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biseq >=1.20.0,<1.22.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biseq >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-rcpp build: @@ -43,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'This package identifies statistically significantly differentially methylated regions of CpGs. It uses kernel methods (the Maximum Mean Discrepancy) to measure differences in methylation profiles, and relates these to inter-replicate changes, whilst accounting for variation in coverage profiles.' extra: identifiers: - biotools:m3d - doi:10.1093/bioinformatics/btu749 + parent_recipe: + name: bioconductor-m3d + path: recipes/bioconductor-m3d + version: 1.14.0 + diff --git a/recipes/bioconductor-m3dexampledata/meta.yaml b/recipes/bioconductor-m3dexampledata/meta.yaml new file mode 100644 index 0000000000000..d2adadca69a85 --- /dev/null +++ b/recipes/bioconductor-m3dexampledata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.8.0" %} +{% set name = "M3DExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 13f405ac3714731aff20afbab68db3f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Example data for M3Drop package.' + diff --git a/recipes/bioconductor-m3dexampledata/post-link.sh b/recipes/bioconductor-m3dexampledata/post-link.sh new file mode 100644 index 0000000000000..05df3f8cafbf3 --- /dev/null +++ b/recipes/bioconductor-m3dexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="M3DExampleData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/M3DExampleData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/M3DExampleData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-m3dexampledata/bioconductor-m3dexampledata_1.8.0_src_all.tar.gz" +) +MD5="13f405ac3714731aff20afbab68db3f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-m3dexampledata/pre-unlink.sh b/recipes/bioconductor-m3dexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..09fca17cfd80f --- /dev/null +++ b/recipes/bioconductor-m3dexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ M3DExampleData diff --git a/recipes/bioconductor-m3drop/build.sh b/recipes/bioconductor-m3drop/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-m3drop/build.sh +++ b/recipes/bioconductor-m3drop/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-m3drop/meta.yaml b/recipes/bioconductor-m3drop/meta.yaml index dc34c1ff3d440..e969f0172ad61 100644 --- a/recipes/bioconductor-m3drop/meta.yaml +++ b/recipes/bioconductor-m3drop/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "M3Drop" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cfe0157b46306c5de17b0f651eb2b4c6a30819b3200fc70093ab2e0f61a89c31 + md5: dae88fe1b86006aa8bea5d18601aec06 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ROCR, knitr, M3DExampleData requirements: host: - r-base @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package fits a Michaelis-Menten model to the pattern of dropouts in single-cell RNASeq data. This model is used as a null to identify significantly variable (i.e. differentially expressed) genes for use in downstream analysis, such as clustering cells.' extra: identifiers: - biotools:m3drop - doi:10.1002/1873-3468.12684 + parent_recipe: + name: bioconductor-m3drop + path: recipes/bioconductor-m3drop + version: 1.6.0 + diff --git a/recipes/bioconductor-maanova/build.sh b/recipes/bioconductor-maanova/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-maanova/build.sh +++ b/recipes/bioconductor-maanova/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maanova/meta.yaml b/recipes/bioconductor-maanova/meta.yaml index 59ec8335899df..5bb581904a787 100644 --- a/recipes/bioconductor-maanova/meta.yaml +++ b/recipes/bioconductor-maanova/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "maanova" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ab170030f4581a7377913e8c27881854dfe69e5c2310b20d7b81be06fb84209d + md5: 98d914299500ad6464eabd0244389b4a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: qvalue, snow requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Analysis of N-dye Micro Array experiment using mixed model effect. Containing analysis of variance, permutation and bootstrap, cluster and consensus tree.' extra: identifiers: - biotools:maanova - doi:10.1007/0-387-21679-0_14 + parent_recipe: + name: bioconductor-maanova + path: recipes/bioconductor-maanova + version: 1.50.0 + diff --git a/recipes/bioconductor-macat/build.sh b/recipes/bioconductor-macat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-macat/build.sh +++ b/recipes/bioconductor-macat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-macat/meta.yaml b/recipes/bioconductor-macat/meta.yaml index 60d4811ba918d..58483bb30a5b4 100644 --- a/recipes/bioconductor-macat/meta.yaml +++ b/recipes/bioconductor-macat/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "macat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5def6e15d502df965e996b04ea5afaa1651fb5d9524afce3608a9018483c7d6c + md5: de0e3159813ba422b6ad6ff8e24776f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2.db, stjudem requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This library contains functions to investigate links between differential gene expression and the chromosomal localization of the genes. MACAT is motivated by the common observation of phenomena involving large chromosomal regions in tumor cells. MACAT is the implementation of a statistical approach for identifying significantly differentially expressed chromosome regions. The functions have been tested on a publicly available data set about acute lymphoblastic leukemia (Yeoh et al.Cancer Cell 2002), which is provided in the library ''stjudem''.' extra: identifiers: - biotools:macat + parent_recipe: + name: bioconductor-macat + path: recipes/bioconductor-macat + version: 1.54.0 + diff --git a/recipes/bioconductor-macorrplot/build.sh b/recipes/bioconductor-macorrplot/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-macorrplot/build.sh +++ b/recipes/bioconductor-macorrplot/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-macorrplot/meta.yaml b/recipes/bioconductor-macorrplot/meta.yaml index cc4e717f88865..6513655044b87 100644 --- a/recipes/bioconductor-macorrplot/meta.yaml +++ b/recipes/bioconductor-macorrplot/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "maCorrPlot" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3b2720f6235214af8dbed9ca8b08ba33f1c65e9d2aba01216976303bbbcdde1e + md5: 2cdfe3ac5b1ab5504522a96ce8fab1b3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Graphically displays correlation in microarray data that is due to insufficient normalization' extra: identifiers: - biotools:macorrplot - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-macorrplot + path: recipes/bioconductor-macorrplot + version: 1.50.0 + diff --git a/recipes/bioconductor-macpet/build.sh b/recipes/bioconductor-macpet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-macpet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-macpet/meta.yaml b/recipes/bioconductor-macpet/meta.yaml new file mode 100644 index 0000000000000..cf1747b4f6273 --- /dev/null +++ b/recipes/bioconductor-macpet/meta.yaml @@ -0,0 +1,81 @@ +{% set version = "1.2.0" %} +{% set name = "MACPET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 30f1bd24dfd02ee23e5b41c72147f57d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: ggplot2 (>= 3.0.0), igraph (>= 1.2.1), rmarkdown (>= 1.10), reshape2 (>= 1.4.3), BiocStyle (>= 2.8.2) +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbowtie >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - 'r-bh >=1.66.0.1' + - 'r-bigmemory >=4.5.33' + - 'r-futile.logger >=1.4.3' + - 'r-gtools >=3.8.1' + - 'r-intervals >=0.15.1' + - 'r-knitr >=1.20' + - 'r-plyr >=1.8.4' + - 'r-rbamtools >=2.16.11' + - 'r-rcpp >=0.12.17' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbowtie >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - 'r-bh >=1.66.0.1' + - 'r-bigmemory >=4.5.33' + - 'r-futile.logger >=1.4.3' + - 'r-gtools >=3.8.1' + - 'r-intervals >=0.15.1' + - 'r-knitr >=1.20' + - 'r-plyr >=1.8.4' + - 'r-rbamtools >=2.16.11' + - 'r-rcpp >=0.12.17' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The MACPET package can be used for complete interaction analysis for ChIA-PET data. MACPET reads ChIA-PET data in BAM or SAM format and separates the data into Self-ligated, Intra- and Inter-chromosomal PETs. Furthermore, MACPET breaks the genome into regions and applies 2D mixture models for identifying candidate peaks/binding sites using skewed generalized students-t distributions (SGT). It then uses a local poisson model for finding significant binding sites. Finally it runs an additive interaction-analysis model for calling for significant interactions between those peaks. MACPET is mainly written in C++, and it also supports the BiocParallel package.' + diff --git a/recipes/bioconductor-made4/build.sh b/recipes/bioconductor-made4/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-made4/build.sh +++ b/recipes/bioconductor-made4/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-made4/meta.yaml b/recipes/bioconductor-made4/meta.yaml index 4815b0ab23272..6246825bb4202 100644 --- a/recipes/bioconductor-made4/meta.yaml +++ b/recipes/bioconductor-made4/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "made4" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b2748031828a253b0b3f77516933af95ee00e80af7720298a4e19cc49ec34a62 + md5: b93783edb8e0c0de6df719e01b79ebfe build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affy requirements: host: - r-ade4 @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Multivariate data analysis and graphical display of microarray data. Functions include between group analysis and coinertia analysis. It contains functions that require ADE4.' extra: identifiers: - biotools:made4 + parent_recipe: + name: bioconductor-made4 + path: recipes/bioconductor-made4 + version: 1.54.0 + diff --git a/recipes/bioconductor-madseq/build.sh b/recipes/bioconductor-madseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-madseq/build.sh +++ b/recipes/bioconductor-madseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-madseq/meta.yaml b/recipes/bioconductor-madseq/meta.yaml index 5ecc3e5885bcf..c89abe2196896 100644 --- a/recipes/bioconductor-madseq/meta.yaml +++ b/recipes/bioconductor-madseq/meta.yaml @@ -1,57 +1,59 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "MADSEQ" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 00b90dd7263a14723a0405319c7a2598b27938f9271d722f51afb468f1857ec6 + md5: 4ca89b5fc53ad2b4b6806b37991fa2ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-coda - 'r-rjags >=4-6' - r-vcfr - r-vgam run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-coda - 'r-rjags >=4-6' @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'The MADSEQ package provides a group of hierarchical Bayeisan models for the detection of mosaic aneuploidy, the inference of the type of aneuploidy and also for the quantification of the fraction of aneuploid cells in the sample.' extra: identifiers: - biotools:madseq - doi:10.1101/142299 + parent_recipe: + name: bioconductor-madseq + path: recipes/bioconductor-madseq + version: 1.6.1 + diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml new file mode 100644 index 0000000000000..b1326c553d3e3 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.1Kgenomes.phase1.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 793705d2a4a4a80a770b436c0df52add +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh new file mode 100644 index 0000000000000..78a8a04f1fb26 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.grch38/bioconductor-mafdb.1kgenomes.phase1.grch38_3.7.0_src_all.tar.gz" +) +MD5="793705d2a4a4a80a770b436c0df52add" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..c0c65622173ad --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.1Kgenomes.phase1.GRCh38 diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml new file mode 100644 index 0000000000000..f3c4c299dead7 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.1" %} +{% set name = "MafDb.1Kgenomes.phase1.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a13d138f00d0f38642f1dfc6cc705050 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Phase 1 of the 1000 Genomes Project for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh new file mode 100644 index 0000000000000..97efcf0908fb2 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase1.hs37d5_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase1.hs37d5/bioconductor-mafdb.1kgenomes.phase1.hs37d5_3.7.1_src_all.tar.gz" +) +MD5="a13d138f00d0f38642f1dfc6cc705050" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..684fa87cc258e --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase1.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.1Kgenomes.phase1.hs37d5 diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml new file mode 100644 index 0000000000000..cf087727df80e --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.1Kgenomes.phase3.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 062f9d00e3f0650806520cf39f3f9dac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh new file mode 100644 index 0000000000000..3aad34029a32a --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.grch38/bioconductor-mafdb.1kgenomes.phase3.grch38_3.7.0_src_all.tar.gz" +) +MD5="062f9d00e3f0650806520cf39f3f9dac" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..fde0d8263f409 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.1Kgenomes.phase3.GRCh38 diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml new file mode 100644 index 0000000000000..02c08fa54f4c8 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.1Kgenomes.phase3.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a659554d3056e019b4f3a179e9628a2d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Phase 3 of the 1000 Genomes Project for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh new file mode 100644 index 0000000000000..2d89a25e964e2 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.1Kgenomes.phase3.hs37d5_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.1kgenomes.phase3.hs37d5/bioconductor-mafdb.1kgenomes.phase3.hs37d5_3.7.0_src_all.tar.gz" +) +MD5="a659554d3056e019b4f3a179e9628a2d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..b96d0f6aaac89 --- /dev/null +++ b/recipes/bioconductor-mafdb.1kgenomes.phase3.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.1Kgenomes.phase3.hs37d5 diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml new file mode 100644 index 0000000000000..4d6b6133f0594 --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ESP6500SI.V2.SSA137.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5c6afa001de76b91bc685c5c4b002b05 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the NHLBI Exome Sequencing Project in the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh new file mode 100644 index 0000000000000..c8e2a66de4eda --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ESP6500SI.V2.SSA137.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/bioconductor-mafdb.esp6500si.v2.ssa137.grch38_3.7.0_src_all.tar.gz" +) +MD5="5c6afa001de76b91bc685c5c4b002b05" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..0e612dacf3f00 --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ESP6500SI.V2.SSA137.GRCh38 diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml new file mode 100644 index 0000000000000..db8c74131ca73 --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ESP6500SI.V2.SSA137.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6ae9642f33195aca7c84240a8642eb8a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the NHLBI Exome Sequencing Project in the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh new file mode 100644 index 0000000000000..0eab40f5ccec3 --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ESP6500SI.V2.SSA137.hs37d5_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5_3.7.0_src_all.tar.gz" +) +MD5="6ae9642f33195aca7c84240a8642eb8a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..786e6150b5e9e --- /dev/null +++ b/recipes/bioconductor-mafdb.esp6500si.v2.ssa137.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ESP6500SI.V2.SSA137.hs37d5 diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml new file mode 100644 index 0000000000000..6f4d3fe786a23 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ExAC.r1.0.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ab8ee4f77c84ecb0f8954f9cec199ef4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh new file mode 100644 index 0000000000000..d565105e88035 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.grch38/bioconductor-mafdb.exac.r1.0.grch38_3.7.0_src_all.tar.gz" +) +MD5="ab8ee4f77c84ecb0f8954f9cec199ef4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.exac.r1.0.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.exac.r1.0.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..fedf3d723851c --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ExAC.r1.0.GRCh38 diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml new file mode 100644 index 0000000000000..c54c9ada1ad6e --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ExAC.r1.0.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a4d494d62a02d808248a058e82e353fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh new file mode 100644 index 0000000000000..d14346cd09d0e --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.hs37d5_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.hs37d5/bioconductor-mafdb.exac.r1.0.hs37d5_3.7.0_src_all.tar.gz" +) +MD5="a4d494d62a02d808248a058e82e353fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..eb1d4430f3466 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ExAC.r1.0.hs37d5 diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml new file mode 100644 index 0000000000000..900d73f75d4ee --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ExAC.r1.0.nonTCGA.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3826e2d43f9b5cc614dec3ca1059b582 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh new file mode 100644 index 0000000000000..1ff36e50f7a34 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.grch38/bioconductor-mafdb.exac.r1.0.nontcga.grch38_3.7.0_src_all.tar.gz" +) +MD5="3826e2d43f9b5cc614dec3ca1059b582" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..93fe9c4e3f5a6 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ExAC.r1.0.nonTCGA.GRCh38 diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml new file mode 100644 index 0000000000000..2ff61d4d283e8 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.ExAC.r1.0.nonTCGA.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f557aba8027c87df7bc0cac088b7eaa2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Exome Aggregation Consortium (ExAC release 1.0 subset of nonTCGA exomes) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh new file mode 100644 index 0000000000000..c6c6a4be1b294 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.ExAC.r1.0.nonTCGA.hs37d5_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5_3.7.0_src_all.tar.gz" +) +MD5="f557aba8027c87df7bc0cac088b7eaa2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..89bd4f22025e7 --- /dev/null +++ b/recipes/bioconductor-mafdb.exac.r1.0.nontcga.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.ExAC.r1.0.nonTCGA.hs37d5 diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml new file mode 100644 index 0000000000000..df33fdd7425a5 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.gnomAD.r2.0.1.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 735178d5c746753c81acfb3023007ac2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.0.1) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh new file mode 100644 index 0000000000000..bed6a7ef28ac7 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.0.1.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.0.1.grch38/bioconductor-mafdb.gnomad.r2.0.1.grch38_3.7.0_src_all.tar.gz" +) +MD5="735178d5c746753c81acfb3023007ac2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..7e58873770018 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomAD.r2.0.1.GRCh38 diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/meta.yaml new file mode 100644 index 0000000000000..63e5af0031178 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.8.0" %} +{% set name = "MafDb.gnomAD.r2.0.1.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f7f9cf73a0b7ae91f7ae986e70827601 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.0.1) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/post-link.sh new file mode 100644 index 0000000000000..e1d465c9d57f1 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomAD.r2.0.1.hs37d5_3.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomAD.r2.0.1.hs37d5_3.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.0.1.hs37d5_3.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/bioconductor-mafdb.gnomad.r2.0.1.hs37d5_3.8.0_src_all.tar.gz" +) +MD5="f7f9cf73a0b7ae91f7ae986e70827601" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..e00c4254c3143 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.0.1.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomAD.r2.0.1.hs37d5 diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml new file mode 100644 index 0000000000000..8011934870c93 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.8.0" %} +{% set name = "MafDb.gnomAD.r2.1.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fd068f564166d58bb18ebd380f6e431e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD release 2.1) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh new file mode 100644 index 0000000000000..6f18fedac9dec --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomAD.r2.1.hs37d5_3.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomad.r2.1.hs37d5/bioconductor-mafdb.gnomad.r2.1.hs37d5_3.8.0_src_all.tar.gz" +) +MD5="fd068f564166d58bb18ebd380f6e431e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..1755dc466bdf3 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomad.r2.1.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomAD.r2.1.hs37d5 diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml new file mode 100644 index 0000000000000..9a634d31fde5e --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.0" %} +{% set name = "MafDb.gnomADex.r2.0.1.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 95070dc7a5d707d63dbb6ae51ad0e68b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.0.1) for the human genome version GRCh38.' + diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh new file mode 100644 index 0000000000000..5e61e9a48c3db --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.0.1.GRCh38_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.0.1.grch38/bioconductor-mafdb.gnomadex.r2.0.1.grch38_3.7.0_src_all.tar.gz" +) +MD5="95070dc7a5d707d63dbb6ae51ad0e68b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..3db26c425e270 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomADex.r2.0.1.GRCh38 diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/meta.yaml new file mode 100644 index 0000000000000..406b6753cd379 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.8.0" %} +{% set name = "MafDb.gnomADex.r2.0.1.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f67e2fe8b9ba5d497b1b7a04432cfee8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.0.1) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/post-link.sh new file mode 100644 index 0000000000000..2bf5048a0fc26 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomADex.r2.0.1.hs37d5_3.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomADex.r2.0.1.hs37d5_3.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.0.1.hs37d5_3.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5_3.8.0_src_all.tar.gz" +) +MD5="f67e2fe8b9ba5d497b1b7a04432cfee8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..e248f92dce8f9 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.0.1.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomADex.r2.0.1.hs37d5 diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml new file mode 100644 index 0000000000000..f22bceb16d329 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.8.0" %} +{% set name = "MafDb.gnomADex.r2.1.hs37d5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 46272d8c1d0d811cf6471a7a6edd1ba2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from the Genome Aggregation Database (gnomAD exomes release 2.1) for the human genome version hs37d5.' + diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh new file mode 100644 index 0000000000000..62033d67ebb27 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.gnomADex.r2.1.hs37d5_3.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.gnomadex.r2.1.hs37d5/bioconductor-mafdb.gnomadex.r2.1.hs37d5_3.8.0_src_all.tar.gz" +) +MD5="46272d8c1d0d811cf6471a7a6edd1ba2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/pre-unlink.sh b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/pre-unlink.sh new file mode 100644 index 0000000000000..f24b8988216b2 --- /dev/null +++ b/recipes/bioconductor-mafdb.gnomadex.r2.1.hs37d5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.gnomADex.r2.1.hs37d5 diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml new file mode 100644 index 0000000000000..bc632baa894cd --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.1" %} +{% set name = "MafDb.TOPMed.freeze5.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: efa58223437a23aa77a4da3d0ae4aa90 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from NHLBI TOPMed for the human genome version hg19.' + diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh new file mode 100644 index 0000000000000..f0caf9817e546 --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg19_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg19/bioconductor-mafdb.topmed.freeze5.hg19_3.7.1_src_all.tar.gz" +) +MD5="efa58223437a23aa77a4da3d0ae4aa90" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg19/pre-unlink.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..5aaed63180259 --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.TOPMed.freeze5.hg19 diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml new file mode 100644 index 0000000000000..6e4bc5d27aff3 --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "3.7.1" %} +{% set name = "MafDb.TOPMed.freeze5.hg38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9d47a5c4e2f94f243c426e4701f6b74a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP149.GRCh38 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store minor allele frequency data from NHLBI TOPMed for the human genome version hg38.' + diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh new file mode 100644 index 0000000000000..7aa46ed82bb79 --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/MafDb.TOPMed.freeze5.hg38_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mafdb.topmed.freeze5.hg38/bioconductor-mafdb.topmed.freeze5.hg38_3.7.1_src_all.tar.gz" +) +MD5="9d47a5c4e2f94f243c426e4701f6b74a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mafdb.topmed.freeze5.hg38/pre-unlink.sh b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..44a78f9ba88e8 --- /dev/null +++ b/recipes/bioconductor-mafdb.topmed.freeze5.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MafDb.TOPMed.freeze5.hg38 diff --git a/recipes/bioconductor-maftools/build.sh b/recipes/bioconductor-maftools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-maftools/build.sh +++ b/recipes/bioconductor-maftools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maftools/meta.yaml b/recipes/bioconductor-maftools/meta.yaml index 9b627b9df2a62..af47a5d8177a3 100644 --- a/recipes/bioconductor-maftools/meta.yaml +++ b/recipes/bioconductor-maftools/meta.yaml @@ -1,29 +1,29 @@ -{% set version = "1.6.15" %} +{% set version = "1.8.0" %} {% set name = "maftools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8d10a210677136232c2a6fb7c1d76fef3ac4387b78ba0aee4edac7c2947d54a3 + md5: 5e5bd8c517982b1d835d07081632c2ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - r-base - - r-changepoint - r-cometexacttest - r-cowplot - r-data.table @@ -37,12 +37,10 @@ requirements: - r-survival - r-wordcloud run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' - r-base - - r-changepoint - r-cometexacttest - r-cowplot - r-data.table @@ -59,8 +57,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Analyze and visualize Mutation Annotation Format (MAF) files from large scale sequencing studies. This package provides various functions to perform most commonly used analyses in cancer genomics and to create feature rich customizable visualzations with minimal effort.' - +extra: + parent_recipe: + name: bioconductor-maftools + path: recipes/bioconductor-maftools + version: 1.6.15 diff --git a/recipes/bioconductor-mageckflute/build.sh b/recipes/bioconductor-mageckflute/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mageckflute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mageckflute/meta.yaml b/recipes/bioconductor-mageckflute/meta.yaml new file mode 100644 index 0000000000000..751f8509aaa73 --- /dev/null +++ b/recipes/bioconductor-mageckflute/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.1" %} +{% set name = "MAGeCKFlute" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 80c61e7aae7789fcd50e2f08b97e1d35 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, org.Mm.eg.db +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-data.table + - r-ggextra + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-gridextra + - r-pheatmap + - r-png + - r-rcolorbrewer + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-data.table + - r-ggextra + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-gridextra + - r-pheatmap + - r-png + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'MAGeCKFlute is designed to surporting downstream analysis, utilizing the gene summary data provided through MAGeCK or MAGeCK-VISPR. Quality control, normalization, and screen hit identification for CRISPR screen data are performed in pipeline. Identified hits within the pipeline are categorized based on experimental design, and are subsequently interpreted by functional enrichment analysis.' + diff --git a/recipes/bioconductor-maigespack/build.sh b/recipes/bioconductor-maigespack/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-maigespack/build.sh +++ b/recipes/bioconductor-maigespack/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maigespack/meta.yaml b/recipes/bioconductor-maigespack/meta.yaml index f4a0de968aec2..8afed60dcd3ab 100644 --- a/recipes/bioconductor-maigespack/meta.yaml +++ b/recipes/bioconductor-maigespack/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "maigesPack" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 98cf2ae3afe8c07e454ad1cc566e5d45b6dfe509d557a2f868d5d95c1ab12207 + md5: 98e206be973a22e3f190a1a3fc044acc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: amap, annotate, class, e1071, MASS, multtest, OLIN, R2HTML, rgl, som requirements: host: - - 'bioconductor-convert >=1.56.0,<1.58.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-convert >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-convert >=1.56.0,<1.58.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-convert >=1.58.0,<1.59.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package uses functions of various other packages together with other functions in a coordinated way to handle and analyse cDNA microarray data' extra: identifiers: - biotools:maigespack - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-maigespack + path: recipes/bioconductor-maigespack + version: 1.44.0 + diff --git a/recipes/bioconductor-mait/build.sh b/recipes/bioconductor-mait/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mait/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mait/meta.yaml b/recipes/bioconductor-mait/meta.yaml new file mode 100644 index 0000000000000..2c6ae59994624 --- /dev/null +++ b/recipes/bioconductor-mait/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.16.0" %} +{% set name = "MAIT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 120be085e8a5f3c3ca11ba1d8c3f8d50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: faahKO +requirements: + host: + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' + - r-agricolae + - r-base + - r-caret + - r-class + - r-e1071 + - r-gplots + - r-mass + - r-pls + - r-plsgenomics + - r-rcpp + run: + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' + - r-agricolae + - r-base + - r-caret + - r-class + - r-e1071 + - r-gplots + - r-mass + - r-pls + - r-plsgenomics + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The MAIT package contains functions to perform end-to-end statistical analysis of LC/MS Metabolomic Data. Special emphasis is put on peak annotation and in modular function design of the functions.' + diff --git a/recipes/bioconductor-maizecdf/meta.yaml b/recipes/bioconductor-maizecdf/meta.yaml new file mode 100644 index 0000000000000..47b078e1775dd --- /dev/null +++ b/recipes/bioconductor-maizecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "maizecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f9dec9e46688d96daf1e07d4e815afb4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Maize.cdf file.' + diff --git a/recipes/bioconductor-maizecdf/post-link.sh b/recipes/bioconductor-maizecdf/post-link.sh new file mode 100644 index 0000000000000..451ea3f66dac3 --- /dev/null +++ b/recipes/bioconductor-maizecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="maizecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/maizecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/maizecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maizecdf/bioconductor-maizecdf_2.18.0_src_all.tar.gz" +) +MD5="f9dec9e46688d96daf1e07d4e815afb4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maizecdf/pre-unlink.sh b/recipes/bioconductor-maizecdf/pre-unlink.sh new file mode 100644 index 0000000000000..24b768f343309 --- /dev/null +++ b/recipes/bioconductor-maizecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ maizecdf diff --git a/recipes/bioconductor-maizeprobe/meta.yaml b/recipes/bioconductor-maizeprobe/meta.yaml new file mode 100644 index 0000000000000..f77009dd337a2 --- /dev/null +++ b/recipes/bioconductor-maizeprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "maizeprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ef7ba47de2346b3552621263399c05d1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Maize\_probe\_tab.' + diff --git a/recipes/bioconductor-maizeprobe/post-link.sh b/recipes/bioconductor-maizeprobe/post-link.sh new file mode 100644 index 0000000000000..4d518932db798 --- /dev/null +++ b/recipes/bioconductor-maizeprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="maizeprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/maizeprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/maizeprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maizeprobe/bioconductor-maizeprobe_2.18.0_src_all.tar.gz" +) +MD5="ef7ba47de2346b3552621263399c05d1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maizeprobe/pre-unlink.sh b/recipes/bioconductor-maizeprobe/pre-unlink.sh new file mode 100644 index 0000000000000..93a81106e4398 --- /dev/null +++ b/recipes/bioconductor-maizeprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ maizeprobe diff --git a/recipes/bioconductor-makecdfenv/build.sh b/recipes/bioconductor-makecdfenv/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-makecdfenv/build.sh +++ b/recipes/bioconductor-makecdfenv/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-makecdfenv/conda_build_config.yaml b/recipes/bioconductor-makecdfenv/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-makecdfenv/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-makecdfenv/meta.yaml b/recipes/bioconductor-makecdfenv/meta.yaml index b721590f5bd54..9f6600a8951e1 100644 --- a/recipes/bioconductor-makecdfenv/meta.yaml +++ b/recipes/bioconductor-makecdfenv/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "makecdfenv" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2bd03184374ccde9683d2b614183918217f9364fa5b51035a67b34dac11d04b5 + md5: 4f1ba6b03964861e6553e52ff5c9cfb3 build: number: 0 rpaths: @@ -18,16 +18,16 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -37,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package has two functions. One reads a Affymetrix chip description file (CDF) and creates a hash table environment containing the location/probe set membership mapping. The other creates a package that automatically loads that environment.' extra: identifiers: - biotools:makecdfenv - doi:10.1186/1471-2105-13-56 + parent_recipe: + name: bioconductor-makecdfenv + path: recipes/bioconductor-makecdfenv + version: 1.56.0 + diff --git a/recipes/bioconductor-malaria.db0/meta.yaml b/recipes/bioconductor-malaria.db0/meta.yaml new file mode 100644 index 0000000000000..8fe2cee1a5e6c --- /dev/null +++ b/recipes/bioconductor-malaria.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "malaria.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 217e4954b728ef55cdb913960d34c63a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for malaria, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-malaria.db0/post-link.sh b/recipes/bioconductor-malaria.db0/post-link.sh new file mode 100644 index 0000000000000..9544599fc59d8 --- /dev/null +++ b/recipes/bioconductor-malaria.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="malaria.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/malaria.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/malaria.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-malaria.db0/bioconductor-malaria.db0_3.7.1_src_all.tar.gz" +) +MD5="217e4954b728ef55cdb913960d34c63a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-malaria.db0/pre-unlink.sh b/recipes/bioconductor-malaria.db0/pre-unlink.sh new file mode 100644 index 0000000000000..3efe851fe5d13 --- /dev/null +++ b/recipes/bioconductor-malaria.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ malaria.db0 diff --git a/recipes/bioconductor-mammaprintdata/meta.yaml b/recipes/bioconductor-mammaprintdata/meta.yaml new file mode 100644 index 0000000000000..a0bf21f6a89e3 --- /dev/null +++ b/recipes/bioconductor-mammaprintdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "mammaPrintData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8bf8e8805b3af4953469a353d305c74c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, gdata, limma +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data for the two breast cancer cohorts published by Glas and Buyse in 2006. This cohorts were used to implement and validate the mammaPrint breast cancer test.' + diff --git a/recipes/bioconductor-mammaprintdata/post-link.sh b/recipes/bioconductor-mammaprintdata/post-link.sh new file mode 100644 index 0000000000000..b1c680319582e --- /dev/null +++ b/recipes/bioconductor-mammaprintdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mammaPrintData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mammaPrintData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mammaPrintData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mammaprintdata/bioconductor-mammaprintdata_1.18.0_src_all.tar.gz" +) +MD5="8bf8e8805b3af4953469a353d305c74c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mammaprintdata/pre-unlink.sh b/recipes/bioconductor-mammaprintdata/pre-unlink.sh new file mode 100644 index 0000000000000..fb34f9f8170be --- /dev/null +++ b/recipes/bioconductor-mammaprintdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mammaPrintData diff --git a/recipes/bioconductor-manor/build.sh b/recipes/bioconductor-manor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-manor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-manor/meta.yaml b/recipes/bioconductor-manor/meta.yaml new file mode 100644 index 0000000000000..c64217b6ca74f --- /dev/null +++ b/recipes/bioconductor-manor/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.54.0" %} +{% set name = "MANOR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f06fe382abee16e0de2e65e43419d59f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-glad >=2.46.0,<2.47.0' + - r-base + run: + - 'bioconductor-glad >=2.46.0,<2.47.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Importation, normalization, visualization, and quality control functions to correct identified sources of variability in array-CGH experiments.' + diff --git a/recipes/bioconductor-manta/build.sh b/recipes/bioconductor-manta/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-manta/build.sh +++ b/recipes/bioconductor-manta/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-manta/meta.yaml b/recipes/bioconductor-manta/meta.yaml index 9267df19495c9..9165c63764673 100644 --- a/recipes/bioconductor-manta/meta.yaml +++ b/recipes/bioconductor-manta/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "manta" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b0790ed4d465257a1bd7edf9318ee8691e668648ddb747fb98768f3f8d221c18 + md5: 695edb2161bca3c0465786e7dfcfe5c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RSQLite, plotrix requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc run: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - 'r-caroline >=0.6.6' - r-hmisc @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for robust comparative metatranscriptomics.' extra: identifiers: - biotools:manta - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-manta + path: recipes/bioconductor-manta + version: 1.26.0 + diff --git a/recipes/bioconductor-mantelcorr/build.sh b/recipes/bioconductor-mantelcorr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mantelcorr/build.sh +++ b/recipes/bioconductor-mantelcorr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mantelcorr/meta.yaml b/recipes/bioconductor-mantelcorr/meta.yaml index 383fc9fdc27ce..d05ae4c49b83d 100644 --- a/recipes/bioconductor-mantelcorr/meta.yaml +++ b/recipes/bioconductor-mantelcorr/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "MantelCorr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d46af1b33116d753766509325dd3df961a77bbdff2cbf50b168a059d61860c31 + md5: 8de0637aa10324d7ff3d37ca1ec4f7d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Computes Mantel cluster correlations from a (p x n) numeric data matrix (e.g. microarray gene-expression data).' extra: identifiers: - biotools:mantelcorr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mantelcorr + path: recipes/bioconductor-mantelcorr + version: 1.50.0 + diff --git a/recipes/bioconductor-mapkl/build.sh b/recipes/bioconductor-mapkl/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mapkl/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapkl/meta.yaml b/recipes/bioconductor-mapkl/meta.yaml new file mode 100644 index 0000000000000..1e9dcb088a022 --- /dev/null +++ b/recipes/bioconductor-mapkl/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.12.0" %} +{% set name = "mAPKL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 99d91da662512e0f50d49ccde0262e5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, mAPKLData, hgu133plus2.db, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-apcluster + - r-base + - r-clustersim + - r-e1071 + - r-igraph + - r-parmigene + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-apcluster + - r-base + - r-clustersim + - r-e1071 + - r-igraph + - r-parmigene +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'We propose a hybrid FS method (mAP-KL), which combines multiple hypothesis testing and affinity propagation (AP)-clustering algorithm along with the Krzanowski & Lai cluster quality index, to select a small yet informative subset of genes.' + diff --git a/recipes/bioconductor-mapkldata/meta.yaml b/recipes/bioconductor-mapkldata/meta.yaml new file mode 100644 index 0000000000000..abc5d454f7bf2 --- /dev/null +++ b/recipes/bioconductor-mapkldata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "mAPKLData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6d044355ab9473e4e724918a054df95c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data from a breast cancer study published by Turashvili et al. in 2007, provided as an eSet.' + diff --git a/recipes/bioconductor-mapkldata/post-link.sh b/recipes/bioconductor-mapkldata/post-link.sh new file mode 100644 index 0000000000000..6dca6e70ecd97 --- /dev/null +++ b/recipes/bioconductor-mapkldata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mAPKLData_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mAPKLData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/mAPKLData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mapkldata/bioconductor-mapkldata_1.14.0_src_all.tar.gz" +) +MD5="6d044355ab9473e4e724918a054df95c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mapkldata/pre-unlink.sh b/recipes/bioconductor-mapkldata/pre-unlink.sh new file mode 100644 index 0000000000000..294b59e03a371 --- /dev/null +++ b/recipes/bioconductor-mapkldata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mAPKLData diff --git a/recipes/bioconductor-mapredictdsc/build.sh b/recipes/bioconductor-mapredictdsc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mapredictdsc/build.sh +++ b/recipes/bioconductor-mapredictdsc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapredictdsc/conda_build_config.yaml b/recipes/bioconductor-mapredictdsc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mapredictdsc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mapredictdsc/meta.yaml b/recipes/bioconductor-mapredictdsc/meta.yaml index c5346a79ff404..168126504742d 100644 --- a/recipes/bioconductor-mapredictdsc/meta.yaml +++ b/recipes/bioconductor-mapredictdsc/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "maPredictDSC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d632461eae6b5153f6962c09fece614f26bd1f93c3dabdc6432d5be4d457a363 + md5: 58b9e88d3fdbb667047c967923367f82 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: parallel requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-lungcanceracvssccgeo >=1.16.0,<1.18.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lungcanceracvssccgeo >=1.18.0,<1.19.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-caret - r-class @@ -32,13 +34,13 @@ requirements: - r-mass - r-rocr run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-lungcanceracvssccgeo >=1.16.0,<1.18.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lungcanceracvssccgeo >=1.18.0,<1.19.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-caret - r-class @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package implements the classification pipeline of the best overall team (Team221) in the IMPROVER Diagnostic Signature Challenge. Additional functionality is added to compare 27 combinations of data preprocessing, feature selection and classifier types.' extra: identifiers: - biotools:mapredictdsc - doi:10.1093/bioinformatics/btt492 + parent_recipe: + name: bioconductor-mapredictdsc + path: recipes/bioconductor-mapredictdsc + version: 1.18.0 + diff --git a/recipes/bioconductor-mapscape/build.sh b/recipes/bioconductor-mapscape/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mapscape/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mapscape/meta.yaml b/recipes/bioconductor-mapscape/meta.yaml new file mode 100644 index 0000000000000..aead67191d8cb --- /dev/null +++ b/recipes/bioconductor-mapscape/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.0" %} +{% set name = "mapscape" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b0155ab540b77d549bf9d403b384e24a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - 'r-base64enc >=0.1-3' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-stringr >=1.0.0' + run: + - r-base + - 'r-base64enc >=0.1-3' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-stringr >=1.0.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MapScape integrates clonal prevalence, clonal hierarchy, anatomic and mutational information to provide interactive visualization of spatial clonal evolution. There are four inputs to MapScape: (i) the clonal phylogeny, (ii) clonal prevalences, (iii) an image reference, which may be a medical image or drawing and (iv) pixel locations for each sample on the referenced image. Optionally, MapScape can accept a data table of mutations for each clone and their variant allele frequencies in each sample. The output of MapScape consists of a cropped anatomical image surrounded by two representations of each tumour sample. The first, a cellular aggregate, visually displays the prevalence of each clone. The second shows a skeleton of the clonal phylogeny while highlighting only those clones present in the sample. Together, these representations enable the analyst to visualize the distribution of clones throughout anatomic space.' + diff --git a/recipes/bioconductor-maqcexpression4plex/meta.yaml b/recipes/bioconductor-maqcexpression4plex/meta.yaml new file mode 100644 index 0000000000000..ecca167818302 --- /dev/null +++ b/recipes/bioconductor-maqcexpression4plex/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.26.0" %} +{% set name = "maqcExpression4plex" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3ce8a0a849ae354153897db598f86fab +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: oligo, pdInfoBuilder +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Data from human (HG18) 4plex NimbleGen array. It has 24k genes with 3 60mer probes per gene.' + diff --git a/recipes/bioconductor-maqcexpression4plex/post-link.sh b/recipes/bioconductor-maqcexpression4plex/post-link.sh new file mode 100644 index 0000000000000..244463616f6a9 --- /dev/null +++ b/recipes/bioconductor-maqcexpression4plex/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="maqcExpression4plex_1.26.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/maqcExpression4plex_1.26.0.tar.gz" + "https://bioarchive.galaxyproject.org/maqcExpression4plex_1.26.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcexpression4plex/bioconductor-maqcexpression4plex_1.26.0_src_all.tar.gz" +) +MD5="3ce8a0a849ae354153897db598f86fab" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maqcexpression4plex/pre-unlink.sh b/recipes/bioconductor-maqcexpression4plex/pre-unlink.sh new file mode 100644 index 0000000000000..a98e2d85a21f2 --- /dev/null +++ b/recipes/bioconductor-maqcexpression4plex/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ maqcExpression4plex diff --git a/recipes/bioconductor-maqcsubset/meta.yaml b/recipes/bioconductor-maqcsubset/meta.yaml new file mode 100644 index 0000000000000..763c126638ee2 --- /dev/null +++ b/recipes/bioconductor-maqcsubset/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.20.0" %} +{% set name = "MAQCsubset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e8b9ec1c5c7aec22ebe396f03e5088ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: genefilter, codelink +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Data Package automatically created on Sun Nov 19 15:59:29 2006.' + diff --git a/recipes/bioconductor-maqcsubset/post-link.sh b/recipes/bioconductor-maqcsubset/post-link.sh new file mode 100644 index 0000000000000..95c431ca92220 --- /dev/null +++ b/recipes/bioconductor-maqcsubset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MAQCsubset_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubset_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubset_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubset/bioconductor-maqcsubset_1.20.0_src_all.tar.gz" +) +MD5="e8b9ec1c5c7aec22ebe396f03e5088ad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maqcsubset/pre-unlink.sh b/recipes/bioconductor-maqcsubset/pre-unlink.sh new file mode 100644 index 0000000000000..4cb7fb55ee2f4 --- /dev/null +++ b/recipes/bioconductor-maqcsubset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MAQCsubset diff --git a/recipes/bioconductor-maqcsubsetafx/meta.yaml b/recipes/bioconductor-maqcsubsetafx/meta.yaml new file mode 100644 index 0000000000000..ed4522079f2bd --- /dev/null +++ b/recipes/bioconductor-maqcsubsetafx/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "MAQCsubsetAFX" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9463855db7431adda8bd920b13a090b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MAQC data subset for the Affymetrix platform' + diff --git a/recipes/bioconductor-maqcsubsetafx/post-link.sh b/recipes/bioconductor-maqcsubsetafx/post-link.sh new file mode 100644 index 0000000000000..29314ceca6865 --- /dev/null +++ b/recipes/bioconductor-maqcsubsetafx/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MAQCsubsetAFX_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubsetAFX_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubsetAFX_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetafx/bioconductor-maqcsubsetafx_1.20.0_src_all.tar.gz" +) +MD5="9463855db7431adda8bd920b13a090b2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maqcsubsetafx/pre-unlink.sh b/recipes/bioconductor-maqcsubsetafx/pre-unlink.sh new file mode 100644 index 0000000000000..b6cba448ba26b --- /dev/null +++ b/recipes/bioconductor-maqcsubsetafx/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MAQCsubsetAFX diff --git a/recipes/bioconductor-maqcsubsetilm/meta.yaml b/recipes/bioconductor-maqcsubsetilm/meta.yaml new file mode 100644 index 0000000000000..2b640b1887fef --- /dev/null +++ b/recipes/bioconductor-maqcsubsetilm/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.20.0" %} +{% set name = "MAQCsubsetILM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 92c3de4c8a84a1ef6f3ef994f9a627f3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'MAQC data subset for the Illumina platform' + diff --git a/recipes/bioconductor-maqcsubsetilm/post-link.sh b/recipes/bioconductor-maqcsubsetilm/post-link.sh new file mode 100644 index 0000000000000..d27ac910087c9 --- /dev/null +++ b/recipes/bioconductor-maqcsubsetilm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MAQCsubsetILM_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MAQCsubsetILM_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MAQCsubsetILM_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-maqcsubsetilm/bioconductor-maqcsubsetilm_1.20.0_src_all.tar.gz" +) +MD5="92c3de4c8a84a1ef6f3ef994f9a627f3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-maqcsubsetilm/pre-unlink.sh b/recipes/bioconductor-maqcsubsetilm/pre-unlink.sh new file mode 100644 index 0000000000000..7a1c352453aa9 --- /dev/null +++ b/recipes/bioconductor-maqcsubsetilm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MAQCsubsetILM diff --git a/recipes/bioconductor-marray/build.sh b/recipes/bioconductor-marray/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-marray/build.sh +++ b/recipes/bioconductor-marray/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-marray/meta.yaml b/recipes/bioconductor-marray/meta.yaml index fda8d59a595e3..89c36182f5546 100644 --- a/recipes/bioconductor-marray/meta.yaml +++ b/recipes/bioconductor-marray/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "marray" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0d019856af63d85064f2618fa10b2be6e838f5e26e56b5c22a1e073f20756914 + md5: 9620bb609afca132e43100410100b934 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: tkWidgets requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Class definitions for two-color spotted microarray data. Fuctions for data input, diagnostic plots, normalization and quality checking.' extra: identifiers: - biotools:marray - doi:10.1007/0-387-21679-0_3 + parent_recipe: + name: bioconductor-marray + path: recipes/bioconductor-marray + version: 1.58.0 + diff --git a/recipes/bioconductor-martini/build.sh b/recipes/bioconductor-martini/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-martini/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-martini/meta.yaml b/recipes/bioconductor-martini/meta.yaml new file mode 100644 index 0000000000000..31212f4778978 --- /dev/null +++ b/recipes/bioconductor-martini/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.2.0" %} +{% set name = "martini" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a700575374a986a0013bff3b1e08a134 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: biomaRt (>= 2.34.1), httr (>= 1.2.1), IRanges (>= 2.8.2), knitr, testthat, tidyverse, rmarkdown +requirements: + host: + - 'bioconductor-rgin >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - 'r-igraph >=1.0.1' + - r-matrix + - 'r-rcpp >=0.12.8' + - 'r-rcppeigen >=0.3.3.3.0' + run: + - 'bioconductor-rgin >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - 'r-igraph >=1.0.1' + - r-matrix + - 'r-rcpp >=0.12.8' + - 'r-rcppeigen >=0.3.3.3.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'martini deals with the low power inherent to GWAS studies by using prior knowledge represented as a network. SNPs are the vertices of the network, and the edges represent biological relationships between them (genomic adjacency, belonging to the same gene, physical interaction between protein products). The network is scanned using SConES, which looks for groups of SNPs maximally associated with the phenotype, that form a close subnetwork.' + diff --git a/recipes/bioconductor-maser/build.sh b/recipes/bioconductor-maser/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-maser/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maser/meta.yaml b/recipes/bioconductor-maser/meta.yaml new file mode 100644 index 0000000000000..12494367ab8b3 --- /dev/null +++ b/recipes/bioconductor-maser/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "maser" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3736c02b9c3b7db33c31da8fa9e72eea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, AnnotationHub +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-reshape2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-dplyr + - r-dt + - r-ggplot2 + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package provides functionalities for analysis, annotation and visualizaton of alternative splicing events.' + diff --git a/recipes/bioconductor-masigpro/build.sh b/recipes/bioconductor-masigpro/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-masigpro/build.sh +++ b/recipes/bioconductor-masigpro/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-masigpro/meta.yaml b/recipes/bioconductor-masigpro/meta.yaml index 6ea20e864dfc8..34f56320bc9bf 100644 --- a/recipes/bioconductor-masigpro/meta.yaml +++ b/recipes/bioconductor-masigpro/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "maSigPro" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c83be0c892cf6ae6852096d794e9a3d65ed96bdadeb7026581598063c6745411 + md5: 4a642f18b31d99eee5b5d7dcd7b54b8e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass - r-mclust - r-venn run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass - r-mclust @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'maSigPro is a regression based approach to find genes for which there are significant gene expression profile differences between experimental groups in time course microarray and RNA-Seq experiments.' extra: identifiers: - biotools:masigpro - doi:10.1093/bioinformatics/btu333 + parent_recipe: + name: bioconductor-masigpro + path: recipes/bioconductor-masigpro + version: 1.52.0 + diff --git a/recipes/bioconductor-maskbad/build.sh b/recipes/bioconductor-maskbad/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-maskbad/build.sh +++ b/recipes/bioconductor-maskbad/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maskbad/conda_build_config.yaml b/recipes/bioconductor-maskbad/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-maskbad/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-maskbad/meta.yaml b/recipes/bioconductor-maskbad/meta.yaml index 802dde7bfbe4e..36318da926a7d 100644 --- a/recipes/bioconductor-maskbad/meta.yaml +++ b/recipes/bioconductor-maskbad/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "maskBAD" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d72601b240e9f5c044c777bff2082ac7dc346fe3c86ed3676e7341b86f4f22de + md5: f4729f51911770bb1448510b43e5e479 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu95av2probe, hgu95av2cdf requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package includes functions to analyze and mask microarray expression data.' extra: identifiers: - biotools:maskbad - doi:10.1093/bioinformatics/btp492 + parent_recipe: + name: bioconductor-maskbad + path: recipes/bioconductor-maskbad + version: 1.24.0 + diff --git a/recipes/bioconductor-massarray/build.sh b/recipes/bioconductor-massarray/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-massarray/build.sh +++ b/recipes/bioconductor-massarray/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-massarray/meta.yaml b/recipes/bioconductor-massarray/meta.yaml index 464e5b81f646d..0bde6d2e4eaa3 100644 --- a/recipes/bioconductor-massarray/meta.yaml +++ b/recipes/bioconductor-massarray/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MassArray" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a1f6e69106e3ce3d2f356703008c580fd63bbe664fc226bd82368b31a6f025da + md5: e993b4abbf29de763c3f3ce2ead2dae6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' - summary: 'This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom''s MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.' + summary: 'This package is designed for the import, quality control, analysis, and visualization of methylation data generated using Sequenom''s MassArray platform. The tools herein contain a highly detailed amplicon prediction for optimal assay design. Also included are quality control measures of data, such as primer dimer and bisulfite conversion efficiency estimation. Methylation data are calculated using the same algorithms contained in the EpiTyper software package. Additionally, automatic SNP-detection can be used to flag potentially confounded data from specific CG sites. Visualization includes barplots of methylation data as well as UCSC Genome Browser-compatible BED tracks. Multiple assays can be positionally combined for integrated analysis.' extra: identifiers: - biotools:massarray - doi:10.1093/bioinformatics/btp382 + parent_recipe: + name: bioconductor-massarray + path: recipes/bioconductor-massarray + version: 1.32.0 + diff --git a/recipes/bioconductor-massir/build.sh b/recipes/bioconductor-massir/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-massir/build.sh +++ b/recipes/bioconductor-massir/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-massir/meta.yaml b/recipes/bioconductor-massir/meta.yaml index a416a99340202..0e6920ec6676f 100644 --- a/recipes/bioconductor-massir/meta.yaml +++ b/recipes/bioconductor-massir/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "massiR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cbe2608b58442c535b78513537ab0e1dea58279fa5af975b5100e4c9ea0600b0 + md5: 155d85624615ff8b2a8dfc5614a8cc78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster - r-diptest - r-gplots run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-cluster - r-diptest @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Predicts the sex of samples in gene expression microarray datasets' extra: identifiers: - biotools:massir + parent_recipe: + name: bioconductor-massir + path: recipes/bioconductor-massir + version: 1.16.0 + diff --git a/recipes/bioconductor-massspecwavelet/build.sh b/recipes/bioconductor-massspecwavelet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-massspecwavelet/build.sh +++ b/recipes/bioconductor-massspecwavelet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-massspecwavelet/meta.yaml b/recipes/bioconductor-massspecwavelet/meta.yaml index 24303bda7fc11..e609caaab30c6 100644 --- a/recipes/bioconductor-massspecwavelet/meta.yaml +++ b/recipes/bioconductor-massspecwavelet/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "MassSpecWavelet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1f028a643031034a21d1c11a3a93bdc994e6f770e9c0bb097dd3c01d3880195e + md5: f2b40bd0d80b1d7161cc6b6a05819c15 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: xcms, caTools requirements: host: - r-base @@ -30,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Processing Mass Spectrometry spectrum by using wavelet based algorithm' extra: identifiers: - biotools:massspecwavelet + parent_recipe: + name: bioconductor-massspecwavelet + path: recipes/bioconductor-massspecwavelet + version: 1.46.0 + diff --git a/recipes/bioconductor-mast/build.sh b/recipes/bioconductor-mast/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mast/build.sh +++ b/recipes/bioconductor-mast/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mast/conda_build_config.yaml b/recipes/bioconductor-mast/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mast/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mast/meta.yaml b/recipes/bioconductor-mast/meta.yaml index 7f5e432a95f82..69c27a2b52816 100644 --- a/recipes/bioconductor-mast/meta.yaml +++ b/recipes/bioconductor-mast/meta.yaml @@ -1,56 +1,65 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.1" %} {% set name = "MAST" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ebaeaf51c011113e3c2871773c3b10e0cd61fc9e4d9f7bb4afe83f40ebf02bff + md5: 2aff93e37d44268b59c52e6f6323e3a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, lme4(>= 1.0), roxygen2(> 4.0.0), numDeriv, car, gdata, lattice, GGally, GSEABase, NMF, TxDb.Hsapiens.UCSC.hg19.knownGene, rsvd, limma, RColorBrewer, BiocStyle, scater requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-abind - r-base - r-data.table - r-ggplot2 - r-plyr + - r-progress - r-reshape2 - r-stringr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-abind - r-base - r-data.table - r-ggplot2 - r-plyr + - r-progress - r-reshape2 - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL(>= 2)' summary: 'Methods and models for handling zero-inflated single cell assay data.' extra: identifiers: - biotools:mast - doi:10.1186/s13059-015-0844-5 + parent_recipe: + name: bioconductor-mast + path: recipes/bioconductor-mast + version: 1.6.1 + diff --git a/recipes/bioconductor-matchbox/build.sh b/recipes/bioconductor-matchbox/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-matchbox/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-matchbox/meta.yaml b/recipes/bioconductor-matchbox/meta.yaml new file mode 100644 index 0000000000000..9e02c85f8458a --- /dev/null +++ b/recipes/bioconductor-matchbox/meta.yaml @@ -0,0 +1,32 @@ +{% set version = "1.24.0" %} +{% set name = "matchBox" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 96cde96f3ff554796874b2a7cc27bdb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The matchBox package enables comparing ranked vectors of features, merging multiple datasets, removing redundant features, using CAT-plots and Venn diagrams, and computing statistical significance.' + diff --git a/recipes/bioconductor-matrixrider/build.sh b/recipes/bioconductor-matrixrider/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-matrixrider/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-matrixrider/meta.yaml b/recipes/bioconductor-matrixrider/meta.yaml new file mode 100644 index 0000000000000..696e634d95523 --- /dev/null +++ b/recipes/bioconductor-matrixrider/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.14.0" %} +{% set name = "MatrixRider" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 96fe9ae1dd48d87fae7b56afd0c4808e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics, BiocStyle, JASPAR2014 +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Calculates a single number for a whole sequence that reflects the propensity of a DNA binding protein to interact with it. The DNA binding protein has to be described with a PFM matrix, for example gotten from Jaspar.' + diff --git a/recipes/bioconductor-matter/build.sh b/recipes/bioconductor-matter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-matter/build.sh +++ b/recipes/bioconductor-matter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-matter/meta.yaml b/recipes/bioconductor-matter/meta.yaml index 2ca0418b609c9..be545003bccc9 100644 --- a/recipes/bioconductor-matter/meta.yaml +++ b/recipes/bioconductor-matter/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "matter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 713c5f73024d38c60d7e457b02dc7a28dba4dcb3b5474d771679bc5960c23d0e + md5: f671a1b4c1379eacdf2fc7c5beb275aa build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-biglm - r-digest - r-irlba run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-biglm - r-digest @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Memory-efficient reading, writing, and manipulation of structured binary data on disk as vectors, matrices, arrays, lists, and data frames.' extra: identifiers: - biotools:matter - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-matter + path: recipes/bioconductor-matter + version: 1.6.0 + diff --git a/recipes/bioconductor-maxcontrastprojection/build.sh b/recipes/bioconductor-maxcontrastprojection/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-maxcontrastprojection/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-maxcontrastprojection/meta.yaml b/recipes/bioconductor-maxcontrastprojection/meta.yaml new file mode 100644 index 0000000000000..1df560a91769f --- /dev/null +++ b/recipes/bioconductor-maxcontrastprojection/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.6.0" %} +{% set name = "MaxContrastProjection" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4fd7e82e9c1214a42db9f0a56b8d622b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, testthat +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-base + run: + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A problem when recording 3D fluorescent microscopy images is how to properly present these results in 2D. Maximum intensity projections are a popular method to determine the focal plane of each pixel in the image. The problem with this approach, however, is that out-of-focus elements will still be visible, making edges and fine structures difficult to detect. This package aims to resolve this problem by using the contrast around a given pixel to determine the focal plane, allowing for a much cleaner structure detection than would be otherwise possible. For convenience, this package also contains functions to perform various other types of projections, including a maximum intensity projection.' + diff --git a/recipes/bioconductor-mbamethyl/build.sh b/recipes/bioconductor-mbamethyl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mbamethyl/build.sh +++ b/recipes/bioconductor-mbamethyl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbamethyl/meta.yaml b/recipes/bioconductor-mbamethyl/meta.yaml index bcf7f107b713b..c6ec254015721 100644 --- a/recipes/bioconductor-mbamethyl/meta.yaml +++ b/recipes/bioconductor-mbamethyl/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MBAmethyl" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ba443711fabff88ce89bd4e723760c6fccefd7b3f8d36d08c21c25716bee4b1d + md5: 6299112309d19ef270d439e7a23ee3ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a function for reconstructing DNA methylation values from raw measurements. It iteratively implements the group fused lars to smooth related-by-location methylation values and the constrained least squares to remove probe affinity effect across multiple sequences.' extra: identifiers: - biotools:mbamethyl - doi:10.1111/biom.12422 + parent_recipe: + name: bioconductor-mbamethyl + path: recipes/bioconductor-mbamethyl + version: 1.14.0 + diff --git a/recipes/bioconductor-mbased/build.sh b/recipes/bioconductor-mbased/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mbased/build.sh +++ b/recipes/bioconductor-mbased/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbased/meta.yaml b/recipes/bioconductor-mbased/meta.yaml index c2ba19b017cc4..586fcb6f38f8c 100644 --- a/recipes/bioconductor-mbased/meta.yaml +++ b/recipes/bioconductor-mbased/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MBASED" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5770fa061f34e461613f9946d4d18d0a1d9b276ab60883060f31f8c199b1ed3 + md5: 503273be8ad6f478d004d993d9f1c054 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-runit run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-runit test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package implements MBASED algorithm for detecting allele-specific gene expression from RNA count data, where allele counts at individual loci (SNVs) are integrated into a gene-specific measure of ASE, and utilizes simulations to appropriately assess the statistical significance of observed ASE.' extra: identifiers: - biotools:mbased - doi:10.1186/s13059-014-0405-3 + parent_recipe: + name: bioconductor-mbased + path: recipes/bioconductor-mbased + version: 1.14.0 + diff --git a/recipes/bioconductor-mbcb/build.sh b/recipes/bioconductor-mbcb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mbcb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbcb/meta.yaml b/recipes/bioconductor-mbcb/meta.yaml new file mode 100644 index 0000000000000..c9c185dd2d6b8 --- /dev/null +++ b/recipes/bioconductor-mbcb/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.36.0" %} +{% set name = "MBCB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 21bf4710d8291d63d7c6615b73000955 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-tcltk2 + run: + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-tcltk2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides a model-based background correction method, which incorporates the negative control beads to pre-process Illumina BeadArray data.' + diff --git a/recipes/bioconductor-mbpcr/build.sh b/recipes/bioconductor-mbpcr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mbpcr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbpcr/meta.yaml b/recipes/bioconductor-mbpcr/meta.yaml new file mode 100644 index 0000000000000..0bdbee69663ba --- /dev/null +++ b/recipes/bioconductor-mbpcr/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.36.0" %} +{% set name = "mBPCR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b429a42900934745c81407e4116c9f54 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xtable +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Estimates the DNA copy number profile using mBPCR to detect regions with copy number changes' + diff --git a/recipes/bioconductor-mbttest/build.sh b/recipes/bioconductor-mbttest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mbttest/build.sh +++ b/recipes/bioconductor-mbttest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mbttest/meta.yaml b/recipes/bioconductor-mbttest/meta.yaml index 135fa3168f50a..c7ca11121081e 100644 --- a/recipes/bioconductor-mbttest/meta.yaml +++ b/recipes/bioconductor-mbttest/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.1" %} +{% set version = "1.10.0" %} {% set name = "MBttest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f971d2ebf2c5e81a1e29a0d05c84392adbe414c4ba3ceba967281c4158008386 + md5: e7f88536245d563302be0374bcdf8009 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'MBttest method was developed from beta t-test method of Baggerly et al(2003). Compared to baySeq (Hard castle and Kelly 2010), DESeq (Anders and Huber 2010) and exact test (Robinson and Smyth 2007, 2008) and the GLM of McCarthy et al(2012), MBttest is of high work efficiency,that is, it has high power, high conservativeness of FDR estimation and high stability. MBttest is suit- able to transcriptomic data, tag data, SAGE data (count data) from small samples or a few replicate libraries. It can be used to identify genes, mRNA isoforms or tags differentially expressed between two conditions.' extra: identifiers: - biotools:mbttest - doi:10.1371/journal.pone.0123658 + parent_recipe: + name: bioconductor-mbttest + path: recipes/bioconductor-mbttest + version: 1.8.1 + diff --git a/recipes/bioconductor-mcagui/build.sh b/recipes/bioconductor-mcagui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mcagui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mcagui/meta.yaml b/recipes/bioconductor-mcagui/meta.yaml new file mode 100644 index 0000000000000..76643d1372d11 --- /dev/null +++ b/recipes/bioconductor-mcagui/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.30.0" %} +{% set name = "mcaGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8375e8dda6d5515700a95ab587d07c2f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-otubase >=1.32.0,<1.33.0' + - r-base + - r-bpca + - r-foreign + - 'r-gwidgets >=0.0-36' + - 'r-gwidgetsrgtk2 >=0.0-53' + - r-lattice + - r-mass + - r-proto + - r-vegan + run: + - 'bioconductor-otubase >=1.32.0,<1.33.0' + - r-base + - r-bpca + - r-foreign + - 'r-gwidgets >=0.0-36' + - 'r-gwidgetsrgtk2 >=0.0-53' + - r-lattice + - r-mass + - r-proto + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Microbial community analysis GUI for R using gWidgets.' + diff --git a/recipes/bioconductor-mcbiclust/build.sh b/recipes/bioconductor-mcbiclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mcbiclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mcbiclust/meta.yaml b/recipes/bioconductor-mcbiclust/meta.yaml new file mode 100644 index 0000000000000..d6f5b2afbda35 --- /dev/null +++ b/recipes/bioconductor-mcbiclust/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.6.0" %} +{% set name = "MCbiclust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 16b7342f3ac123ba54e0efc7df2ba492 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gplots, knitr, rmarkdown, BiocStyle, gProfileR, MASS, dplyr, pander, devtools, testthat, GSVA +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - r-cluster + - r-ggally + - r-ggplot2 + - r-scales + - r-wgcna + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - r-cluster + - r-ggally + - r-ggplot2 + - r-scales + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Custom made algorithm and associated methods for finding, visualising and analysing biclusters in large gene expression data sets. Algorithm is based on with a supplied gene set of size n, finding the maximum strength correlation matrix containing m samples from the data set.' + diff --git a/recipes/bioconductor-mcrestimate/build.sh b/recipes/bioconductor-mcrestimate/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mcrestimate/build.sh +++ b/recipes/bioconductor-mcrestimate/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mcrestimate/meta.yaml b/recipes/bioconductor-mcrestimate/meta.yaml index 5b9fc46483c72..54cd5ff2db504 100644 --- a/recipes/bioconductor-mcrestimate/meta.yaml +++ b/recipes/bioconductor-mcrestimate/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "MCRestimate" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f9bd512483fa6b8fd4e1b1d55ae50a722fec4528f20e846b621e396c951b36fb + md5: f72686ef3ef87989030a376fec562d0f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: xtable (>= 1.2-1), ROC (>= 1.8.0), genefilter (>= 1.12.0), gpls (>= 1.6.0) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-golubesets >=1.22.0,<1.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-golubesets >=1.24.0,<1.25.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' - 'r-randomforest >=3.9-6' - 'r-rcolorbrewer >=0.1-3' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-golubesets >=1.22.0,<1.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-golubesets >=1.24.0,<1.25.0' - r-base - 'r-e1071 >=1.5-12' - 'r-pamr >=1.22' @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package includes a function for combining preprocessing and classification methods to calculate misclassification errors' extra: identifiers: - biotools:mcrestimate - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mcrestimate + path: recipes/bioconductor-mcrestimate + version: 2.36.0 + diff --git a/recipes/bioconductor-mcsea/build.sh b/recipes/bioconductor-mcsea/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mcsea/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mcsea/meta.yaml b/recipes/bioconductor-mcsea/meta.yaml new file mode 100644 index 0000000000000..13c4b41cf4fcb --- /dev/null +++ b/recipes/bioconductor-mcsea/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "mCSEA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1511621e7aa960674da610667a7ea6e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocGenerics, BiocStyle, knitr, leukemiasEset, rmarkdown, RUnit +requirements: + host: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mcseadata >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mcseadata >=1.2.0,<1.3.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identification of diferentially methylated regions (DMRs) in predefined regions (promoters, CpG islands...) from the human genome using Illumina''s 450K or EPIC microarray data. Provides methods to rank CpG probes based on linear models and includes plotting functions.' + diff --git a/recipes/bioconductor-mcseadata/meta.yaml b/recipes/bioconductor-mcseadata/meta.yaml new file mode 100644 index 0000000000000..48b233cec7373 --- /dev/null +++ b/recipes/bioconductor-mcseadata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "mCSEAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 45eb34bc0dcb1414abbd892e3d4f70ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Data objects necessary to some mCSEA package functions. There are also example data objects to illustrate mCSEA package functionality.' + diff --git a/recipes/bioconductor-mcseadata/post-link.sh b/recipes/bioconductor-mcseadata/post-link.sh new file mode 100644 index 0000000000000..c022f8111626e --- /dev/null +++ b/recipes/bioconductor-mcseadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mCSEAdata_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mCSEAdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/mCSEAdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mcseadata/bioconductor-mcseadata_1.2.0_src_all.tar.gz" +) +MD5="45eb34bc0dcb1414abbd892e3d4f70ec" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mcseadata/pre-unlink.sh b/recipes/bioconductor-mcseadata/pre-unlink.sh new file mode 100644 index 0000000000000..95dfb62b04c76 --- /dev/null +++ b/recipes/bioconductor-mcseadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mCSEAdata diff --git a/recipes/bioconductor-mcsurvdata/meta.yaml b/recipes/bioconductor-mcsurvdata/meta.yaml new file mode 100644 index 0000000000000..3be365e4351ca --- /dev/null +++ b/recipes/bioconductor-mcsurvdata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "mcsurvdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b58022a7e2590ccf7b3a38d4587d7f50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package stores two merged expressionSet objects that contain the gene expression profile and clinical information of -a- six breast cancer cohorts and -b- four colorectal cancer cohorts. Breast cancer data are employed in the vignette of the hrunbiased package for survival analysis of gene signatures.' + diff --git a/recipes/bioconductor-mcsurvdata/post-link.sh b/recipes/bioconductor-mcsurvdata/post-link.sh new file mode 100644 index 0000000000000..55b2ecc2d32c2 --- /dev/null +++ b/recipes/bioconductor-mcsurvdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mcsurvdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mcsurvdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/mcsurvdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mcsurvdata/bioconductor-mcsurvdata_1.0.0_src_all.tar.gz" +) +MD5="b58022a7e2590ccf7b3a38d4587d7f50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mcsurvdata/pre-unlink.sh b/recipes/bioconductor-mcsurvdata/pre-unlink.sh new file mode 100644 index 0000000000000..7b4591a61f5dd --- /dev/null +++ b/recipes/bioconductor-mcsurvdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mcsurvdata diff --git a/recipes/bioconductor-mdgsa/build.sh b/recipes/bioconductor-mdgsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mdgsa/build.sh +++ b/recipes/bioconductor-mdgsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mdgsa/meta.yaml b/recipes/bioconductor-mdgsa/meta.yaml index 6e59c0a694701..41586f5c203cf 100644 --- a/recipes/bioconductor-mdgsa/meta.yaml +++ b/recipes/bioconductor-mdgsa/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "mdgsa" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 26a2dfe9c83daf777cf76c0f452fe19baffc9080c4e7043edccd3ee3091a8fe7 + md5: 28668e2ddf14e96380fbe1961c10e357 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, limma, ALL, hgu95av2.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-cluster - r-dbi - r-matrix run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base - r-cluster - r-dbi @@ -37,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Functions to preform a Gene Set Analysis in several genomic dimensions. Including methods for miRNAs.' extra: identifiers: - biotools:mdgsa + parent_recipe: + name: bioconductor-mdgsa + path: recipes/bioconductor-mdgsa + version: 1.12.1 + diff --git a/recipes/bioconductor-mdp/build.sh b/recipes/bioconductor-mdp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mdp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mdp/meta.yaml b/recipes/bioconductor-mdp/meta.yaml new file mode 100644 index 0000000000000..24b4c42b92c4f --- /dev/null +++ b/recipes/bioconductor-mdp/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "mdp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 51954cabceb7d8de92fe7b889a2da705 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, fgsea +requirements: + host: + - r-base + - r-ggplot2 + run: + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The Molecular Degree of Perturbation webtool quantifies the heterogeneity of samples. It takes a data.frame of omic data that contains at least two classes (control and test) and assigns a score to all samples based on how perturbed they are compared to the controls. It is based on the Molecular Distance to Health (Pankla et al. 2009), and expands on this algorithm by adding the options to calculate the z-score using the modified z-score (using median absolute deviation), change the z-score zeroing threshold, and look at genes that are most perturbed in the test versus control classes.' + diff --git a/recipes/bioconductor-mdqc/build.sh b/recipes/bioconductor-mdqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mdqc/build.sh +++ b/recipes/bioconductor-mdqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mdqc/meta.yaml b/recipes/bioconductor-mdqc/meta.yaml index cb74c51677b73..8bf7a07e195bb 100644 --- a/recipes/bioconductor-mdqc/meta.yaml +++ b/recipes/bioconductor-mdqc/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "mdqc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 651ef51f80b42aee74ae6fcedd34c0bc44261b8c6dd828e7a38a01f5cde68d98 + md5: d82132337f2ad3520bf49b73cb29c6f8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'MDQC is a multivariate quality assessment method for microarrays based on quality control (QC) reports. The Mahalanobis distance of an array''s quality attributes is used to measure the similarity of the quality of that array against the quality of the other arrays. Then, arrays with unusually high distances can be flagged as potentially low-quality.' extra: identifiers: - biotools:mdqc - doi:10.1093/bioinformatics/btm487 + parent_recipe: + name: bioconductor-mdqc + path: recipes/bioconductor-mdqc + version: 1.42.0 + diff --git a/recipes/bioconductor-mdts/build.sh b/recipes/bioconductor-mdts/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mdts/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mdts/meta.yaml b/recipes/bioconductor-mdts/meta.yaml new file mode 100644 index 0000000000000..7869cb39a5303 --- /dev/null +++ b/recipes/bioconductor-mdts/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.2.0" %} +{% set name = "MDTS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 509a06e8a0f6897ed1edb83f5687b479 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-stringr + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package for the detection of de novo copy number deletions in targeted sequencing of trios with high sensitivity and positive predictive value.' + diff --git a/recipes/bioconductor-meal/build.sh b/recipes/bioconductor-meal/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-meal/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meal/meta.yaml b/recipes/bioconductor-meal/meta.yaml new file mode 100644 index 0000000000000..15c35deb1f867 --- /dev/null +++ b/recipes/bioconductor-meal/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.12.0" %} +{% set name = "MEAL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fa53c8e7918242e6fadea0f6c9894496 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylation450kanno.ilmn12.hg19, knitr, minfiData, BiocStyle, rmarkdown, brgedata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dmrcate >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-multidataset >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-ggplot2 >=2.0.0' + - r-isva + - r-matrixstats + - r-permute + - r-smartsva + - r-vegan + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dmrcate >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-multidataset >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-ggplot2 >=2.0.0' + - r-isva + - r-matrixstats + - r-permute + - r-smartsva + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package to integrate methylation and expression data. It can also perform methylation or expression analysis alone. Several plotting functionalities are included as well as a new region analysis based on redundancy analysis. Effect of SNPs on a region can also be estimated.' + diff --git a/recipes/bioconductor-measurementerror.cor/build.sh b/recipes/bioconductor-measurementerror.cor/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-measurementerror.cor/build.sh +++ b/recipes/bioconductor-measurementerror.cor/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-measurementerror.cor/meta.yaml b/recipes/bioconductor-measurementerror.cor/meta.yaml index ba4a286abb21e..af177793b3873 100644 --- a/recipes/bioconductor-measurementerror.cor/meta.yaml +++ b/recipes/bioconductor-measurementerror.cor/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MeasurementError.cor" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e1f6fd5283877bffd2dadf347b4c8e2d18a4053c6dc13b4ebcfba90447143496 + md5: fca8d3daecf480356153659e0a0c1e74 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Two-stage measurement error model for correlation estimation with smaller bias than the usual sample correlation' extra: identifiers: - biotools:measurementerror.cor - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-measurementerror.cor + path: recipes/bioconductor-measurementerror.cor + version: 1.52.0 + diff --git a/recipes/bioconductor-medicagocdf/meta.yaml b/recipes/bioconductor-medicagocdf/meta.yaml new file mode 100644 index 0000000000000..2bcf7256dc864 --- /dev/null +++ b/recipes/bioconductor-medicagocdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "medicagocdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1fbb2e4c070344d18e65f1b3993867db +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Medicago.cdf file.' + diff --git a/recipes/bioconductor-medicagocdf/post-link.sh b/recipes/bioconductor-medicagocdf/post-link.sh new file mode 100644 index 0000000000000..498fab6c724cf --- /dev/null +++ b/recipes/bioconductor-medicagocdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="medicagocdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/medicagocdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/medicagocdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medicagocdf/bioconductor-medicagocdf_2.18.0_src_all.tar.gz" +) +MD5="1fbb2e4c070344d18e65f1b3993867db" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-medicagocdf/pre-unlink.sh b/recipes/bioconductor-medicagocdf/pre-unlink.sh new file mode 100644 index 0000000000000..13bdf15d128fc --- /dev/null +++ b/recipes/bioconductor-medicagocdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ medicagocdf diff --git a/recipes/bioconductor-medicagoprobe/meta.yaml b/recipes/bioconductor-medicagoprobe/meta.yaml new file mode 100644 index 0000000000000..b9a14995a4a65 --- /dev/null +++ b/recipes/bioconductor-medicagoprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "medicagoprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83b9887ad2ed26c704b0ca7115e5838d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Medicago\_probe\_tab.' + diff --git a/recipes/bioconductor-medicagoprobe/post-link.sh b/recipes/bioconductor-medicagoprobe/post-link.sh new file mode 100644 index 0000000000000..2baf145f7f87b --- /dev/null +++ b/recipes/bioconductor-medicagoprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="medicagoprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/medicagoprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/medicagoprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medicagoprobe/bioconductor-medicagoprobe_2.18.0_src_all.tar.gz" +) +MD5="83b9887ad2ed26c704b0ca7115e5838d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-medicagoprobe/pre-unlink.sh b/recipes/bioconductor-medicagoprobe/pre-unlink.sh new file mode 100644 index 0000000000000..cbcdb34940802 --- /dev/null +++ b/recipes/bioconductor-medicagoprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ medicagoprobe diff --git a/recipes/bioconductor-medips/build.sh b/recipes/bioconductor-medips/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-medips/build.sh +++ b/recipes/bioconductor-medips/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-medips/meta.yaml b/recipes/bioconductor-medips/meta.yaml index d0e2837c93207..2d8385a1f2737 100644 --- a/recipes/bioconductor-medips/meta.yaml +++ b/recipes/bioconductor-medips/meta.yaml @@ -1,55 +1,62 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "MEDIPS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 455c89e4898263be0ee3d937cec61a1d6e2e75b4f6e373d97bc8020ef751acce + md5: 20d8d11b858c8912edff6d11917faa5c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, BiocStyle requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-gtools run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-gtools test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'MEDIPS was developed for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, MEDIPS provides functionalities for the analysis of any kind of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential coverage between groups of samples and saturation and correlation analysis.' extra: identifiers: - biotools:medips + parent_recipe: + name: bioconductor-medips + path: recipes/bioconductor-medips + version: 1.32.0 + diff --git a/recipes/bioconductor-medipsdata/meta.yaml b/recipes/bioconductor-medipsdata/meta.yaml new file mode 100644 index 0000000000000..0d91901836195 --- /dev/null +++ b/recipes/bioconductor-medipsdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "MEDIPSData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 80c0076eae9f53aeda545a4e2716ab69 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Example data for MEDIPS and QSEA packages, consisting of chromosome 22 MeDIP and control/Input sample data. Additionally, the package contains MeDIP seq data from 3 NSCLC samples and adjacent normal tissue (chr 20-22). All data has been aligned to human genome hg19.' + diff --git a/recipes/bioconductor-medipsdata/post-link.sh b/recipes/bioconductor-medipsdata/post-link.sh new file mode 100644 index 0000000000000..8096af1f47262 --- /dev/null +++ b/recipes/bioconductor-medipsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MEDIPSData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MEDIPSData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/MEDIPSData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-medipsdata/bioconductor-medipsdata_1.18.0_src_all.tar.gz" +) +MD5="80c0076eae9f53aeda545a4e2716ab69" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-medipsdata/pre-unlink.sh b/recipes/bioconductor-medipsdata/pre-unlink.sh new file mode 100644 index 0000000000000..683a08e1ab5e6 --- /dev/null +++ b/recipes/bioconductor-medipsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MEDIPSData diff --git a/recipes/bioconductor-medme/build.sh b/recipes/bioconductor-medme/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-medme/build.sh +++ b/recipes/bioconductor-medme/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-medme/meta.yaml b/recipes/bioconductor-medme/meta.yaml index d921758ea592f..a13d5a1e9e558 100644 --- a/recipes/bioconductor-medme/meta.yaml +++ b/recipes/bioconductor-medme/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "MEDME" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6720cc486f736e58f350f0b7a7f8b685cacfbc12660575b3b7865db3eb1f5973 + md5: a77cb873abc5ef82394b847801debb3a build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg18, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-drc - r-mass run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-drc - r-mass @@ -34,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Description: MEDME allows the prediction of absolute and relative methylation levels based on measures obtained by MeDIP-microarray experiments' extra: identifiers: - biotools:medme - doi:10.1101/gr.080721.108 + parent_recipe: + name: bioconductor-medme + path: recipes/bioconductor-medme + version: 1.40.0 + diff --git a/recipes/bioconductor-meebodata/meta.yaml b/recipes/bioconductor-meebodata/meta.yaml new file mode 100644 index 0000000000000..b9125d8bed339 --- /dev/null +++ b/recipes/bioconductor-meebodata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "MEEBOdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f406364f10353a1a634a4d726c66a22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'R objects describing the MEEBO set.' + diff --git a/recipes/bioconductor-meebodata/post-link.sh b/recipes/bioconductor-meebodata/post-link.sh new file mode 100644 index 0000000000000..57c69c607fe50 --- /dev/null +++ b/recipes/bioconductor-meebodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MEEBOdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MEEBOdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/MEEBOdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-meebodata/bioconductor-meebodata_1.20.0_src_all.tar.gz" +) +MD5="6f406364f10353a1a634a4d726c66a22" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-meebodata/pre-unlink.sh b/recipes/bioconductor-meebodata/pre-unlink.sh new file mode 100644 index 0000000000000..654dbc8727082 --- /dev/null +++ b/recipes/bioconductor-meebodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MEEBOdata diff --git a/recipes/bioconductor-meigor/build.sh b/recipes/bioconductor-meigor/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-meigor/build.sh +++ b/recipes/bioconductor-meigor/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meigor/meta.yaml b/recipes/bioconductor-meigor/meta.yaml index 43eef27b964c1..85d48333fe30b 100644 --- a/recipes/bioconductor-meigor/meta.yaml +++ b/recipes/bioconductor-meigor/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MEIGOR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3498f08b7d834c7b8f879d0a074261325870490d2df69e07672a83ade172a912 + md5: 3ebe8603dbf28a32751dc0e048d0b2c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: CellNOptR requirements: host: - - 'bioconductor-cnorode >=1.22.0,<1.24.0' + - 'bioconductor-cnorode >=1.24.0,<1.25.0' - r-base - r-desolve - r-rsolnp - r-snowfall run: - - 'bioconductor-cnorode >=1.22.0,<1.24.0' + - 'bioconductor-cnorode >=1.24.0,<1.25.0' - r-base - r-desolve - r-rsolnp @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Global Optimization' extra: identifiers: - biotools:meigor - doi:10.1186/1471-2105-15-136 + parent_recipe: + name: bioconductor-meigor + path: recipes/bioconductor-meigor + version: 1.14.0 + diff --git a/recipes/bioconductor-mergemaid/build.sh b/recipes/bioconductor-mergemaid/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mergemaid/build.sh +++ b/recipes/bioconductor-mergemaid/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mergemaid/meta.yaml b/recipes/bioconductor-mergemaid/meta.yaml index 01588439c286d..66c1dbc7dde4f 100644 --- a/recipes/bioconductor-mergemaid/meta.yaml +++ b/recipes/bioconductor-mergemaid/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "2.52.0" %} +{% set version = "2.54.0" %} {% set name = "MergeMaid" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c27c0907ec96bd2fab59c072e58a0a45d0b74b736858935fd9e8f0dda23a7b14 + md5: 11c316392b5fb033937ab626cc4a1054 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass - r-survival run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass - r-survival @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The functions in this R extension are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be ''list'',''matrix'', or ''ExpressionSet''. The main function is ''mergeExprs'' which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function ''intcor'' calculate the correlation coefficients. Other functions use the output from ''modelOutcome'' to graphically display the results and cross-validate associations of gene expression data with survival.' extra: identifiers: - biotools:mergemaid - doi:10.2202/1544-6115.1046 + parent_recipe: + name: bioconductor-mergemaid + path: recipes/bioconductor-mergemaid + version: 2.52.0 + diff --git a/recipes/bioconductor-mergeomics/build.sh b/recipes/bioconductor-mergeomics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mergeomics/build.sh +++ b/recipes/bioconductor-mergeomics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mergeomics/meta.yaml b/recipes/bioconductor-mergeomics/meta.yaml index 74bfa1edca90d..707061a2b257f 100644 --- a/recipes/bioconductor-mergeomics/meta.yaml +++ b/recipes/bioconductor-mergeomics/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "Mergeomics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 19e07d1023d86f5d2debae383e4ef5e5ac51044ce90698b6c248771a76887f86 + md5: 042173c4efb0b75209df2bf35cbf70d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).' + summary: 'The Mergeomics pipeline serves as a flexible framework for integrating multidimensional omics-disease associations, functional genomics, canonical pathways and gene-gene interaction networks to generate mechanistic hypotheses. It includes two main parts, 1) Marker set enrichment analysis (MSEA); 2) Weighted Key Driver Analysis (wKDA).' extra: identifiers: - biotools:mergeomics - doi:10.1101/036012 + parent_recipe: + name: bioconductor-mergeomics + path: recipes/bioconductor-mergeomics + version: 1.8.0 + diff --git a/recipes/bioconductor-mesh.aca.eg.db/meta.yaml b/recipes/bioconductor-mesh.aca.eg.db/meta.yaml new file mode 100644 index 0000000000000..f2d989a44e661 --- /dev/null +++ b/recipes/bioconductor-mesh.aca.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Aca.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ccbcbec0fe189c42c94ee382a4f91e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.aca.eg.db/post-link.sh b/recipes/bioconductor-mesh.aca.eg.db/post-link.sh new file mode 100644 index 0000000000000..253d81a4ff07f --- /dev/null +++ b/recipes/bioconductor-mesh.aca.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Aca.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aca.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aca.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aca.eg.db/bioconductor-mesh.aca.eg.db_1.11.0_src_all.tar.gz" +) +MD5="9ccbcbec0fe189c42c94ee382a4f91e9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.aca.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.aca.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..9c6b96e3bfee9 --- /dev/null +++ b/recipes/bioconductor-mesh.aca.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Aca.eg.db diff --git a/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml b/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml new file mode 100644 index 0000000000000..bed17797dc65a --- /dev/null +++ b/recipes/bioconductor-mesh.aga.pest.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Aga.PEST.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a4743af6866821a43a0dca3b32ddb5a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh b/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh new file mode 100644 index 0000000000000..5141ce98b1df4 --- /dev/null +++ b/recipes/bioconductor-mesh.aga.pest.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aga.PEST.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aga.pest.eg.db/bioconductor-mesh.aga.pest.eg.db_1.11.0_src_all.tar.gz" +) +MD5="a4743af6866821a43a0dca3b32ddb5a5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.aga.pest.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.aga.pest.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..54a0554288252 --- /dev/null +++ b/recipes/bioconductor-mesh.aga.pest.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Aga.PEST.eg.db diff --git a/recipes/bioconductor-mesh.ame.eg.db/meta.yaml b/recipes/bioconductor-mesh.ame.eg.db/meta.yaml new file mode 100644 index 0000000000000..fc0ab677503f9 --- /dev/null +++ b/recipes/bioconductor-mesh.ame.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ame.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: caac4a2dbb385e12508b9b783301a108 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ame.eg.db/post-link.sh b/recipes/bioconductor-mesh.ame.eg.db/post-link.sh new file mode 100644 index 0000000000000..e38db8ad8d0ca --- /dev/null +++ b/recipes/bioconductor-mesh.ame.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ame.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ame.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ame.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ame.eg.db/bioconductor-mesh.ame.eg.db_1.11.0_src_all.tar.gz" +) +MD5="caac4a2dbb385e12508b9b783301a108" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ame.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ame.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..fc1d0a90ff1db --- /dev/null +++ b/recipes/bioconductor-mesh.ame.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ame.eg.db diff --git a/recipes/bioconductor-mesh.aml.eg.db/meta.yaml b/recipes/bioconductor-mesh.aml.eg.db/meta.yaml new file mode 100644 index 0000000000000..6ef712f202b21 --- /dev/null +++ b/recipes/bioconductor-mesh.aml.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Aml.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0d4213a8c23de5feaea66f809b4cfe5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.aml.eg.db/post-link.sh b/recipes/bioconductor-mesh.aml.eg.db/post-link.sh new file mode 100644 index 0000000000000..759b15c6e6d21 --- /dev/null +++ b/recipes/bioconductor-mesh.aml.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Aml.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Aml.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Aml.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aml.eg.db/bioconductor-mesh.aml.eg.db_1.11.0_src_all.tar.gz" +) +MD5="0d4213a8c23de5feaea66f809b4cfe5f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.aml.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.aml.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..7caaa7f342e4a --- /dev/null +++ b/recipes/bioconductor-mesh.aml.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Aml.eg.db diff --git a/recipes/bioconductor-mesh.ana.eg.db/meta.yaml b/recipes/bioconductor-mesh.ana.eg.db/meta.yaml new file mode 100644 index 0000000000000..2d98afe433160 --- /dev/null +++ b/recipes/bioconductor-mesh.ana.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ana.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3d146c598a66e6e40081517169bda1e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ana.eg.db/post-link.sh b/recipes/bioconductor-mesh.ana.eg.db/post-link.sh new file mode 100644 index 0000000000000..16ee1b23e937f --- /dev/null +++ b/recipes/bioconductor-mesh.ana.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ana.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ana.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ana.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ana.eg.db/bioconductor-mesh.ana.eg.db_1.11.0_src_all.tar.gz" +) +MD5="3d146c598a66e6e40081517169bda1e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ana.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ana.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..f585991239e0f --- /dev/null +++ b/recipes/bioconductor-mesh.ana.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ana.eg.db diff --git a/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml b/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml new file mode 100644 index 0000000000000..5e55e3525b2cd --- /dev/null +++ b/recipes/bioconductor-mesh.ani.fgsc.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ani.FGSC.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 719ef69619c7ff3e69eb14ac01777450 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh b/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh new file mode 100644 index 0000000000000..52a7f377f8bfa --- /dev/null +++ b/recipes/bioconductor-mesh.ani.fgsc.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ani.FGSC.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ani.fgsc.eg.db/bioconductor-mesh.ani.fgsc.eg.db_1.11.0_src_all.tar.gz" +) +MD5="719ef69619c7ff3e69eb14ac01777450" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ani.fgsc.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ani.fgsc.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..c8e563139ecc7 --- /dev/null +++ b/recipes/bioconductor-mesh.ani.fgsc.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ani.FGSC.eg.db diff --git a/recipes/bioconductor-mesh.aor.db/meta.yaml b/recipes/bioconductor-mesh.aor.db/meta.yaml new file mode 100644 index 0000000000000..1a1dc8318ddcd --- /dev/null +++ b/recipes/bioconductor-mesh.aor.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.AOR.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1f10237a8a9140ee1f6da72ca1308427 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of AOR (ancestor-offspring relationship) in MeSH.' + diff --git a/recipes/bioconductor-mesh.aor.db/post-link.sh b/recipes/bioconductor-mesh.aor.db/post-link.sh new file mode 100644 index 0000000000000..47c5e3143895b --- /dev/null +++ b/recipes/bioconductor-mesh.aor.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.AOR.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.AOR.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.AOR.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.aor.db/bioconductor-mesh.aor.db_1.11.0_src_all.tar.gz" +) +MD5="1f10237a8a9140ee1f6da72ca1308427" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.aor.db/pre-unlink.sh b/recipes/bioconductor-mesh.aor.db/pre-unlink.sh new file mode 100644 index 0000000000000..f8772969909cc --- /dev/null +++ b/recipes/bioconductor-mesh.aor.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.AOR.db diff --git a/recipes/bioconductor-mesh.ath.eg.db/meta.yaml b/recipes/bioconductor-mesh.ath.eg.db/meta.yaml new file mode 100644 index 0000000000000..abd54b28a5c0b --- /dev/null +++ b/recipes/bioconductor-mesh.ath.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ath.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 73520c331ee0fd50fb21b62dc8b81e0f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ath.eg.db/post-link.sh b/recipes/bioconductor-mesh.ath.eg.db/post-link.sh new file mode 100644 index 0000000000000..d3afe0409b789 --- /dev/null +++ b/recipes/bioconductor-mesh.ath.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ath.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ath.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ath.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ath.eg.db/bioconductor-mesh.ath.eg.db_1.11.0_src_all.tar.gz" +) +MD5="73520c331ee0fd50fb21b62dc8b81e0f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ath.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ath.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1d7c3696c5495 --- /dev/null +++ b/recipes/bioconductor-mesh.ath.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ath.eg.db diff --git a/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml b/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml new file mode 100644 index 0000000000000..7d478380c9bc2 --- /dev/null +++ b/recipes/bioconductor-mesh.bfl.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Bfl.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e3d17146970aba917ffa2e75a4b61668 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh b/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh new file mode 100644 index 0000000000000..a1944e9d34b50 --- /dev/null +++ b/recipes/bioconductor-mesh.bfl.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Bfl.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bfl.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bfl.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bfl.eg.db/bioconductor-mesh.bfl.eg.db_1.11.0_src_all.tar.gz" +) +MD5="e3d17146970aba917ffa2e75a4b61668" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.bfl.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.bfl.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..9782fdc076e4a --- /dev/null +++ b/recipes/bioconductor-mesh.bfl.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Bfl.eg.db diff --git a/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml b/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml new file mode 100644 index 0000000000000..c4a9431679d4b --- /dev/null +++ b/recipes/bioconductor-mesh.bsu.168.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Bsu.168.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a65d23890cee17d4c2eff1e4a8d39714 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh b/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh new file mode 100644 index 0000000000000..0b036154e6c3d --- /dev/null +++ b/recipes/bioconductor-mesh.bsu.168.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Bsu.168.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bsu.168.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bsu.168.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bsu.168.eg.db/bioconductor-mesh.bsu.168.eg.db_1.11.0_src_all.tar.gz" +) +MD5="a65d23890cee17d4c2eff1e4a8d39714" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.bsu.168.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.bsu.168.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..73cc8fc229661 --- /dev/null +++ b/recipes/bioconductor-mesh.bsu.168.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Bsu.168.eg.db diff --git a/recipes/bioconductor-mesh.bta.eg.db/meta.yaml b/recipes/bioconductor-mesh.bta.eg.db/meta.yaml new file mode 100644 index 0000000000000..a115407306393 --- /dev/null +++ b/recipes/bioconductor-mesh.bta.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Bta.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8ed09310cb68d0b8ea7e075c669c69cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.bta.eg.db/post-link.sh b/recipes/bioconductor-mesh.bta.eg.db/post-link.sh new file mode 100644 index 0000000000000..054ffdd5b37bf --- /dev/null +++ b/recipes/bioconductor-mesh.bta.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Bta.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Bta.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Bta.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.bta.eg.db/bioconductor-mesh.bta.eg.db_1.11.0_src_all.tar.gz" +) +MD5="8ed09310cb68d0b8ea7e075c669c69cf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.bta.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.bta.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..c743682075a8c --- /dev/null +++ b/recipes/bioconductor-mesh.bta.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Bta.eg.db diff --git a/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml b/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml new file mode 100644 index 0000000000000..777b8513b6f35 --- /dev/null +++ b/recipes/bioconductor-mesh.cal.sc5314.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cal.SC5314.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: abe3f60190131f0a2a65e7408b829fbd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh b/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh new file mode 100644 index 0000000000000..f8602e85d0e15 --- /dev/null +++ b/recipes/bioconductor-mesh.cal.sc5314.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cal.SC5314.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cal.sc5314.eg.db/bioconductor-mesh.cal.sc5314.eg.db_1.11.0_src_all.tar.gz" +) +MD5="abe3f60190131f0a2a65e7408b829fbd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cal.sc5314.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cal.sc5314.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..d75d2a3b9e3a2 --- /dev/null +++ b/recipes/bioconductor-mesh.cal.sc5314.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cal.SC5314.eg.db diff --git a/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml b/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml new file mode 100644 index 0000000000000..0d5cdb7fc37d5 --- /dev/null +++ b/recipes/bioconductor-mesh.cbr.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cbr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f7376562bb5b90f71142bc6430e39c6d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh b/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh new file mode 100644 index 0000000000000..738f2d5c77ebc --- /dev/null +++ b/recipes/bioconductor-mesh.cbr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cbr.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cbr.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cbr.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cbr.eg.db/bioconductor-mesh.cbr.eg.db_1.11.0_src_all.tar.gz" +) +MD5="f7376562bb5b90f71142bc6430e39c6d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cbr.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cbr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..161da5b41e18d --- /dev/null +++ b/recipes/bioconductor-mesh.cbr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cbr.eg.db diff --git a/recipes/bioconductor-mesh.cel.eg.db/meta.yaml b/recipes/bioconductor-mesh.cel.eg.db/meta.yaml new file mode 100644 index 0000000000000..f9f7e1cbab73f --- /dev/null +++ b/recipes/bioconductor-mesh.cel.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cel.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40395428c53ccc5bed4a5720f13c1126 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cel.eg.db/post-link.sh b/recipes/bioconductor-mesh.cel.eg.db/post-link.sh new file mode 100644 index 0000000000000..31c2ca7fda244 --- /dev/null +++ b/recipes/bioconductor-mesh.cel.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cel.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cel.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cel.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cel.eg.db/bioconductor-mesh.cel.eg.db_1.11.0_src_all.tar.gz" +) +MD5="40395428c53ccc5bed4a5720f13c1126" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cel.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cel.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..fe34e7c377ee5 --- /dev/null +++ b/recipes/bioconductor-mesh.cel.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cel.eg.db diff --git a/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml b/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml new file mode 100644 index 0000000000000..75196d6ae9273 --- /dev/null +++ b/recipes/bioconductor-mesh.cfa.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cfa.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1a51d80a9c253fdc7037a4a4d23f7429 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh b/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh new file mode 100644 index 0000000000000..578c5f564a89c --- /dev/null +++ b/recipes/bioconductor-mesh.cfa.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cfa.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cfa.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cfa.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cfa.eg.db/bioconductor-mesh.cfa.eg.db_1.11.0_src_all.tar.gz" +) +MD5="1a51d80a9c253fdc7037a4a4d23f7429" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cfa.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cfa.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1cda67c39ff48 --- /dev/null +++ b/recipes/bioconductor-mesh.cfa.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cfa.eg.db diff --git a/recipes/bioconductor-mesh.cin.eg.db/meta.yaml b/recipes/bioconductor-mesh.cin.eg.db/meta.yaml new file mode 100644 index 0000000000000..35bd2bd234bb9 --- /dev/null +++ b/recipes/bioconductor-mesh.cin.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cin.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d3eee14d64663fdc86f9e1f8964341b9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cin.eg.db/post-link.sh b/recipes/bioconductor-mesh.cin.eg.db/post-link.sh new file mode 100644 index 0000000000000..6c41fdad037bd --- /dev/null +++ b/recipes/bioconductor-mesh.cin.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cin.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cin.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cin.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cin.eg.db/bioconductor-mesh.cin.eg.db_1.11.0_src_all.tar.gz" +) +MD5="d3eee14d64663fdc86f9e1f8964341b9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cin.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cin.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..6dae8905e4da4 --- /dev/null +++ b/recipes/bioconductor-mesh.cin.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cin.eg.db diff --git a/recipes/bioconductor-mesh.cja.eg.db/meta.yaml b/recipes/bioconductor-mesh.cja.eg.db/meta.yaml new file mode 100644 index 0000000000000..f4f5f20ede484 --- /dev/null +++ b/recipes/bioconductor-mesh.cja.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cja.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 202f330085d91903e587263de9e3f0c0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cja.eg.db/post-link.sh b/recipes/bioconductor-mesh.cja.eg.db/post-link.sh new file mode 100644 index 0000000000000..3fc96dade47cb --- /dev/null +++ b/recipes/bioconductor-mesh.cja.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cja.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cja.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cja.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cja.eg.db/bioconductor-mesh.cja.eg.db_1.11.0_src_all.tar.gz" +) +MD5="202f330085d91903e587263de9e3f0c0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cja.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cja.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..8b5ddffa3241c --- /dev/null +++ b/recipes/bioconductor-mesh.cja.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cja.eg.db diff --git a/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml b/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml new file mode 100644 index 0000000000000..920485cc7a3a4 --- /dev/null +++ b/recipes/bioconductor-mesh.cpo.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cpo.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e2dc546ff799e5a99f0a521e682d62fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh b/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh new file mode 100644 index 0000000000000..c498b9beeea6a --- /dev/null +++ b/recipes/bioconductor-mesh.cpo.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cpo.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cpo.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cpo.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cpo.eg.db/bioconductor-mesh.cpo.eg.db_1.11.0_src_all.tar.gz" +) +MD5="e2dc546ff799e5a99f0a521e682d62fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cpo.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cpo.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b779fd3a322dd --- /dev/null +++ b/recipes/bioconductor-mesh.cpo.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cpo.eg.db diff --git a/recipes/bioconductor-mesh.cre.eg.db/meta.yaml b/recipes/bioconductor-mesh.cre.eg.db/meta.yaml new file mode 100644 index 0000000000000..3e4e6e6e2f254 --- /dev/null +++ b/recipes/bioconductor-mesh.cre.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Cre.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9f1aa5546a1f7b2164c92ad0262d5f5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.cre.eg.db/post-link.sh b/recipes/bioconductor-mesh.cre.eg.db/post-link.sh new file mode 100644 index 0000000000000..798e307c0a05d --- /dev/null +++ b/recipes/bioconductor-mesh.cre.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Cre.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Cre.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Cre.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.cre.eg.db/bioconductor-mesh.cre.eg.db_1.11.0_src_all.tar.gz" +) +MD5="9f1aa5546a1f7b2164c92ad0262d5f5f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.cre.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.cre.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ecb40669cb664 --- /dev/null +++ b/recipes/bioconductor-mesh.cre.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Cre.eg.db diff --git a/recipes/bioconductor-mesh.dan.eg.db/meta.yaml b/recipes/bioconductor-mesh.dan.eg.db/meta.yaml new file mode 100644 index 0000000000000..892ff68e2aa91 --- /dev/null +++ b/recipes/bioconductor-mesh.dan.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dan.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06ceff65e0124447a748a20c90034f1f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dan.eg.db/post-link.sh b/recipes/bioconductor-mesh.dan.eg.db/post-link.sh new file mode 100644 index 0000000000000..049c4f8899f2c --- /dev/null +++ b/recipes/bioconductor-mesh.dan.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dan.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dan.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dan.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dan.eg.db/bioconductor-mesh.dan.eg.db_1.11.0_src_all.tar.gz" +) +MD5="06ceff65e0124447a748a20c90034f1f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dan.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dan.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..dbff3405f43e5 --- /dev/null +++ b/recipes/bioconductor-mesh.dan.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dan.eg.db diff --git a/recipes/bioconductor-mesh.db/meta.yaml b/recipes/bioconductor-mesh.db/meta.yaml index 5aeb6bfef0983..d5a610d4e5242 100644 --- a/recipes/bioconductor-mesh.db/meta.yaml +++ b/recipes/bioconductor-mesh.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.10.0" %} +{% set version = "1.11.0" %} {% set name = "MeSH.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bf8fc760ff396641bea95f73a8688adc43efa18d827cb2c537e4181b9bc807ee + md5: c6b74bfc2623be738b9ac6ed981f8810 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-meshdbi >=1.16.0,<1.18.0' + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-meshdbi >=1.16.0,<1.18.0' + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire MeSH assembled using data from MeSH.' - +extra: + parent_recipe: + name: bioconductor-mesh.db + path: recipes/bioconductor-mesh.db + version: 1.10.0 diff --git a/recipes/bioconductor-mesh.db/post-link.sh b/recipes/bioconductor-mesh.db/post-link.sh index 702d0ead2a246..a3b5b92a936bc 100644 --- a/recipes/bioconductor-mesh.db/post-link.sh +++ b/recipes/bioconductor-mesh.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="MeSH.db_1.10.0.tar.gz" +FN="MeSH.db_1.11.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/MeSH.db_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/MeSH.db_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.db/bioconductor-mesh.db_1.11.0_src_all.tar.gz" ) -MD5="f47e271183018989338e75970620ce41" +MD5="c6b74bfc2623be738b9ac6ed981f8810" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml b/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml new file mode 100644 index 0000000000000..c4da70c823471 --- /dev/null +++ b/recipes/bioconductor-mesh.dda.3937.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dda.3937.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fa6921643753b56290fefb57274a59be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh b/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh new file mode 100644 index 0000000000000..60fd411cacc62 --- /dev/null +++ b/recipes/bioconductor-mesh.dda.3937.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dda.3937.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dda.3937.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dda.3937.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dda.3937.eg.db/bioconductor-mesh.dda.3937.eg.db_1.11.0_src_all.tar.gz" +) +MD5="fa6921643753b56290fefb57274a59be" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dda.3937.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dda.3937.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..2f88613ac2f75 --- /dev/null +++ b/recipes/bioconductor-mesh.dda.3937.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dda.3937.eg.db diff --git a/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml b/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml new file mode 100644 index 0000000000000..606a7d8508ac6 --- /dev/null +++ b/recipes/bioconductor-mesh.ddi.ax4.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ddi.AX4.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f16d5ae80376c352f770a6ace7ca5c78 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh b/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh new file mode 100644 index 0000000000000..ff7478efb0112 --- /dev/null +++ b/recipes/bioconductor-mesh.ddi.ax4.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ddi.AX4.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ddi.ax4.eg.db/bioconductor-mesh.ddi.ax4.eg.db_1.11.0_src_all.tar.gz" +) +MD5="f16d5ae80376c352f770a6ace7ca5c78" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ddi.ax4.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ddi.ax4.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b4facf6f05fc3 --- /dev/null +++ b/recipes/bioconductor-mesh.ddi.ax4.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ddi.AX4.eg.db diff --git a/recipes/bioconductor-mesh.der.eg.db/meta.yaml b/recipes/bioconductor-mesh.der.eg.db/meta.yaml new file mode 100644 index 0000000000000..0ff9384570578 --- /dev/null +++ b/recipes/bioconductor-mesh.der.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Der.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6e983cc8b9eea0dfa80d34d1dcc427f3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.der.eg.db/post-link.sh b/recipes/bioconductor-mesh.der.eg.db/post-link.sh new file mode 100644 index 0000000000000..a9401798130c5 --- /dev/null +++ b/recipes/bioconductor-mesh.der.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Der.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Der.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Der.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.der.eg.db/bioconductor-mesh.der.eg.db_1.11.0_src_all.tar.gz" +) +MD5="6e983cc8b9eea0dfa80d34d1dcc427f3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.der.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.der.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..e65eabf4bf0cb --- /dev/null +++ b/recipes/bioconductor-mesh.der.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Der.eg.db diff --git a/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml b/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml new file mode 100644 index 0000000000000..d9ce9492c5cd0 --- /dev/null +++ b/recipes/bioconductor-mesh.dgr.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dgr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: af40bdddd4d0d2596b085605734ba4d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh b/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh new file mode 100644 index 0000000000000..10e18b03a8280 --- /dev/null +++ b/recipes/bioconductor-mesh.dgr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dgr.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dgr.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dgr.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dgr.eg.db/bioconductor-mesh.dgr.eg.db_1.11.0_src_all.tar.gz" +) +MD5="af40bdddd4d0d2596b085605734ba4d3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dgr.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dgr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..5b10681a3ad25 --- /dev/null +++ b/recipes/bioconductor-mesh.dgr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dgr.eg.db diff --git a/recipes/bioconductor-mesh.dme.eg.db/meta.yaml b/recipes/bioconductor-mesh.dme.eg.db/meta.yaml new file mode 100644 index 0000000000000..1898226eeb2de --- /dev/null +++ b/recipes/bioconductor-mesh.dme.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dme.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b9f1b8e5882366a3362fe861a7f366e6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dme.eg.db/post-link.sh b/recipes/bioconductor-mesh.dme.eg.db/post-link.sh new file mode 100644 index 0000000000000..820f1608c7fbf --- /dev/null +++ b/recipes/bioconductor-mesh.dme.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dme.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dme.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dme.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dme.eg.db/bioconductor-mesh.dme.eg.db_1.11.0_src_all.tar.gz" +) +MD5="b9f1b8e5882366a3362fe861a7f366e6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dme.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dme.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..edd517b8ee739 --- /dev/null +++ b/recipes/bioconductor-mesh.dme.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dme.eg.db diff --git a/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml b/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml new file mode 100644 index 0000000000000..e49625f33c1af --- /dev/null +++ b/recipes/bioconductor-mesh.dmo.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dmo.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e5267e6a3961a67f289b3f58e484a508 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh b/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh new file mode 100644 index 0000000000000..71faacbab346c --- /dev/null +++ b/recipes/bioconductor-mesh.dmo.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dmo.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dmo.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dmo.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dmo.eg.db/bioconductor-mesh.dmo.eg.db_1.11.0_src_all.tar.gz" +) +MD5="e5267e6a3961a67f289b3f58e484a508" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dmo.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dmo.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..f42ca5a353b73 --- /dev/null +++ b/recipes/bioconductor-mesh.dmo.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dmo.eg.db diff --git a/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml b/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml new file mode 100644 index 0000000000000..bf4ad8be08607 --- /dev/null +++ b/recipes/bioconductor-mesh.dpe.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dpe.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89bc6448d7420b8808260bbd2fce5c6a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh b/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh new file mode 100644 index 0000000000000..38a032961b4c0 --- /dev/null +++ b/recipes/bioconductor-mesh.dpe.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dpe.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dpe.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dpe.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dpe.eg.db/bioconductor-mesh.dpe.eg.db_1.11.0_src_all.tar.gz" +) +MD5="89bc6448d7420b8808260bbd2fce5c6a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dpe.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dpe.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1103dd4ec0cd0 --- /dev/null +++ b/recipes/bioconductor-mesh.dpe.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dpe.eg.db diff --git a/recipes/bioconductor-mesh.dre.eg.db/meta.yaml b/recipes/bioconductor-mesh.dre.eg.db/meta.yaml new file mode 100644 index 0000000000000..41a8305740b78 --- /dev/null +++ b/recipes/bioconductor-mesh.dre.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dre.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4776847a50cbd8afe46626f3c3437b45 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dre.eg.db/post-link.sh b/recipes/bioconductor-mesh.dre.eg.db/post-link.sh new file mode 100644 index 0000000000000..f94885bb5ff8d --- /dev/null +++ b/recipes/bioconductor-mesh.dre.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dre.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dre.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dre.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dre.eg.db/bioconductor-mesh.dre.eg.db_1.11.0_src_all.tar.gz" +) +MD5="4776847a50cbd8afe46626f3c3437b45" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dre.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dre.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..712fd9eba3cda --- /dev/null +++ b/recipes/bioconductor-mesh.dre.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dre.eg.db diff --git a/recipes/bioconductor-mesh.dse.eg.db/meta.yaml b/recipes/bioconductor-mesh.dse.eg.db/meta.yaml new file mode 100644 index 0000000000000..56396c7c7cf69 --- /dev/null +++ b/recipes/bioconductor-mesh.dse.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dse.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 583f5f954ed715f511317f9dc424b9d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dse.eg.db/post-link.sh b/recipes/bioconductor-mesh.dse.eg.db/post-link.sh new file mode 100644 index 0000000000000..b3cfccb2128ca --- /dev/null +++ b/recipes/bioconductor-mesh.dse.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dse.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dse.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dse.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dse.eg.db/bioconductor-mesh.dse.eg.db_1.11.0_src_all.tar.gz" +) +MD5="583f5f954ed715f511317f9dc424b9d4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dse.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dse.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..a82a23b931740 --- /dev/null +++ b/recipes/bioconductor-mesh.dse.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dse.eg.db diff --git a/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml b/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml new file mode 100644 index 0000000000000..2efafb2462a53 --- /dev/null +++ b/recipes/bioconductor-mesh.dsi.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dsi.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cf96a96c3f2f869956b7c02d68b0dbbd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh b/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh new file mode 100644 index 0000000000000..d41ad8c49f28e --- /dev/null +++ b/recipes/bioconductor-mesh.dsi.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dsi.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dsi.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dsi.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dsi.eg.db/bioconductor-mesh.dsi.eg.db_1.11.0_src_all.tar.gz" +) +MD5="cf96a96c3f2f869956b7c02d68b0dbbd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dsi.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dsi.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b5974f2da11b0 --- /dev/null +++ b/recipes/bioconductor-mesh.dsi.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dsi.eg.db diff --git a/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml b/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml new file mode 100644 index 0000000000000..7972264a0f260 --- /dev/null +++ b/recipes/bioconductor-mesh.dvi.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dvi.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e26b6b84d33832c1d2b19c5406bd4ddf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh b/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh new file mode 100644 index 0000000000000..5b9e6e3b25459 --- /dev/null +++ b/recipes/bioconductor-mesh.dvi.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dvi.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dvi.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dvi.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dvi.eg.db/bioconductor-mesh.dvi.eg.db_1.11.0_src_all.tar.gz" +) +MD5="e26b6b84d33832c1d2b19c5406bd4ddf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dvi.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dvi.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..868f89c284dec --- /dev/null +++ b/recipes/bioconductor-mesh.dvi.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dvi.eg.db diff --git a/recipes/bioconductor-mesh.dya.eg.db/meta.yaml b/recipes/bioconductor-mesh.dya.eg.db/meta.yaml new file mode 100644 index 0000000000000..400868bf282ca --- /dev/null +++ b/recipes/bioconductor-mesh.dya.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Dya.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2407944d8054f00a17cf922d7bdf58b6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.dya.eg.db/post-link.sh b/recipes/bioconductor-mesh.dya.eg.db/post-link.sh new file mode 100644 index 0000000000000..e929a5495a2ce --- /dev/null +++ b/recipes/bioconductor-mesh.dya.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Dya.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Dya.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Dya.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.dya.eg.db/bioconductor-mesh.dya.eg.db_1.11.0_src_all.tar.gz" +) +MD5="2407944d8054f00a17cf922d7bdf58b6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.dya.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.dya.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..e681b47b56eff --- /dev/null +++ b/recipes/bioconductor-mesh.dya.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Dya.eg.db diff --git a/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml new file mode 100644 index 0000000000000..124dfdbc9e380 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.55989.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.55989.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89c5cff5ae86667b6a515f1314e28ce5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh new file mode 100644 index 0000000000000..e01046dd0a460 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.55989.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.55989.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.55989.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.55989.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.55989.eg.db/bioconductor-mesh.eco.55989.eg.db_1.11.0_src_all.tar.gz" +) +MD5="89c5cff5ae86667b6a515f1314e28ce5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.55989.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.55989.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..d44ecf45e5cb2 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.55989.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.55989.eg.db diff --git a/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml new file mode 100644 index 0000000000000..57426719a6ff0 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.ed1a.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.ED1a.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 48e7ade0744cc673ddddadbe55967ad3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh new file mode 100644 index 0000000000000..b7ed21ec8fa08 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.ed1a.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.ED1a.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.ed1a.eg.db/bioconductor-mesh.eco.ed1a.eg.db_1.11.0_src_all.tar.gz" +) +MD5="48e7ade0744cc673ddddadbe55967ad3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.ed1a.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.ed1a.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..23332fee8c7bb --- /dev/null +++ b/recipes/bioconductor-mesh.eco.ed1a.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.ED1a.eg.db diff --git a/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml new file mode 100644 index 0000000000000..cf53d4024a3a0 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.iai39.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.IAI39.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ba2f514da060d4315d09567829a78d3a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh new file mode 100644 index 0000000000000..cf1828f8f85b8 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.iai39.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.IAI39.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.iai39.eg.db/bioconductor-mesh.eco.iai39.eg.db_1.11.0_src_all.tar.gz" +) +MD5="ba2f514da060d4315d09567829a78d3a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.iai39.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.iai39.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..c9bc3667456e0 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.iai39.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.IAI39.eg.db diff --git a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml new file mode 100644 index 0000000000000..ddbcd76c3c021 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.K12.MG1655.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d0f3c397bbe677efa0e4cfebc6e6eead +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh new file mode 100644 index 0000000000000..748c583d55531 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.K12.MG1655.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.k12.mg1655.eg.db/bioconductor-mesh.eco.k12.mg1655.eg.db_1.11.0_src_all.tar.gz" +) +MD5="d0f3c397bbe677efa0e4cfebc6e6eead" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..d84bcfe3f37b0 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.k12.mg1655.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.K12.MG1655.eg.db diff --git a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml new file mode 100644 index 0000000000000..fc72de194e578 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.O157.H7.Sakai.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 80d4f81563edbdf16da37e6e67cd2e04 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh new file mode 100644 index 0000000000000..2c491a1886a71 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.O157.H7.Sakai.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.o157.h7.sakai.eg.db/bioconductor-mesh.eco.o157.h7.sakai.eg.db_1.11.0_src_all.tar.gz" +) +MD5="80d4f81563edbdf16da37e6e67cd2e04" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ca7dccd94edb8 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.o157.h7.sakai.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.O157.H7.Sakai.eg.db diff --git a/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml b/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml new file mode 100644 index 0000000000000..9e4336987a168 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.umn026.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eco.UMN026.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 557a999dfe0e422cf01efd2ba9735450 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh b/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh new file mode 100644 index 0000000000000..62bf265f0ca51 --- /dev/null +++ b/recipes/bioconductor-mesh.eco.umn026.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eco.UMN026.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eco.umn026.eg.db/bioconductor-mesh.eco.umn026.eg.db_1.11.0_src_all.tar.gz" +) +MD5="557a999dfe0e422cf01efd2ba9735450" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eco.umn026.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eco.umn026.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ec548978f643a --- /dev/null +++ b/recipes/bioconductor-mesh.eco.umn026.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eco.UMN026.eg.db diff --git a/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml b/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml new file mode 100644 index 0000000000000..844349aabc7d6 --- /dev/null +++ b/recipes/bioconductor-mesh.eqc.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Eqc.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 16c88a92bc3f91d93cffed92f420f92f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh b/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh new file mode 100644 index 0000000000000..50a610c1890fc --- /dev/null +++ b/recipes/bioconductor-mesh.eqc.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Eqc.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Eqc.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Eqc.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.eqc.eg.db/bioconductor-mesh.eqc.eg.db_1.11.0_src_all.tar.gz" +) +MD5="16c88a92bc3f91d93cffed92f420f92f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.eqc.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.eqc.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..305d61981b790 --- /dev/null +++ b/recipes/bioconductor-mesh.eqc.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Eqc.eg.db diff --git a/recipes/bioconductor-mesh.gga.eg.db/meta.yaml b/recipes/bioconductor-mesh.gga.eg.db/meta.yaml new file mode 100644 index 0000000000000..46c0d2973577f --- /dev/null +++ b/recipes/bioconductor-mesh.gga.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Gga.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7fc1e66d6029ba8b6c615265b3ce9de0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.gga.eg.db/post-link.sh b/recipes/bioconductor-mesh.gga.eg.db/post-link.sh new file mode 100644 index 0000000000000..72a6936bc1aef --- /dev/null +++ b/recipes/bioconductor-mesh.gga.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Gga.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Gga.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Gga.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.gga.eg.db/bioconductor-mesh.gga.eg.db_1.11.0_src_all.tar.gz" +) +MD5="7fc1e66d6029ba8b6c615265b3ce9de0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.gga.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.gga.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..166bfb4ca82f2 --- /dev/null +++ b/recipes/bioconductor-mesh.gga.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Gga.eg.db diff --git a/recipes/bioconductor-mesh.gma.eg.db/meta.yaml b/recipes/bioconductor-mesh.gma.eg.db/meta.yaml new file mode 100644 index 0000000000000..8e0443ec705fb --- /dev/null +++ b/recipes/bioconductor-mesh.gma.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Gma.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4ea83c4f59c36cd57129650b97902776 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.gma.eg.db/post-link.sh b/recipes/bioconductor-mesh.gma.eg.db/post-link.sh new file mode 100644 index 0000000000000..58b07098ba39f --- /dev/null +++ b/recipes/bioconductor-mesh.gma.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Gma.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Gma.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Gma.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.gma.eg.db/bioconductor-mesh.gma.eg.db_1.11.0_src_all.tar.gz" +) +MD5="4ea83c4f59c36cd57129650b97902776" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.gma.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.gma.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..afbb6ac29da9f --- /dev/null +++ b/recipes/bioconductor-mesh.gma.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Gma.eg.db diff --git a/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml b/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml new file mode 100644 index 0000000000000..77e7f4eddcebd --- /dev/null +++ b/recipes/bioconductor-mesh.hsa.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Hsa.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ca0da5b6e8cf66b6b796fe64cf7a1a66 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh b/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh new file mode 100644 index 0000000000000..b792187370f0a --- /dev/null +++ b/recipes/bioconductor-mesh.hsa.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Hsa.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Hsa.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Hsa.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.hsa.eg.db/bioconductor-mesh.hsa.eg.db_1.11.0_src_all.tar.gz" +) +MD5="ca0da5b6e8cf66b6b796fe64cf7a1a66" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.hsa.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.hsa.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..16ac06f2a9b4c --- /dev/null +++ b/recipes/bioconductor-mesh.hsa.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Hsa.eg.db diff --git a/recipes/bioconductor-mesh.laf.eg.db/meta.yaml b/recipes/bioconductor-mesh.laf.eg.db/meta.yaml new file mode 100644 index 0000000000000..71356d030401e --- /dev/null +++ b/recipes/bioconductor-mesh.laf.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Laf.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9fd4415f7d81a0158923d6e9bb582dd8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.laf.eg.db/post-link.sh b/recipes/bioconductor-mesh.laf.eg.db/post-link.sh new file mode 100644 index 0000000000000..571ef095c7502 --- /dev/null +++ b/recipes/bioconductor-mesh.laf.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Laf.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Laf.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Laf.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.laf.eg.db/bioconductor-mesh.laf.eg.db_1.11.0_src_all.tar.gz" +) +MD5="9fd4415f7d81a0158923d6e9bb582dd8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.laf.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.laf.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..84412286ffd4f --- /dev/null +++ b/recipes/bioconductor-mesh.laf.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Laf.eg.db diff --git a/recipes/bioconductor-mesh.lma.eg.db/meta.yaml b/recipes/bioconductor-mesh.lma.eg.db/meta.yaml new file mode 100644 index 0000000000000..3607c5b791c71 --- /dev/null +++ b/recipes/bioconductor-mesh.lma.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Lma.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 196be5e739ac7537272bc5511196cd4b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.lma.eg.db/post-link.sh b/recipes/bioconductor-mesh.lma.eg.db/post-link.sh new file mode 100644 index 0000000000000..d0410e9ce4c99 --- /dev/null +++ b/recipes/bioconductor-mesh.lma.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Lma.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Lma.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Lma.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.lma.eg.db/bioconductor-mesh.lma.eg.db_1.11.0_src_all.tar.gz" +) +MD5="196be5e739ac7537272bc5511196cd4b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.lma.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.lma.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..8c6380af669f0 --- /dev/null +++ b/recipes/bioconductor-mesh.lma.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Lma.eg.db diff --git a/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml b/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml new file mode 100644 index 0000000000000..521acb26025e7 --- /dev/null +++ b/recipes/bioconductor-mesh.mdo.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mdo.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ac78f04e3d382e622e8f711b304299d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh b/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh new file mode 100644 index 0000000000000..29f65c5c8529e --- /dev/null +++ b/recipes/bioconductor-mesh.mdo.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mdo.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mdo.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mdo.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mdo.eg.db/bioconductor-mesh.mdo.eg.db_1.11.0_src_all.tar.gz" +) +MD5="ac78f04e3d382e622e8f711b304299d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mdo.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mdo.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ec8a4a118aa05 --- /dev/null +++ b/recipes/bioconductor-mesh.mdo.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mdo.eg.db diff --git a/recipes/bioconductor-mesh.mes.eg.db/meta.yaml b/recipes/bioconductor-mesh.mes.eg.db/meta.yaml new file mode 100644 index 0000000000000..5f8611e8af930 --- /dev/null +++ b/recipes/bioconductor-mesh.mes.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mes.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 79ddb75c5d270505271411f89ac3a5d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mes.eg.db/post-link.sh b/recipes/bioconductor-mesh.mes.eg.db/post-link.sh new file mode 100644 index 0000000000000..ab4440cea524f --- /dev/null +++ b/recipes/bioconductor-mesh.mes.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mes.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mes.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mes.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mes.eg.db/bioconductor-mesh.mes.eg.db_1.11.0_src_all.tar.gz" +) +MD5="79ddb75c5d270505271411f89ac3a5d2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mes.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mes.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..aef234cbb4f59 --- /dev/null +++ b/recipes/bioconductor-mesh.mes.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mes.eg.db diff --git a/recipes/bioconductor-mesh.mga.eg.db/meta.yaml b/recipes/bioconductor-mesh.mga.eg.db/meta.yaml new file mode 100644 index 0000000000000..1acb7a9a9db26 --- /dev/null +++ b/recipes/bioconductor-mesh.mga.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mga.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8052f93acc2adbec71a2759e41302b73 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mga.eg.db/post-link.sh b/recipes/bioconductor-mesh.mga.eg.db/post-link.sh new file mode 100644 index 0000000000000..3b37019c1a3be --- /dev/null +++ b/recipes/bioconductor-mesh.mga.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mga.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mga.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mga.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mga.eg.db/bioconductor-mesh.mga.eg.db_1.11.0_src_all.tar.gz" +) +MD5="8052f93acc2adbec71a2759e41302b73" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mga.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mga.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..20c11a13087b5 --- /dev/null +++ b/recipes/bioconductor-mesh.mga.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mga.eg.db diff --git a/recipes/bioconductor-mesh.miy.eg.db/meta.yaml b/recipes/bioconductor-mesh.miy.eg.db/meta.yaml new file mode 100644 index 0000000000000..09245ee79d01d --- /dev/null +++ b/recipes/bioconductor-mesh.miy.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Miy.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0940dec688bc7d05a45d4167affb05cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.miy.eg.db/post-link.sh b/recipes/bioconductor-mesh.miy.eg.db/post-link.sh new file mode 100644 index 0000000000000..fefc147e71087 --- /dev/null +++ b/recipes/bioconductor-mesh.miy.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Miy.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Miy.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Miy.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.miy.eg.db/bioconductor-mesh.miy.eg.db_1.11.0_src_all.tar.gz" +) +MD5="0940dec688bc7d05a45d4167affb05cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.miy.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.miy.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..71e2f14f8fdad --- /dev/null +++ b/recipes/bioconductor-mesh.miy.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Miy.eg.db diff --git a/recipes/bioconductor-mesh.mml.eg.db/meta.yaml b/recipes/bioconductor-mesh.mml.eg.db/meta.yaml new file mode 100644 index 0000000000000..66ac8e55f5f3d --- /dev/null +++ b/recipes/bioconductor-mesh.mml.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mml.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ace49003b51dac2903cd6d52984a69f7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mml.eg.db/post-link.sh b/recipes/bioconductor-mesh.mml.eg.db/post-link.sh new file mode 100644 index 0000000000000..940ede69a52c7 --- /dev/null +++ b/recipes/bioconductor-mesh.mml.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mml.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mml.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mml.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mml.eg.db/bioconductor-mesh.mml.eg.db_1.11.0_src_all.tar.gz" +) +MD5="ace49003b51dac2903cd6d52984a69f7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mml.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mml.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..7362c6474c654 --- /dev/null +++ b/recipes/bioconductor-mesh.mml.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mml.eg.db diff --git a/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml b/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml new file mode 100644 index 0000000000000..80cd8cd7bf874 --- /dev/null +++ b/recipes/bioconductor-mesh.mmu.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mmu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: da945297c55815c252c935f913564dd9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh b/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh new file mode 100644 index 0000000000000..290e8b73b4b05 --- /dev/null +++ b/recipes/bioconductor-mesh.mmu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mmu.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mmu.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mmu.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mmu.eg.db/bioconductor-mesh.mmu.eg.db_1.11.0_src_all.tar.gz" +) +MD5="da945297c55815c252c935f913564dd9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mmu.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mmu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..48198b46b85b2 --- /dev/null +++ b/recipes/bioconductor-mesh.mmu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mmu.eg.db diff --git a/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml b/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml new file mode 100644 index 0000000000000..836882486dc0c --- /dev/null +++ b/recipes/bioconductor-mesh.mtr.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Mtr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c255db3b10a80bab983401965723419e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh b/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh new file mode 100644 index 0000000000000..31805e0c1ae72 --- /dev/null +++ b/recipes/bioconductor-mesh.mtr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Mtr.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Mtr.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Mtr.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.mtr.eg.db/bioconductor-mesh.mtr.eg.db_1.11.0_src_all.tar.gz" +) +MD5="c255db3b10a80bab983401965723419e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.mtr.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.mtr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..82c6e4d1a85ad --- /dev/null +++ b/recipes/bioconductor-mesh.mtr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Mtr.eg.db diff --git a/recipes/bioconductor-mesh.nle.eg.db/meta.yaml b/recipes/bioconductor-mesh.nle.eg.db/meta.yaml new file mode 100644 index 0000000000000..50ed29686ede2 --- /dev/null +++ b/recipes/bioconductor-mesh.nle.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Nle.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 27b9882d18e1a078f65a58fba142dbcb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.nle.eg.db/post-link.sh b/recipes/bioconductor-mesh.nle.eg.db/post-link.sh new file mode 100644 index 0000000000000..b32c327324c98 --- /dev/null +++ b/recipes/bioconductor-mesh.nle.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Nle.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Nle.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Nle.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.nle.eg.db/bioconductor-mesh.nle.eg.db_1.11.0_src_all.tar.gz" +) +MD5="27b9882d18e1a078f65a58fba142dbcb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.nle.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.nle.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1fa9e89e6a6b2 --- /dev/null +++ b/recipes/bioconductor-mesh.nle.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Nle.eg.db diff --git a/recipes/bioconductor-mesh.oan.eg.db/meta.yaml b/recipes/bioconductor-mesh.oan.eg.db/meta.yaml new file mode 100644 index 0000000000000..79c208b902a01 --- /dev/null +++ b/recipes/bioconductor-mesh.oan.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Oan.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 18dbb385493d99c5b1b61e297afca5bc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.oan.eg.db/post-link.sh b/recipes/bioconductor-mesh.oan.eg.db/post-link.sh new file mode 100644 index 0000000000000..93745716a0a40 --- /dev/null +++ b/recipes/bioconductor-mesh.oan.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Oan.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Oan.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Oan.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.oan.eg.db/bioconductor-mesh.oan.eg.db_1.11.0_src_all.tar.gz" +) +MD5="18dbb385493d99c5b1b61e297afca5bc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.oan.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.oan.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..8531991b7bb28 --- /dev/null +++ b/recipes/bioconductor-mesh.oan.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Oan.eg.db diff --git a/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml b/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml new file mode 100644 index 0000000000000..0c00407b09bfa --- /dev/null +++ b/recipes/bioconductor-mesh.ocu.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ocu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c01c62fe2154b4bde7f261f6d549206 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh b/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh new file mode 100644 index 0000000000000..93ceb0f56a9b1 --- /dev/null +++ b/recipes/bioconductor-mesh.ocu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ocu.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ocu.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ocu.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ocu.eg.db/bioconductor-mesh.ocu.eg.db_1.11.0_src_all.tar.gz" +) +MD5="3c01c62fe2154b4bde7f261f6d549206" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ocu.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ocu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1c5651e08d98d --- /dev/null +++ b/recipes/bioconductor-mesh.ocu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ocu.eg.db diff --git a/recipes/bioconductor-mesh.oni.eg.db/meta.yaml b/recipes/bioconductor-mesh.oni.eg.db/meta.yaml new file mode 100644 index 0000000000000..2457b38b61b06 --- /dev/null +++ b/recipes/bioconductor-mesh.oni.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Oni.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4ffafa6e1d30aef16245f01cffaea20a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.oni.eg.db/post-link.sh b/recipes/bioconductor-mesh.oni.eg.db/post-link.sh new file mode 100644 index 0000000000000..550d51b2c0f9d --- /dev/null +++ b/recipes/bioconductor-mesh.oni.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Oni.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Oni.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Oni.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.oni.eg.db/bioconductor-mesh.oni.eg.db_1.11.0_src_all.tar.gz" +) +MD5="4ffafa6e1d30aef16245f01cffaea20a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.oni.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.oni.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..5cb159f6dd348 --- /dev/null +++ b/recipes/bioconductor-mesh.oni.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Oni.eg.db diff --git a/recipes/bioconductor-mesh.osa.eg.db/meta.yaml b/recipes/bioconductor-mesh.osa.eg.db/meta.yaml new file mode 100644 index 0000000000000..d954655f64d7a --- /dev/null +++ b/recipes/bioconductor-mesh.osa.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Osa.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89027273281c37a56cb0c53123c3ac86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.osa.eg.db/post-link.sh b/recipes/bioconductor-mesh.osa.eg.db/post-link.sh new file mode 100644 index 0000000000000..cd83fb298e6f8 --- /dev/null +++ b/recipes/bioconductor-mesh.osa.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Osa.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Osa.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Osa.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.osa.eg.db/bioconductor-mesh.osa.eg.db_1.11.0_src_all.tar.gz" +) +MD5="89027273281c37a56cb0c53123c3ac86" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.osa.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.osa.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..72e64783881d7 --- /dev/null +++ b/recipes/bioconductor-mesh.osa.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Osa.eg.db diff --git a/recipes/bioconductor-mesh.pab.eg.db/meta.yaml b/recipes/bioconductor-mesh.pab.eg.db/meta.yaml new file mode 100644 index 0000000000000..04a457e825716 --- /dev/null +++ b/recipes/bioconductor-mesh.pab.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Pab.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b156e5aab93facda91f391d174968450 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.pab.eg.db/post-link.sh b/recipes/bioconductor-mesh.pab.eg.db/post-link.sh new file mode 100644 index 0000000000000..1c810c130327d --- /dev/null +++ b/recipes/bioconductor-mesh.pab.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Pab.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pab.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pab.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pab.eg.db/bioconductor-mesh.pab.eg.db_1.11.0_src_all.tar.gz" +) +MD5="b156e5aab93facda91f391d174968450" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.pab.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.pab.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..af4358807227b --- /dev/null +++ b/recipes/bioconductor-mesh.pab.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Pab.eg.db diff --git a/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml b/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml new file mode 100644 index 0000000000000..ed5b2397e1aff --- /dev/null +++ b/recipes/bioconductor-mesh.pae.pao1.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Pae.PAO1.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 281b4562470d51760d4e0d039229a09d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh b/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh new file mode 100644 index 0000000000000..35d3c84cf5eaa --- /dev/null +++ b/recipes/bioconductor-mesh.pae.pao1.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pae.PAO1.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pae.pao1.eg.db/bioconductor-mesh.pae.pao1.eg.db_1.11.0_src_all.tar.gz" +) +MD5="281b4562470d51760d4e0d039229a09d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.pae.pao1.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.pae.pao1.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..86917093b5a24 --- /dev/null +++ b/recipes/bioconductor-mesh.pae.pao1.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Pae.PAO1.eg.db diff --git a/recipes/bioconductor-mesh.pcr.db/meta.yaml b/recipes/bioconductor-mesh.pcr.db/meta.yaml new file mode 100644 index 0000000000000..828e51e886b86 --- /dev/null +++ b/recipes/bioconductor-mesh.pcr.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.PCR.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9783b11c1f930c575a7a1cd62050484d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of PCR (parent-child relationship) in MeSH.' + diff --git a/recipes/bioconductor-mesh.pcr.db/post-link.sh b/recipes/bioconductor-mesh.pcr.db/post-link.sh new file mode 100644 index 0000000000000..951a099cf1741 --- /dev/null +++ b/recipes/bioconductor-mesh.pcr.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.PCR.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.PCR.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.PCR.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pcr.db/bioconductor-mesh.pcr.db_1.11.0_src_all.tar.gz" +) +MD5="9783b11c1f930c575a7a1cd62050484d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.pcr.db/pre-unlink.sh b/recipes/bioconductor-mesh.pcr.db/pre-unlink.sh new file mode 100644 index 0000000000000..59ed34388acc7 --- /dev/null +++ b/recipes/bioconductor-mesh.pcr.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.PCR.db diff --git a/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml b/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml new file mode 100644 index 0000000000000..3bf7c5d933fa6 --- /dev/null +++ b/recipes/bioconductor-mesh.pfa.3d7.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Pfa.3D7.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 749aa5c6f52653c81258acb10b4c1e7a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh b/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh new file mode 100644 index 0000000000000..09a8d29b59b87 --- /dev/null +++ b/recipes/bioconductor-mesh.pfa.3d7.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pfa.3D7.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pfa.3d7.eg.db/bioconductor-mesh.pfa.3d7.eg.db_1.11.0_src_all.tar.gz" +) +MD5="749aa5c6f52653c81258acb10b4c1e7a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.pfa.3d7.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.pfa.3d7.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..23b1071e8922e --- /dev/null +++ b/recipes/bioconductor-mesh.pfa.3d7.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Pfa.3D7.eg.db diff --git a/recipes/bioconductor-mesh.pto.eg.db/meta.yaml b/recipes/bioconductor-mesh.pto.eg.db/meta.yaml new file mode 100644 index 0000000000000..588c15e3cf550 --- /dev/null +++ b/recipes/bioconductor-mesh.pto.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Pto.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0448b207fbf726ff6f62ef739864aa2d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.pto.eg.db/post-link.sh b/recipes/bioconductor-mesh.pto.eg.db/post-link.sh new file mode 100644 index 0000000000000..dab4a4c03fd32 --- /dev/null +++ b/recipes/bioconductor-mesh.pto.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Pto.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Pto.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Pto.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.pto.eg.db/bioconductor-mesh.pto.eg.db_1.11.0_src_all.tar.gz" +) +MD5="0448b207fbf726ff6f62ef739864aa2d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.pto.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.pto.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ffad2a80cd0e7 --- /dev/null +++ b/recipes/bioconductor-mesh.pto.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Pto.eg.db diff --git a/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml b/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml new file mode 100644 index 0000000000000..fd18a5ad6e23f --- /dev/null +++ b/recipes/bioconductor-mesh.ptr.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ptr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b497c8bfc04f1a2101c498100dbd9f0f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh b/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh new file mode 100644 index 0000000000000..2fe9c70039395 --- /dev/null +++ b/recipes/bioconductor-mesh.ptr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ptr.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ptr.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ptr.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ptr.eg.db/bioconductor-mesh.ptr.eg.db_1.11.0_src_all.tar.gz" +) +MD5="b497c8bfc04f1a2101c498100dbd9f0f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ptr.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ptr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..a269b315c4689 --- /dev/null +++ b/recipes/bioconductor-mesh.ptr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ptr.eg.db diff --git a/recipes/bioconductor-mesh.rno.eg.db/meta.yaml b/recipes/bioconductor-mesh.rno.eg.db/meta.yaml new file mode 100644 index 0000000000000..0934cfdf3c851 --- /dev/null +++ b/recipes/bioconductor-mesh.rno.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Rno.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b821144643cc233cca92148617566b31 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.rno.eg.db/post-link.sh b/recipes/bioconductor-mesh.rno.eg.db/post-link.sh new file mode 100644 index 0000000000000..9c2940f3eb214 --- /dev/null +++ b/recipes/bioconductor-mesh.rno.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Rno.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Rno.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Rno.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.rno.eg.db/bioconductor-mesh.rno.eg.db_1.11.0_src_all.tar.gz" +) +MD5="b821144643cc233cca92148617566b31" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.rno.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.rno.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ab4c47cdb5303 --- /dev/null +++ b/recipes/bioconductor-mesh.rno.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Rno.eg.db diff --git a/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml b/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml new file mode 100644 index 0000000000000..c9abead0aadab --- /dev/null +++ b/recipes/bioconductor-mesh.sce.s288c.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Sce.S288c.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4db271c6a1df2c4e438ca4405f4bf8ce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh b/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh new file mode 100644 index 0000000000000..dbd809204f616 --- /dev/null +++ b/recipes/bioconductor-mesh.sce.s288c.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sce.S288c.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sce.s288c.eg.db/bioconductor-mesh.sce.s288c.eg.db_1.11.0_src_all.tar.gz" +) +MD5="4db271c6a1df2c4e438ca4405f4bf8ce" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.sce.s288c.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.sce.s288c.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..3f516c1006750 --- /dev/null +++ b/recipes/bioconductor-mesh.sce.s288c.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Sce.S288c.eg.db diff --git a/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml b/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml new file mode 100644 index 0000000000000..a2b8bea9432d3 --- /dev/null +++ b/recipes/bioconductor-mesh.sco.a32.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Sco.A32.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a89a8bf1179059f69eeb32ba0dfff796 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh b/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh new file mode 100644 index 0000000000000..d90b9b675522c --- /dev/null +++ b/recipes/bioconductor-mesh.sco.a32.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Sco.A32.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sco.A32.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sco.A32.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sco.a32.eg.db/bioconductor-mesh.sco.a32.eg.db_1.11.0_src_all.tar.gz" +) +MD5="a89a8bf1179059f69eeb32ba0dfff796" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.sco.a32.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.sco.a32.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..c8fd2f1de4c70 --- /dev/null +++ b/recipes/bioconductor-mesh.sco.a32.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Sco.A32.eg.db diff --git a/recipes/bioconductor-mesh.sil.eg.db/meta.yaml b/recipes/bioconductor-mesh.sil.eg.db/meta.yaml new file mode 100644 index 0000000000000..0051845e602a2 --- /dev/null +++ b/recipes/bioconductor-mesh.sil.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Sil.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2fd601ed25adfdd2412d9c723a2f72d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.sil.eg.db/post-link.sh b/recipes/bioconductor-mesh.sil.eg.db/post-link.sh new file mode 100644 index 0000000000000..d514d9a5a8ba9 --- /dev/null +++ b/recipes/bioconductor-mesh.sil.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Sil.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Sil.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Sil.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.sil.eg.db/bioconductor-mesh.sil.eg.db_1.11.0_src_all.tar.gz" +) +MD5="2fd601ed25adfdd2412d9c723a2f72d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.sil.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.sil.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..d513e56cf4251 --- /dev/null +++ b/recipes/bioconductor-mesh.sil.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Sil.eg.db diff --git a/recipes/bioconductor-mesh.spu.eg.db/meta.yaml b/recipes/bioconductor-mesh.spu.eg.db/meta.yaml new file mode 100644 index 0000000000000..fa8b0965384d2 --- /dev/null +++ b/recipes/bioconductor-mesh.spu.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Spu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f0c6530bbd904a55c1a34fb61ccfd61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.spu.eg.db/post-link.sh b/recipes/bioconductor-mesh.spu.eg.db/post-link.sh new file mode 100644 index 0000000000000..92f7b891cecc8 --- /dev/null +++ b/recipes/bioconductor-mesh.spu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Spu.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Spu.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Spu.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.spu.eg.db/bioconductor-mesh.spu.eg.db_1.11.0_src_all.tar.gz" +) +MD5="6f0c6530bbd904a55c1a34fb61ccfd61" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.spu.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.spu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..840e5f0698b67 --- /dev/null +++ b/recipes/bioconductor-mesh.spu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Spu.eg.db diff --git a/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml b/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml new file mode 100644 index 0000000000000..42413888a5fbd --- /dev/null +++ b/recipes/bioconductor-mesh.ssc.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Ssc.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8641af272a45c721a9cbd9c229776de5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh b/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh new file mode 100644 index 0000000000000..ab2e93c4ab684 --- /dev/null +++ b/recipes/bioconductor-mesh.ssc.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Ssc.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Ssc.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Ssc.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.ssc.eg.db/bioconductor-mesh.ssc.eg.db_1.11.0_src_all.tar.gz" +) +MD5="8641af272a45c721a9cbd9c229776de5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.ssc.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.ssc.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..3cdd7dc7fd99f --- /dev/null +++ b/recipes/bioconductor-mesh.ssc.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Ssc.eg.db diff --git a/recipes/bioconductor-mesh.syn.eg.db/meta.yaml b/recipes/bioconductor-mesh.syn.eg.db/meta.yaml new file mode 100644 index 0000000000000..f85e557d1b141 --- /dev/null +++ b/recipes/bioconductor-mesh.syn.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Syn.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec4df33cef0022929018947d66c0e024 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.syn.eg.db/post-link.sh b/recipes/bioconductor-mesh.syn.eg.db/post-link.sh new file mode 100644 index 0000000000000..14f5b8218368e --- /dev/null +++ b/recipes/bioconductor-mesh.syn.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Syn.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Syn.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Syn.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.syn.eg.db/bioconductor-mesh.syn.eg.db_1.11.0_src_all.tar.gz" +) +MD5="ec4df33cef0022929018947d66c0e024" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.syn.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.syn.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..5dda672dca12b --- /dev/null +++ b/recipes/bioconductor-mesh.syn.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Syn.eg.db diff --git a/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml b/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml new file mode 100644 index 0000000000000..3d2c4a009b3b8 --- /dev/null +++ b/recipes/bioconductor-mesh.tbr.9274.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Tbr.9274.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9465b3f70608a6f5363ede1c075aa1f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh b/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh new file mode 100644 index 0000000000000..534f6685c803f --- /dev/null +++ b/recipes/bioconductor-mesh.tbr.9274.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tbr.9274.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tbr.9274.eg.db/bioconductor-mesh.tbr.9274.eg.db_1.11.0_src_all.tar.gz" +) +MD5="9465b3f70608a6f5363ede1c075aa1f1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.tbr.9274.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.tbr.9274.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..bad2f77d37278 --- /dev/null +++ b/recipes/bioconductor-mesh.tbr.9274.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Tbr.9274.eg.db diff --git a/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml b/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml new file mode 100644 index 0000000000000..3f9ab81b476e6 --- /dev/null +++ b/recipes/bioconductor-mesh.tgo.me49.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Tgo.ME49.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 437d5be6e97f4b2cc2cee1972e3be115 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh b/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh new file mode 100644 index 0000000000000..7b0de41fc077e --- /dev/null +++ b/recipes/bioconductor-mesh.tgo.me49.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tgo.ME49.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tgo.me49.eg.db/bioconductor-mesh.tgo.me49.eg.db_1.11.0_src_all.tar.gz" +) +MD5="437d5be6e97f4b2cc2cee1972e3be115" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.tgo.me49.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.tgo.me49.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b708a46d2fcb3 --- /dev/null +++ b/recipes/bioconductor-mesh.tgo.me49.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Tgo.ME49.eg.db diff --git a/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml b/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml new file mode 100644 index 0000000000000..7fd95b34ad556 --- /dev/null +++ b/recipes/bioconductor-mesh.tgu.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Tgu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b75f668b61550b675aa3fdd3d556a935 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh b/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh new file mode 100644 index 0000000000000..b0549e1be73f3 --- /dev/null +++ b/recipes/bioconductor-mesh.tgu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Tgu.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Tgu.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Tgu.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.tgu.eg.db/bioconductor-mesh.tgu.eg.db_1.11.0_src_all.tar.gz" +) +MD5="b75f668b61550b675aa3fdd3d556a935" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.tgu.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.tgu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..ba09835961ff2 --- /dev/null +++ b/recipes/bioconductor-mesh.tgu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Tgu.eg.db diff --git a/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml b/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml new file mode 100644 index 0000000000000..a0d534a17ecd2 --- /dev/null +++ b/recipes/bioconductor-mesh.vvi.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Vvi.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fdf974109135d9569d7d2c280f71716c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh b/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh new file mode 100644 index 0000000000000..847ae005673a3 --- /dev/null +++ b/recipes/bioconductor-mesh.vvi.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Vvi.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Vvi.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Vvi.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.vvi.eg.db/bioconductor-mesh.vvi.eg.db_1.11.0_src_all.tar.gz" +) +MD5="fdf974109135d9569d7d2c280f71716c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.vvi.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.vvi.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..0f7f292b24e11 --- /dev/null +++ b/recipes/bioconductor-mesh.vvi.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Vvi.eg.db diff --git a/recipes/bioconductor-mesh.xla.eg.db/meta.yaml b/recipes/bioconductor-mesh.xla.eg.db/meta.yaml new file mode 100644 index 0000000000000..b24e121242d1e --- /dev/null +++ b/recipes/bioconductor-mesh.xla.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Xla.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 624c4086857259bb0f77e588a9ee4eb3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.xla.eg.db/post-link.sh b/recipes/bioconductor-mesh.xla.eg.db/post-link.sh new file mode 100644 index 0000000000000..82bc34b741bd4 --- /dev/null +++ b/recipes/bioconductor-mesh.xla.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Xla.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Xla.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Xla.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.xla.eg.db/bioconductor-mesh.xla.eg.db_1.11.0_src_all.tar.gz" +) +MD5="624c4086857259bb0f77e588a9ee4eb3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.xla.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.xla.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..b5412c0809d90 --- /dev/null +++ b/recipes/bioconductor-mesh.xla.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Xla.eg.db diff --git a/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml b/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml new file mode 100644 index 0000000000000..c326785ccaa42 --- /dev/null +++ b/recipes/bioconductor-mesh.xtr.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Xtr.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b49f5370146697faef0d8ae965f7e29 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh b/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh new file mode 100644 index 0000000000000..f58171f1e1e36 --- /dev/null +++ b/recipes/bioconductor-mesh.xtr.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Xtr.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Xtr.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Xtr.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.xtr.eg.db/bioconductor-mesh.xtr.eg.db_1.11.0_src_all.tar.gz" +) +MD5="1b49f5370146697faef0d8ae965f7e29" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.xtr.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.xtr.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..d14029bb5ee22 --- /dev/null +++ b/recipes/bioconductor-mesh.xtr.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Xtr.eg.db diff --git a/recipes/bioconductor-mesh.zma.eg.db/meta.yaml b/recipes/bioconductor-mesh.zma.eg.db/meta.yaml new file mode 100644 index 0000000000000..6a5d4be8108e2 --- /dev/null +++ b/recipes/bioconductor-mesh.zma.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.11.0" %} +{% set name = "MeSH.Zma.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f15886b139eac087d5c183f8643f4c5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Entrez Gene ID to MeSH ID table.' + diff --git a/recipes/bioconductor-mesh.zma.eg.db/post-link.sh b/recipes/bioconductor-mesh.zma.eg.db/post-link.sh new file mode 100644 index 0000000000000..a4ce4cd0dc214 --- /dev/null +++ b/recipes/bioconductor-mesh.zma.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MeSH.Zma.eg.db_1.11.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MeSH.Zma.eg.db_1.11.0.tar.gz" + "https://bioarchive.galaxyproject.org/MeSH.Zma.eg.db_1.11.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mesh.zma.eg.db/bioconductor-mesh.zma.eg.db_1.11.0_src_all.tar.gz" +) +MD5="f15886b139eac087d5c183f8643f4c5d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mesh.zma.eg.db/pre-unlink.sh b/recipes/bioconductor-mesh.zma.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..886cb5551ed6b --- /dev/null +++ b/recipes/bioconductor-mesh.zma.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MeSH.Zma.eg.db diff --git a/recipes/bioconductor-meshdbi/build.sh b/recipes/bioconductor-meshdbi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-meshdbi/build.sh +++ b/recipes/bioconductor-meshdbi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meshdbi/meta.yaml b/recipes/bioconductor-meshdbi/meta.yaml index fdeb406290a93..7dfc8426142d3 100644 --- a/recipes/bioconductor-meshdbi/meta.yaml +++ b/recipes/bioconductor-meshdbi/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MeSHDbi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aa4b5dea29fe4853eaf22b592ebf27b6fc47551614aa9f095e666ca47b9523d0 + md5: 0a8007f98154bf5d6dc7399938c4c143 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-rsqlite test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package is unified implementation of MeSH.db, MeSH.AOR.db, and MeSH.PCR.db and also is interface to construct Gene-MeSH package (MeSH.XXX.eg.db). loadMeSHDbiPkg import sqlite file and generate MeSH.XXX.eg.db.' extra: identifiers: - biotools:meshdbi + parent_recipe: + name: bioconductor-meshdbi + path: recipes/bioconductor-meshdbi + version: 1.16.0 + diff --git a/recipes/bioconductor-meshes/build.sh b/recipes/bioconductor-meshes/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-meshes/build.sh +++ b/recipes/bioconductor-meshes/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meshes/meta.yaml b/recipes/bioconductor-meshes/meta.yaml index b36be7b608a67..81ec30f6b0a8d 100644 --- a/recipes/bioconductor-meshes/meta.yaml +++ b/recipes/bioconductor-meshes/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "meshes" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89c8ec6bb5917e010e0db16eaad2129931df482b3b2472dd4ffd52a55b2959c0 + md5: 82fde49d4067c7941020d0da49df8f1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, MeSH.Cel.eg.db, MeSH.Hsa.eg.db, prettydoc requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-mesh.db >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-mesh.db >=1.11.0,<1.12.0' - r-base - r-rvcheck run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-mesh.db >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-mesh.db >=1.11.0,<1.12.0' - r-base - r-rvcheck test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MeSH (Medical Subject Headings) is the NLM controlled vocabulary used to manually index articles for MEDLINE/PubMed. MeSH terms were associated by Entrez Gene ID by three methods, gendoo, gene2pubmed and RBBH. This association is fundamental for enrichment and semantic analyses. meshes supports enrichment analysis (over-representation and gene set enrichment analysis) of gene list or whole expression profile. The semantic comparisons of MeSH terms provide quantitative ways to compute similarities between genes and gene groups. meshes implemented five methods proposed by Resnik, Schlicker, Jiang, Lin and Wang respectively and supports more than 70 species.' extra: identifiers: - biotools:meshes - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-meshes + path: recipes/bioconductor-meshes + version: 1.6.1 + diff --git a/recipes/bioconductor-meshr/build.sh b/recipes/bioconductor-meshr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-meshr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-meshr/meta.yaml b/recipes/bioconductor-meshr/meta.yaml new file mode 100644 index 0000000000000..7afc0501d0ff3 --- /dev/null +++ b/recipes/bioconductor-meshr/meta.yaml @@ -0,0 +1,62 @@ +{% set version = "1.18.0" %} +{% set name = "meshr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2949ce68968d8e93325b2e4081038246 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-cummerbund >=2.24.0,<2.25.0' + - 'bioconductor-mesh.aca.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.aor.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.bsu.168.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.hsa.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.pcr.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.syn.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-fdrtool + - r-rsqlite + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-cummerbund >=2.24.0,<2.25.0' + - 'bioconductor-mesh.aca.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.aor.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.bsu.168.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.hsa.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.pcr.db >=1.11.0,<1.12.0' + - 'bioconductor-mesh.syn.eg.db >=1.11.0,<1.12.0' + - 'bioconductor-meshdbi >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-fdrtool + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of annotation maps describing the entire MeSH assembled using data from MeSH.' + diff --git a/recipes/bioconductor-messina/build.sh b/recipes/bioconductor-messina/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-messina/build.sh +++ b/recipes/bioconductor-messina/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-messina/meta.yaml b/recipes/bioconductor-messina/meta.yaml index 7ba2acc0311e5..80c4eee637924 100644 --- a/recipes/bioconductor-messina/meta.yaml +++ b/recipes/bioconductor-messina/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "messina" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 10c4fc3c43d7efe7d4338ea2a86ac2a537466449927f875c7df4ac5585bba2d6 + md5: 9e461e240fdb0e98fb3eac38288e5014 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr (>= 1.5), antiProfilesData (>= 0.99.2), Biobase (>= 2.22.0), BiocStyle requirements: host: - r-base @@ -39,9 +40,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'EPL (>= 1.0)' summary: 'Messina is a collection of algorithms for constructing optimally robust single-gene classifiers, and for identifying differential expression in the presence of outliers or unknown sample subgroups. The methods have application in identifying lead features to develop into clinical tests (both diagnostic and prognostic), and in identifying differential expression when a fraction of samples show unusual patterns of expression.' extra: identifiers: - biotools:messina + parent_recipe: + name: bioconductor-messina + path: recipes/bioconductor-messina + version: 1.16.0 + diff --git a/recipes/bioconductor-metaarray/build.sh b/recipes/bioconductor-metaarray/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metaarray/build.sh +++ b/recipes/bioconductor-metaarray/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metaarray/meta.yaml b/recipes/bioconductor-metaarray/meta.yaml index 3e5f9b33ce70f..61eeabf016060 100644 --- a/recipes/bioconductor-metaarray/meta.yaml +++ b/recipes/bioconductor-metaarray/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "metaArray" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6d17b3fe4860060594b99b873e476217e7c9f2f4e30501c9f16ca252accaaaea + md5: e6157bb8e824426a8762f4b0779f3eb8 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-mergemaid >=2.52.0,<2.54.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mergemaid >=2.54.0,<2.55.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-mergemaid >=2.52.0,<2.54.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mergemaid >=2.54.0,<2.55.0' - r-base build: - {{ compiler('c') }} @@ -32,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: '1) Data transformation for meta-analysis of microarray Data: Transformation of gene expression data to signed probability scale (MCMC/EM methods) 2) Combined differential expression on raw scale: Weighted Z-score after stabilizing mean-variance relation within platform' extra: identifiers: - biotools:metaarray - doi:10.1186/1471-2105-8-364 + parent_recipe: + name: bioconductor-metaarray + path: recipes/bioconductor-metaarray + version: 1.58.0 + diff --git a/recipes/bioconductor-metab/build.sh b/recipes/bioconductor-metab/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metab/build.sh +++ b/recipes/bioconductor-metab/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metab/meta.yaml b/recipes/bioconductor-metab/meta.yaml index b20639b56a207..12fc1700b5ff4 100644 --- a/recipes/bioconductor-metab/meta.yaml +++ b/recipes/bioconductor-metab/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Metab" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a18734efc0f37beebe0a7f64fe896630d62e8919dda375c0c92257f6297dd62a + md5: 17d57f56b906189a511c1a646ed7f6f0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-pander - r-svdialogs run: - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-pander - r-svdialogs @@ -31,9 +33,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Metab is an R package for high-throughput processing of metabolomics data analysed by the Automated Mass Spectral Deconvolution and Identification System (AMDIS) (http://chemdata.nist.gov/mass-spc/amdis/downloads/). In addition, it performs statistical hypothesis test (t-test) and analysis of variance (ANOVA). Doing so, Metab considerably speed up the data mining process in metabolomics and produces better quality results. Metab was developed using interactive features, allowing users with lack of R knowledge to appreciate its functionalities.' extra: identifiers: - biotools:metab + parent_recipe: + name: bioconductor-metab + path: recipes/bioconductor-metab + version: 1.14.0 + diff --git a/recipes/bioconductor-metabomxtr/build.sh b/recipes/bioconductor-metabomxtr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metabomxtr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metabomxtr/meta.yaml b/recipes/bioconductor-metabomxtr/meta.yaml new file mode 100644 index 0000000000000..8a01170ffca4e --- /dev/null +++ b/recipes/bioconductor-metabomxtr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.16.0" %} +{% set name = "metabomxtr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cbd341ea534e6f6667ac57fd3ef853e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xtable, reshape2 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-formula + - r-ggplot2 + - r-optimx + - r-plyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-formula + - r-ggplot2 + - r-optimx + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The functions in this package return optimized parameter estimates and log likelihoods for mixture models of truncated data with normal or lognormal distributions.' + diff --git a/recipes/bioconductor-metabosignal/build.sh b/recipes/bioconductor-metabosignal/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metabosignal/build.sh +++ b/recipes/bioconductor-metabosignal/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metabosignal/meta.yaml b/recipes/bioconductor-metabosignal/meta.yaml index 95a21acd4d4ea..4380d8a95e8c3 100644 --- a/recipes/bioconductor-metabosignal/meta.yaml +++ b/recipes/bioconductor-metabosignal/meta.yaml @@ -1,45 +1,47 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MetaboSignal" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 36a9dc2ccebcc22046a6f57f4708ad3a3e6572df8aa01c1eb0eb89e0281543fe + md5: cde3fdfabbe4271392c9c5a5b6b0827f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.101.0' - - 'bioconductor-hpar >=1.22.2,<1.24.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-mwastools >=1.4.0,<1.6.0' - - 'bioconductor-mygene >=1.16.2,<1.18.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' + - 'bioconductor-hpar >=1.24.0,<1.25.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-mwastools >=1.6.0,<1.7.0' + - 'bioconductor-mygene >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-igraph - r-rcurl run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.101.0' - - 'bioconductor-hpar >=1.22.2,<1.24.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-mwastools >=1.4.0,<1.6.0' - - 'bioconductor-mygene >=1.16.2,<1.18.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-ensdb.hsapiens.v75 >=2.99.0,<2.100.0' + - 'bioconductor-hpar >=1.24.0,<1.25.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-mwastools >=1.6.0,<1.7.0' + - 'bioconductor-mygene >=1.18.0,<1.19.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-igraph - r-rcurl @@ -47,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'MetaboSignal is an R package that allows merging, analyzing and customizing metabolic and signaling KEGG pathways. It is a network-based approach designed to explore the topological relationship between genes (signaling- or enzymatic-genes) and metabolites, representing a powerful tool to investigate the genetic landscape and regulatory networks of metabolic phenotypes.' extra: identifiers: - biotools:metabosignal + parent_recipe: + name: bioconductor-metabosignal + path: recipes/bioconductor-metabosignal + version: 1.10.0 + diff --git a/recipes/bioconductor-metacca/build.sh b/recipes/bioconductor-metacca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metacca/build.sh +++ b/recipes/bioconductor-metacca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metacca/meta.yaml b/recipes/bioconductor-metacca/meta.yaml index b4cff6184c4b5..9bbbae46c74e8 100644 --- a/recipes/bioconductor-metacca/meta.yaml +++ b/recipes/bioconductor-metacca/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "metaCCA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b68b951ccb5e5e4f0091545315c566649ac82ec4bc818a7ebe23b65de7ad64b6 + md5: 50c6cad7861b8a8c9d42e5ee6cba4a4f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'metaCCA performs multivariate analysis of a single or multiple GWAS based on univariate regression coefficients. It allows multivariate representation of both phenotype and genotype. metaCCA extends the statistical technique of canonical correlation analysis to the setting where original individual-level records are not available, and employs a covariance shrinkage algorithm to achieve robustness.' extra: identifiers: - biotools:metacca + parent_recipe: + name: bioconductor-metacca + path: recipes/bioconductor-metacca + version: 1.8.0 + diff --git a/recipes/bioconductor-metacyto/build.sh b/recipes/bioconductor-metacyto/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metacyto/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metacyto/meta.yaml b/recipes/bioconductor-metacyto/meta.yaml new file mode 100644 index 0000000000000..4a23af5e4668b --- /dev/null +++ b/recipes/bioconductor-metacyto/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.0" %} +{% set name = "MetaCyto" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d1b83e2ab5e29d72dcf77268f3f8dc26 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, dplyr +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-fastcluster + - r-ggplot2 + - r-metafor + - 'r-tidyr >=0.7' + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowsom >=1.14.0,<1.15.0' + - r-base + - r-cluster + - r-fastcluster + - r-ggplot2 + - r-metafor + - 'r-tidyr >=0.7' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides functions for preprocessing, automated gating and meta-analysis of cytometry data. It also provides functions that facilitate the collection of cytometry data from the ImmPort database.' + diff --git a/recipes/bioconductor-metagene/build.sh b/recipes/bioconductor-metagene/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metagene/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metagene/meta.yaml b/recipes/bioconductor-metagene/meta.yaml new file mode 100644 index 0000000000000..13a33b99f14d6 --- /dev/null +++ b/recipes/bioconductor-metagene/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "2.14.0" %} +{% set name = "metagene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5a33016df96518252fa9483efbea65f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, similaRpeak, RUnit, knitr, BiocStyle, rmarkdown, similaRpeak +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-dbchip >=1.26.0,<1.27.0' + - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gplots + - r-magrittr + - r-matrixstats + - r-mustat + - r-purrr + - 'r-r6 >=2.0' + - r-stringr + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-dbchip >=1.26.0,<1.27.0' + - 'bioconductor-ensdb.hsapiens.v86 >=2.99.0,<2.100.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gplots + - r-magrittr + - r-matrixstats + - r-mustat + - r-purrr + - 'r-r6 >=2.0' + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic-2.0 | file LICENSE' + summary: 'This package produces metagene plots to compare the behavior of DNA-interacting proteins at selected groups of genes/features. Bam files are used to increase the resolution. Multiple combination of group of bam files and/or group of genomic regions can be compared in a single analysis. Bootstraping analysis is used to compare the groups and locate regions with statistically different enrichment profiles.' + diff --git a/recipes/bioconductor-metagenomefeatures/build.sh b/recipes/bioconductor-metagenomefeatures/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metagenomefeatures/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metagenomefeatures/meta.yaml b/recipes/bioconductor-metagenomefeatures/meta.yaml new file mode 100644 index 0000000000000..c6336316eb7fc --- /dev/null +++ b/recipes/bioconductor-metagenomefeatures/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "2.2.0" %} +{% set name = "metagenomeFeatures" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 751c0d0ab00c437e3b87e2c068f83f39 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.11), testthat (>= 0.10.0), rmarkdown (>= 1.3), tidyverse (>= 1.2.1), devtools (>= 1.13.5), ggtree(>= 1.8.2) +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-ape >=3.5' + - r-base + - 'r-dbplyr >=1.0.0' + - 'r-dplyr >=0.7.0' + - 'r-lattice >=0.20.33' + - 'r-lazyeval >=0.1.10' + - 'r-magrittr >=1.5' + - 'r-purrr >=0.2.2' + - 'r-rsqlite >=1.0.0' + - 'r-stringr >=1.0.0' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-ape >=3.5' + - r-base + - 'r-dbplyr >=1.0.0' + - 'r-dplyr >=0.7.0' + - 'r-lattice >=0.20.33' + - 'r-lazyeval >=0.1.10' + - 'r-magrittr >=1.5' + - 'r-purrr >=0.2.2' + - 'r-rsqlite >=1.0.0' + - 'r-stringr >=1.0.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'metagenomeFeatures was developed for use in exploring the taxonomic annotations for a marker-gene metagenomic sequence dataset. The package can be used to explore the taxonomic composition of a marker-gene database or annotated sequences from a marker-gene metagenome experiment.' + diff --git a/recipes/bioconductor-metagenomeseq/build.sh b/recipes/bioconductor-metagenomeseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metagenomeseq/build.sh +++ b/recipes/bioconductor-metagenomeseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metagenomeseq/meta.yaml b/recipes/bioconductor-metagenomeseq/meta.yaml index 4b04416b81d7c..863b64c116cb3 100644 --- a/recipes/bioconductor-metagenomeseq/meta.yaml +++ b/recipes/bioconductor-metagenomeseq/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "metagenomeSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1e1e3933f47c7867b3654cd918870c86f7d411b96525bf3cb8ffb4cb7eb47ce1 + md5: 118d3d6d0a1abe00cb13245ef88c5781 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: annotate, BiocGenerics, biomformat, knitr, gss, testthat (>= 0.8), vegan, interactiveDisplay requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-foreach - r-glmnet @@ -28,8 +30,8 @@ requirements: - r-matrixstats - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-foreach - r-glmnet @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'metagenomeSeq is designed to determine features (be it Operational Taxanomic Unit (OTU), species, etc.) that are differentially abundant between two or more groups of multiple samples. metagenomeSeq is designed to address the effects of both normalization and under-sampling of microbial communities on disease association detection and the testing of feature correlations.' extra: identifiers: - biotools:metagenomeseq - doi:10.1038/nmeth.2658 + parent_recipe: + name: bioconductor-metagenomeseq + path: recipes/bioconductor-metagenomeseq + version: 1.22.0 + diff --git a/recipes/bioconductor-metagxbreast/meta.yaml b/recipes/bioconductor-metagxbreast/meta.yaml new file mode 100644 index 0000000000000..02457e3758156 --- /dev/null +++ b/recipes/bioconductor-metagxbreast/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.2.0" %} +{% set name = "MetaGxBreast" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1157831dd3b4e2b789b5833c1586b7a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, xtable +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A collection of Breast Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.' + diff --git a/recipes/bioconductor-metagxbreast/post-link.sh b/recipes/bioconductor-metagxbreast/post-link.sh new file mode 100644 index 0000000000000..819dd8ea34b6d --- /dev/null +++ b/recipes/bioconductor-metagxbreast/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MetaGxBreast_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxBreast_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxBreast_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxbreast/bioconductor-metagxbreast_1.2.0_src_all.tar.gz" +) +MD5="1157831dd3b4e2b789b5833c1586b7a6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-metagxbreast/pre-unlink.sh b/recipes/bioconductor-metagxbreast/pre-unlink.sh new file mode 100644 index 0000000000000..9b57e96f26e44 --- /dev/null +++ b/recipes/bioconductor-metagxbreast/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MetaGxBreast diff --git a/recipes/bioconductor-metagxovarian/meta.yaml b/recipes/bioconductor-metagxovarian/meta.yaml new file mode 100644 index 0000000000000..16c37921b28db --- /dev/null +++ b/recipes/bioconductor-metagxovarian/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.2.0" %} +{% set name = "MetaGxOvarian" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fc131f6eb1d2c6317560da14ff12c06d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, xtable +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A collection of Ovarian Cancer Transcriptomic Datasets that are part of the MetaGxData package compendium.' + diff --git a/recipes/bioconductor-metagxovarian/post-link.sh b/recipes/bioconductor-metagxovarian/post-link.sh new file mode 100644 index 0000000000000..0a3daf8cf07a0 --- /dev/null +++ b/recipes/bioconductor-metagxovarian/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MetaGxOvarian_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxOvarian_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxOvarian_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxovarian/bioconductor-metagxovarian_1.2.0_src_all.tar.gz" +) +MD5="fc131f6eb1d2c6317560da14ff12c06d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-metagxovarian/pre-unlink.sh b/recipes/bioconductor-metagxovarian/pre-unlink.sh new file mode 100644 index 0000000000000..c94d1174836ad --- /dev/null +++ b/recipes/bioconductor-metagxovarian/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MetaGxOvarian diff --git a/recipes/bioconductor-metagxpancreas/meta.yaml b/recipes/bioconductor-metagxpancreas/meta.yaml new file mode 100644 index 0000000000000..d929faf294d2a --- /dev/null +++ b/recipes/bioconductor-metagxpancreas/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.2.0" %} +{% set name = "MetaGxPancreas" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 974a7f5e6f82070585bdc35cc843ccea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, xtable +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - r-base + - r-lattice + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A collection of pancreatic Cancer transcriptomic datasets that are part of the MetaGxData package compendium.' + diff --git a/recipes/bioconductor-metagxpancreas/post-link.sh b/recipes/bioconductor-metagxpancreas/post-link.sh new file mode 100644 index 0000000000000..21aab26b9027a --- /dev/null +++ b/recipes/bioconductor-metagxpancreas/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MetaGxPancreas_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MetaGxPancreas_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MetaGxPancreas_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metagxpancreas/bioconductor-metagxpancreas_1.2.0_src_all.tar.gz" +) +MD5="974a7f5e6f82070585bdc35cc843ccea" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-metagxpancreas/pre-unlink.sh b/recipes/bioconductor-metagxpancreas/pre-unlink.sh new file mode 100644 index 0000000000000..338a283278523 --- /dev/null +++ b/recipes/bioconductor-metagxpancreas/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MetaGxPancreas diff --git a/recipes/bioconductor-metahdep/build.sh b/recipes/bioconductor-metahdep/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metahdep/build.sh +++ b/recipes/bioconductor-metahdep/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metahdep/meta.yaml b/recipes/bioconductor-metahdep/meta.yaml index 0ad1d65a1b9ac..24f27d92ca270 100644 --- a/recipes/bioconductor-metahdep/meta.yaml +++ b/recipes/bioconductor-metahdep/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "metahdep" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fbe74ec3a8b05e7fb6e27a329f401740e9517d860cb819dc9d551172170ab224 + md5: 1ec5c00ecd70c4a2989f0ef02ae1e868 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affyPLM requirements: host: - r-base @@ -28,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Tools for meta-analysis in the presence of hierarchical (and/or sampling) dependence, including with gene expression studies' extra: identifiers: - biotools:metahdep - doi:10.1093/bioinformatics/btp468 + parent_recipe: + name: bioconductor-metahdep + path: recipes/bioconductor-metahdep + version: 1.38.0 + diff --git a/recipes/bioconductor-metams/build.sh b/recipes/bioconductor-metams/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metams/build.sh +++ b/recipes/bioconductor-metams/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metams/meta.yaml b/recipes/bioconductor-metams/meta.yaml index 8dbd387804c81..5a6bc47935eb0 100644 --- a/recipes/bioconductor-metams/meta.yaml +++ b/recipes/bioconductor-metams/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "metaMS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d5a22f272df23f75c69da2d4cd1505772e4cfdf1a209be4f07b1e489f4cae3f0 + md5: 1a9e09b66ffd6bd52572e58e8568718c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: metaMSdata, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-matrix - r-robustbase run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-camera >=1.36.0,<1.38.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-matrix - r-robustbase @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'MS-based metabolomics data processing and compound annotation pipeline.' extra: identifiers: - biotools:metams + parent_recipe: + name: bioconductor-metams + path: recipes/bioconductor-metams + version: 1.16.0 + diff --git a/recipes/bioconductor-metamsdata/meta.yaml b/recipes/bioconductor-metamsdata/meta.yaml new file mode 100644 index 0000000000000..4734a887f56a5 --- /dev/null +++ b/recipes/bioconductor-metamsdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "metaMSdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c2755dd8852d556ae98deb6d06d355af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Example CDF data for the metaMS package' + diff --git a/recipes/bioconductor-metamsdata/post-link.sh b/recipes/bioconductor-metamsdata/post-link.sh new file mode 100644 index 0000000000000..ee1e7a247348d --- /dev/null +++ b/recipes/bioconductor-metamsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="metaMSdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/metaMSdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/metaMSdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-metamsdata/bioconductor-metamsdata_1.18.0_src_all.tar.gz" +) +MD5="c2755dd8852d556ae98deb6d06d355af" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-metamsdata/pre-unlink.sh b/recipes/bioconductor-metamsdata/pre-unlink.sh new file mode 100644 index 0000000000000..a2603058b1817 --- /dev/null +++ b/recipes/bioconductor-metamsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ metaMSdata diff --git a/recipes/bioconductor-metaneighbor/build.sh b/recipes/bioconductor-metaneighbor/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metaneighbor/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metaneighbor/meta.yaml b/recipes/bioconductor-metaneighbor/meta.yaml new file mode 100644 index 0000000000000..8ec51b14f57aa --- /dev/null +++ b/recipes/bioconductor-metaneighbor/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.2.0" %} +{% set name = "MetaNeighbor" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cdfa4ea9e41f76e1cd208d5dbcb182d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.17), rmarkdown (>= 1.6), testthat (>= 1.0.2) +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-beanplot >=1.2' + - 'r-gplots >=3.0.1' + - 'r-rcolorbrewer >=1.1' + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-beanplot >=1.2' + - 'r-gplots >=3.0.1' + - 'r-rcolorbrewer >=1.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'MetaNeighbor allows users to quantify cell type replicability across datasets using neighbor voting.' + diff --git a/recipes/bioconductor-metaseq/build.sh b/recipes/bioconductor-metaseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metaseq/build.sh +++ b/recipes/bioconductor-metaseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metaseq/meta.yaml b/recipes/bioconductor-metaseq/meta.yaml index 775b1dc8eda78..1df553df8f1f6 100644 --- a/recipes/bioconductor-metaseq/meta.yaml +++ b/recipes/bioconductor-metaseq/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "metaSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d493c972e22285478ad115544e85eeb52ae06b2955d55ca1eec014a0f2dfeb1e + md5: 524028c02437bc7f07237cf2a83f727f build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-noiseq >=2.24.0,<2.26.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' - r-base - r-rcpp - r-snow run: - - 'bioconductor-noiseq >=2.24.0,<2.26.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' - r-base - r-rcpp - r-snow @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The probabilities by one-sided NOISeq are combined by Fisher''s method or Stouffer''s method' extra: identifiers: - biotools:metaseq - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-metaseq + path: recipes/bioconductor-metaseq + version: 1.20.0 + diff --git a/recipes/bioconductor-metaseqr/build.sh b/recipes/bioconductor-metaseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metaseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metaseqr/meta.yaml b/recipes/bioconductor-metaseqr/meta.yaml new file mode 100644 index 0000000000000..90e5f450fd55f --- /dev/null +++ b/recipes/bioconductor-metaseqr/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.22.0" %} +{% set name = "metaseqR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5a180e620a8676c71a16a0b5a4ec5bf5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, GenomicRanges, rtracklayer, Rsamtools, survcomp, VennDiagram, knitr, zoo, RUnit, BiocManager, BSgenome, RSQLite +requirements: + host: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-brew + - r-corrplot + - r-gplots + - r-log4r + - r-nbpseq + - r-rjson + run: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-noiseq >=2.26.0,<2.27.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-brew + - r-corrplot + - r-gplots + - r-log4r + - r-nbpseq + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Provides an interface to several normalization and statistical testing packages for RNA-Seq gene expression data. Additionally, it creates several diagnostic plots, performs meta-analysis by combinining the results of several statistical tests and reports the results in an interactive way.' + diff --git a/recipes/bioconductor-metavizr/build.sh b/recipes/bioconductor-metavizr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metavizr/build.sh +++ b/recipes/bioconductor-metavizr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metavizr/meta.yaml b/recipes/bioconductor-metavizr/meta.yaml index ebb3f3f37f0dd..07853c4c3b549 100644 --- a/recipes/bioconductor-metavizr/meta.yaml +++ b/recipes/bioconductor-metavizr/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "1.2.1" %} +{% set version = "1.6.1" %} {% set name = "metavizr" %} -{% set bioc = "3.6" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2c2b4ad681d2fc0c326462021fc3246ed5b813546603fcd0c2d172b46cc89684 + md5: a9f2fa64aa45b79c822c284ae5205d1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, matrixStats, msd16s (>= 0.109.1), etec16s, testthat, gss, curatedMetagenomicData requirements: host: - - bioconductor-biobase - - bioconductor-epivizr - - bioconductor-epivizrdata - - bioconductor-epivizrserver - - bioconductor-epivizrstandalone - - bioconductor-genomeinfodb - - 'bioconductor-metagenomeseq >=1.17.1' - - bioconductor-phyloseq - - 'r-base <=3.4.1' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-epivizr >=2.12.0,<2.13.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-epivizrstandalone >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - r-base - r-data.table - r-digest - r-httr - r-vegan run: - - bioconductor-biobase - - bioconductor-epivizr - - bioconductor-epivizrdata - - bioconductor-epivizrserver - - bioconductor-epivizrstandalone - - bioconductor-genomeinfodb - - 'bioconductor-metagenomeseq >=1.17.1' - - bioconductor-phyloseq - - 'r-base <=3.4.1' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-epivizr >=2.12.0,<2.13.0' + - 'bioconductor-epivizrdata >=1.10.0,<1.11.0' + - 'bioconductor-epivizrserver >=1.10.0,<1.11.0' + - 'bioconductor-epivizrstandalone >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - r-base - r-data.table - r-digest - r-httr @@ -49,6 +51,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides Websocket communication to the metaviz web app (http://metaviz.cbcb.umd.edu) for interactive visualization of metagenomics data. Objects in R/bioc interactive sessions can be displayed in plots and data can be explored using a facetzoom visualization. Fundamental Bioconductor data structures are supported (e.g., MRexperiment objects), while providing an easy mechanism to support other data structures. Visualizations (using d3.js) can be easily added to the web app as well.' +extra: + parent_recipe: + name: bioconductor-metavizr + path: recipes/bioconductor-metavizr + version: 1.2.1 + diff --git a/recipes/bioconductor-metcirc/build.sh b/recipes/bioconductor-metcirc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-metcirc/build.sh +++ b/recipes/bioconductor-metcirc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metcirc/meta.yaml b/recipes/bioconductor-metcirc/meta.yaml index 752abe81b3e5a..a51f1fe79f653 100644 --- a/recipes/bioconductor-metcirc/meta.yaml +++ b/recipes/bioconductor-metcirc/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "MetCirc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06a75184e2424e261730d58ad8f4b7ee511f1a9075a41af997c6693a55b9817a + md5: 3f23d9efb9d1897dc1fd44012d8dfe7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, knitr (>= 1.11) requirements: host: - 'r-amap >=0.8' @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'MetCirc comprises a workflow to interactively explore high-resolution MS/MS metabolomics data: create an MSP object, a format for MS/MS library data, bin m/z values of precursors, calculate similarity between precursors based on the normalised dot product and visualise similarities in a circular layout. Within the interactive framework the user can annotate MS/MS features based on their similarity to (known) related MS/MS features.' extra: identifiers: - biotools:metcirc - doi:10.1093/bioinformatics/btx159 + parent_recipe: + name: bioconductor-metcirc + path: recipes/bioconductor-metcirc + version: 1.10.0 + diff --git a/recipes/bioconductor-methimpute/build.sh b/recipes/bioconductor-methimpute/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methimpute/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methimpute/meta.yaml b/recipes/bioconductor-methimpute/meta.yaml new file mode 100644 index 0000000000000..f4972f25e7338 --- /dev/null +++ b/recipes/bioconductor-methimpute/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "1.4.0" %} +{% set name = "methimpute" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e072c861115fb41c461876d548cd6968 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, BiocStyle +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-data.table + - r-ggplot2 + - r-minpack.lm + - 'r-rcpp >=0.12.4.5' + - r-reshape2 + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-data.table + - r-ggplot2 + - r-minpack.lm + - 'r-rcpp >=0.12.4.5' + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package implements functions for calling methylation for all cytosines in the genome.' + diff --git a/recipes/bioconductor-methinheritsim/build.sh b/recipes/bioconductor-methinheritsim/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methinheritsim/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methinheritsim/meta.yaml b/recipes/bioconductor-methinheritsim/meta.yaml new file mode 100644 index 0000000000000..644696f844b4f --- /dev/null +++ b/recipes/bioconductor-methinheritsim/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.1" %} +{% set name = "methInheritSim" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 70da35403445ef588556718166474bc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, methylInheritance +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylkit >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-msm + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylkit >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-msm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Simulate a multigeneration methylation case versus control experiment with inheritance relation using a real control dataset.' + diff --git a/recipes/bioconductor-methped/build.sh b/recipes/bioconductor-methped/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methped/build.sh +++ b/recipes/bioconductor-methped/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methped/meta.yaml b/recipes/bioconductor-methped/meta.yaml index 4e11dae6f5057..9dc2ee314c146 100644 --- a/recipes/bioconductor-methped/meta.yaml +++ b/recipes/bioconductor-methped/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MethPed" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6f8a451a4402d9b9ca298e596932a978f13679cbaf0c906647dc354a119270e6 + md5: d81703a17f7dbc8f21bc4782de4c42de build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, markdown, impute requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-randomforest run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-randomforest test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Classification of pediatric tumors into biologically defined subtypes is challenging and multifaceted approaches are needed. For this aim, we developed a diagnostic classifier based on DNA methylation profiles. We offer MethPed as an easy-to-use toolbox that allows researchers and clinical diagnosticians to test single samples as well as large cohorts for subclass prediction of pediatric brain tumors. The current version of MethPed can classify the following tumor diagnoses/subgroups: Diffuse Intrinsic Pontine Glioma (DIPG), Ependymoma, Embryonal tumors with multilayered rosettes (ETMR), Glioblastoma (GBM), Medulloblastoma (MB) - Group 3 (MB_Gr3), Group 4 (MB_Gr3), Group WNT (MB_WNT), Group SHH (MB_SHH) and Pilocytic Astrocytoma (PiloAstro).' extra: identifiers: - biotools:methped - doi:10.1186/s13148-015-0103-3 + parent_recipe: + name: bioconductor-methped + path: recipes/bioconductor-methped + version: 1.8.0 + diff --git a/recipes/bioconductor-methtargetedngs/build.sh b/recipes/bioconductor-methtargetedngs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methtargetedngs/build.sh +++ b/recipes/bioconductor-methtargetedngs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methtargetedngs/meta.yaml b/recipes/bioconductor-methtargetedngs/meta.yaml index 1544dc7b545e6..b9cfbb9ff32ec 100644 --- a/recipes/bioconductor-methtargetedngs/meta.yaml +++ b/recipes/bioconductor-methtargetedngs/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "MethTargetedNGS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 35a8ee457c74f7d65edf9f626f3469493b9fe42aab9577d1b8631d208b933f73 + md5: ade70d7cd180adfcc0cbb28eec6345ef build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# SystemRequirements: HMMER3 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-gplots - r-seqinr - r-stringr run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-gplots - r-seqinr @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Perform step by step methylation analysis of Next Generation Sequencing data.' extra: identifiers: - biotools:methtargetedngs - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-methtargetedngs + path: recipes/bioconductor-methtargetedngs + version: 1.12.0 + diff --git a/recipes/bioconductor-methvisual/build.sh b/recipes/bioconductor-methvisual/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methvisual/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methvisual/meta.yaml b/recipes/bioconductor-methvisual/meta.yaml new file mode 100644 index 0000000000000..5ce814c2e9e65 --- /dev/null +++ b/recipes/bioconductor-methvisual/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.34.0" %} +{% set name = "methVisual" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec537978bc45ab9ada43c3b429825362 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-ca + - r-gridbase + - r-gsubfn + - r-plotrix + - r-sqldf + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-ca + - r-gridbase + - r-gsubfn + - r-plotrix + - r-sqldf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package ''methVisual'' allows the visualization of DNA methylation data after bisulfite sequencing.' + diff --git a/recipes/bioconductor-methyanalysis/build.sh b/recipes/bioconductor-methyanalysis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methyanalysis/build.sh +++ b/recipes/bioconductor-methyanalysis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methyanalysis/conda_build_config.yaml b/recipes/bioconductor-methyanalysis/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-methyanalysis/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-methyanalysis/meta.yaml b/recipes/bioconductor-methyanalysis/meta.yaml index 62f04996595da..dc6de15927ea3 100644 --- a/recipes/bioconductor-methyanalysis/meta.yaml +++ b/recipes/bioconductor-methyanalysis/meta.yaml @@ -1,70 +1,77 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "methyAnalysis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 71a4c455b3588f58cf259bdc4227f8a86549be36017de5df36515b3a9d9dba87 + md5: 3075fef8d84c73154ba460e1390106af build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: FDb.InfiniumMethylation.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genoset >=1.36.0,<1.38.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genoset >=1.38.0,<1.39.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genoset >=1.36.0,<1.38.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genoset >=1.38.0,<1.39.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The methyAnalysis package aims for the DNA methylation data analysis and visualization. A MethyGenoSet class is defined to keep the chromosome location information together with the data. The package also includes functions of estimating the methylation levels from Methy-Seq data.' extra: identifiers: - biotools:methyanalysis - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-methyanalysis + path: recipes/bioconductor-methyanalysis + version: 1.22.0 + diff --git a/recipes/bioconductor-methylaid/build.sh b/recipes/bioconductor-methylaid/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methylaid/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylaid/meta.yaml b/recipes/bioconductor-methylaid/meta.yaml new file mode 100644 index 0000000000000..d721c75925542 --- /dev/null +++ b/recipes/bioconductor-methylaid/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.16.0" %} +{% set name = "MethylAid" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c654109f11f3e32cf050cee84dbb956f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, MethylAidData, minfiData, minfiDataEPIC, RUnit +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridbase + - r-hexbin + - r-matrixstats + - r-rcolorbrewer + - r-shiny + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-gridbase + - r-hexbin + - r-matrixstats + - r-rcolorbrewer + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A visual and interactive web application using RStudio''s shiny package. Bad quality samples are detected using sample-dependent and sample-independent controls present on the array and user adjustable thresholds. In depth exploration of bad quality samples can be performed using several interactive diagnostic plots of the quality control probes present on the array. Furthermore, the impact of any batch effect provided by the user can be explored.' + diff --git a/recipes/bioconductor-methylaiddata/meta.yaml b/recipes/bioconductor-methylaiddata/meta.yaml new file mode 100644 index 0000000000000..9086ad93a5f85 --- /dev/null +++ b/recipes/bioconductor-methylaiddata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.14.0" %} +{% set name = "MethylAidData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b7445efd87e21834a9a35e92bae6bbad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocParallel, BiocStyle, knitr, minfiData, minfiDataEPIC +requirements: + host: + - 'bioconductor-methylaid >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-methylaid >=1.16.0,<1.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A data package containing summarized Illumina 450k array data on 2800 samples and summarized EPIC data for 2620 samples. The data can be use as a background data set in the interactive application.' + diff --git a/recipes/bioconductor-methylaiddata/post-link.sh b/recipes/bioconductor-methylaiddata/post-link.sh new file mode 100644 index 0000000000000..1da5185e259de --- /dev/null +++ b/recipes/bioconductor-methylaiddata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MethylAidData_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MethylAidData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/MethylAidData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-methylaiddata/bioconductor-methylaiddata_1.14.0_src_all.tar.gz" +) +MD5="b7445efd87e21834a9a35e92bae6bbad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-methylaiddata/pre-unlink.sh b/recipes/bioconductor-methylaiddata/pre-unlink.sh new file mode 100644 index 0000000000000..0c25b05af3d1d --- /dev/null +++ b/recipes/bioconductor-methylaiddata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MethylAidData diff --git a/recipes/bioconductor-methylgsa/build.sh b/recipes/bioconductor-methylgsa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methylgsa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylgsa/meta.yaml b/recipes/bioconductor-methylgsa/meta.yaml new file mode 100644 index 0000000000000..5023284c3f2f5 --- /dev/null +++ b/recipes/bioconductor-methylgsa/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.0" %} +{% set name = "methylGSA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 12017f8e0a2e33ae773b213c7426f23c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, enrichplot +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-base + - r-ggplot2 + - r-robustrankaggreg + - r-stringr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-missmethyl >=1.16.0,<1.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - r-base + - r-ggplot2 + - r-robustrankaggreg + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The main functions for methylGSA are methylglm and methylRRA. methylGSA implements logistic regression adjusting number of probes as a covariate. methylRRA adjusts multiple p-values of each gene by Robust Rank Aggregation. For more detailed help information, please see the vignette.' + diff --git a/recipes/bioconductor-methylinheritance/build.sh b/recipes/bioconductor-methylinheritance/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methylinheritance/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylinheritance/meta.yaml b/recipes/bioconductor-methylinheritance/meta.yaml new file mode 100644 index 0000000000000..622927c611b01 --- /dev/null +++ b/recipes/bioconductor-methylinheritance/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.6.1" %} +{% set name = "methylInheritance" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 21df16eb1d54500c0e3b1f7de6405a1d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit, methInheritSim +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylkit >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-rebus + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-methylkit >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gridextra + - r-rebus +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Permutation analysis, based on Monte Carlo sampling, for testing the hypothesis that the number of conserved differentially methylated elements, between several generations, is associated to an effect inherited from a treatment and that stochastic effect can be dismissed.' + diff --git a/recipes/bioconductor-methylkit/build.sh b/recipes/bioconductor-methylkit/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methylkit/build.sh +++ b/recipes/bioconductor-methylkit/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylkit/meta.yaml b/recipes/bioconductor-methylkit/meta.yaml index de4aacf2e0e23..b5756dabfd7dd 100644 --- a/recipes/bioconductor-methylkit/meta.yaml +++ b/recipes/bioconductor-methylkit/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.0" %} {% set name = "methylKit" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 33590c69b9a36d913730f2cb7daf4a1cd601141ac0f5bdbd0f454b2d1a398ada + md5: 541833aff30364b6568449ae16019f5e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat,knitr, rmarkdown, genomation, BiocManager requirements: host: - - 'bioconductor-fastseg >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-fastseg >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -38,17 +39,17 @@ requirements: - r-r.utils - r-rcpp run: - - 'bioconductor-fastseg >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-fastseg >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-data.table >=1.9.6' - r-emdbook @@ -65,9 +66,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'methylKit is an R package for DNA methylation analysis and annotation from high-throughput bisulfite sequencing. The package is designed to deal with sequencing data from RRBS and its variants, but also target-capture methods and whole genome bisulfite sequencing. It also has functions to analyze base-pair resolution 5hmC data from experimental protocols such as oxBS-Seq and TAB-Seq. Perl is needed to read SAM files only.' extra: identifiers: - biotools:methylkit + parent_recipe: + name: bioconductor-methylkit + path: recipes/bioconductor-methylkit + version: 1.6.3 + diff --git a/recipes/bioconductor-methylmix/build.sh b/recipes/bioconductor-methylmix/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methylmix/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylmix/meta.yaml b/recipes/bioconductor-methylmix/meta.yaml new file mode 100644 index 0000000000000..7899e6e513ea6 --- /dev/null +++ b/recipes/bioconductor-methylmix/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "2.12.0" %} +{% set name = "MethylMix" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e894baa2827b774cc07acc38faa8d6d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, doParallel, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-data.table + - r-digest + - r-foreach + - r-ggplot2 + - r-r.matlab + - r-rcolorbrewer + - r-rcurl + - r-rpmm + run: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-data.table + - r-digest + - r-foreach + - r-ggplot2 + - r-r.matlab + - r-rcolorbrewer + - r-rcurl + - r-rpmm +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'MethylMix is an algorithm implemented to identify hyper and hypomethylated genes for a disease. MethylMix is based on a beta mixture model to identify methylation states and compares them with the normal DNA methylation state. MethylMix uses a novel statistic, the Differential Methylation value or DM-value defined as the difference of a methylation state with the normal methylation state. Finally, matched gene expression data is used to identify, besides differential, functional methylation states by focusing on methylation changes that effect gene expression. References: Gevaert 0. MethylMix: an R package for identifying DNA methylation-driven genes. Bioinformatics (Oxford, England). 2015;31(11):1839-41. doi:10.1093/bioinformatics/btv020. Gevaert O, Tibshirani R, Plevritis SK. Pancancer analysis of DNA methylation-driven genes using MethylMix. Genome Biology. 2015;16(1):17. doi:10.1186/s13059-014-0579-8.' + diff --git a/recipes/bioconductor-methylmnm/build.sh b/recipes/bioconductor-methylmnm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methylmnm/build.sh +++ b/recipes/bioconductor-methylmnm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylmnm/meta.yaml b/recipes/bioconductor-methylmnm/meta.yaml index 3974004b3836d..8fe29eb0741b0 100644 --- a/recipes/bioconductor-methylmnm/meta.yaml +++ b/recipes/bioconductor-methylmnm/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "methylMnM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 22584a7d451e4a7c7114c0372f3fc420e3c81f6511362f21e65cf57c77011cbe + md5: 595ea0397f953ec93b06932e0e724dd4 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - r-statmod run: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - r-statmod build: @@ -32,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'To give the exactly p-value and q-value of MeDIP-seq and MRE-seq data for different samples comparation.' extra: identifiers: - biotools:methylmnm - doi:10.1101/gr.156539.113 + parent_recipe: + name: bioconductor-methylmnm + path: recipes/bioconductor-methylmnm + version: 1.18.0 + diff --git a/recipes/bioconductor-methylpipe/build.sh b/recipes/bioconductor-methylpipe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methylpipe/build.sh +++ b/recipes/bioconductor-methylpipe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylpipe/meta.yaml b/recipes/bioconductor-methylpipe/meta.yaml index d918e99a3351b..5aea45bd3151c 100644 --- a/recipes/bioconductor-methylpipe/meta.yaml +++ b/recipes/bioconductor-methylpipe/meta.yaml @@ -1,49 +1,50 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "methylPipe" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1e05797af340863c335d3537282025e0c7092cae9aaa85b6dc8b030cc673622c + md5: 0174e17c1fbcf664052973c8be3f5c79 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg18, TxDb.Hsapiens.UCSC.hg18.knownGene, knitr, MethylSeekR requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-gplots run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-gplots @@ -54,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'Memory efficient analysis of base resolution DNA methylation data in both the CpG and non-CpG sequence context. Integration of DNA methylation data derived from any methodology providing base- or low-resolution data.' extra: identifiers: - biotools:methylpipe + parent_recipe: + name: bioconductor-methylpipe + path: recipes/bioconductor-methylpipe + version: 1.14.0 + diff --git a/recipes/bioconductor-methylseekr/build.sh b/recipes/bioconductor-methylseekr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methylseekr/build.sh +++ b/recipes/bioconductor-methylseekr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylseekr/meta.yaml b/recipes/bioconductor-methylseekr/meta.yaml index 4b5fa59c34a7c..3c6f4df600029 100644 --- a/recipes/bioconductor-methylseekr/meta.yaml +++ b/recipes/bioconductor-methylseekr/meta.yaml @@ -1,45 +1,52 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MethylSeekR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a77c81e78e8bdfe9fef27d56af407467395fcfad4d8e42a64e891acf65cfeda5 + md5: 19080118abe4bf6ba3aed35b2643764b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - 'r-mhsmm >=0.4.4' run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - 'r-mhsmm >=0.4.4' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This is a package for the discovery of regulatory regions from Bis-seq data' extra: identifiers: - biotools:methylseekr + parent_recipe: + name: bioconductor-methylseekr + path: recipes/bioconductor-methylseekr + version: 1.20.0 + diff --git a/recipes/bioconductor-methylumi/build.sh b/recipes/bioconductor-methylumi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-methylumi/build.sh +++ b/recipes/bioconductor-methylumi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methylumi/meta.yaml b/recipes/bioconductor-methylumi/meta.yaml index 90edd5fb2aa44..285ab12014b43 100644 --- a/recipes/bioconductor-methylumi/meta.yaml +++ b/recipes/bioconductor-methylumi/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "methylumi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 57c7dd21135f97eb787d09ed8807eb5c5971b0c43dd55627208d9b0256ab662d + md5: f1a2ca6160d851c6db5797cf4636058e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: lumi, lattice, limma, xtable, SQN, MASS, matrixStats, parallel, rtracklayer, Biostrings, methyAnalysis, TCGAMethylation450k, IlluminaHumanMethylation450kanno.ilmn12.hg19, FDb.InfiniumMethylation.hg18 (>= 2.2.0), Homo.sapiens, knitr requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.4.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-lattice @@ -38,19 +40,19 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.4.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-fdb.infiniummethylation.hg19 >=2.2.0,<2.3.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-lattice @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.' + summary: 'This package provides classes for holding and manipulating Illumina methylation data. Based on eSet, it can contain MIAME information, sample information, feature information, and multiple matrices of data. An "intelligent" import function, methylumiR can read the Illumina text files and create a MethyLumiSet. methylumIDAT can directly read raw IDAT files from HumanMethylation27 and HumanMethylation450 microarrays. Normalization, background correction, and quality control features for GoldenGate, Infinium, and Infinium HD arrays are also included.' extra: identifiers: - biotools:methylumi - doi:10.1186/1471-2164-14-293 + parent_recipe: + name: bioconductor-methylumi + path: recipes/bioconductor-methylumi + version: 2.26.0 + diff --git a/recipes/bioconductor-methyvim/build.sh b/recipes/bioconductor-methyvim/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-methyvim/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-methyvim/meta.yaml b/recipes/bioconductor-methyvim/meta.yaml new file mode 100644 index 0000000000000..fe8982b5580c3 --- /dev/null +++ b/recipes/bioconductor-methyvim/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.4.0" %} +{% set name = "methyvim" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c8c7263ae8d200c1780273158bfda8fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, SuperLearner, earth, nnet, gam, arm, snow, parallel, BatchJobs, minfiData, methyvimData +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-dofuture + - r-dplyr + - r-future + - r-ggplot2 + - r-ggsci + - r-gridextra + - r-gtools + - r-superheat + - r-tmle + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-dofuture + - r-dplyr + - r-future + - r-ggplot2 + - r-ggsci + - r-gridextra + - r-gtools + - r-superheat + - r-tmle +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'This package provides facilities for differential methylation analysis based on variable importance measures (VIMs), a class of statistical target parameters that arise in causal inference. The estimation and inference procedures provided are nonparametric, relying on ensemble machine learning to flexibly assess functional relationships among covariates and the outcome of interest. These tools can be applied to differential methylation at the level of CpG sites, to obtain valid statistical inference even after corrections for multiple hypothesis testing.' + diff --git a/recipes/bioconductor-methyvimdata/meta.yaml b/recipes/bioconductor-methyvimdata/meta.yaml new file mode 100644 index 0000000000000..b204fed4bd36c --- /dev/null +++ b/recipes/bioconductor-methyvimdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "methyvimData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2d04580044269f4e9f1f904aed11ff6f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocStyle, SummarizedExperiment, knitr, rmarkdown +requirements: + host: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Contains a reduced set of simulated data inspired by data produced by the Infinium EPIC BeadChip assays by Illumina. The example data set is made available to highlight many of the key procedures that are available within the core functions of the methyvim package.' + diff --git a/recipes/bioconductor-methyvimdata/post-link.sh b/recipes/bioconductor-methyvimdata/post-link.sh new file mode 100644 index 0000000000000..b88aa59ae16e3 --- /dev/null +++ b/recipes/bioconductor-methyvimdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="methyvimData_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/methyvimData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/methyvimData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-methyvimdata/bioconductor-methyvimdata_1.4.0_src_all.tar.gz" +) +MD5="2d04580044269f4e9f1f904aed11ff6f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-methyvimdata/pre-unlink.sh b/recipes/bioconductor-methyvimdata/pre-unlink.sh new file mode 100644 index 0000000000000..635432241c4bc --- /dev/null +++ b/recipes/bioconductor-methyvimdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ methyvimData diff --git a/recipes/bioconductor-metid/build.sh b/recipes/bioconductor-metid/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metid/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metid/meta.yaml b/recipes/bioconductor-metid/meta.yaml new file mode 100644 index 0000000000000..7cbd25413f1a3 --- /dev/null +++ b/recipes/bioconductor-metid/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.0.0" %} +{% set name = "MetID" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c5b7dea163a632b9626c4b3db70334bf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.19), rmarkdown (>= 1.8) +requirements: + host: + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - 'r-devtools >=1.13.0' + - 'r-igraph >=1.2.1' + - 'r-matrix >=1.2-12' + - 'r-stringr >=1.3.0' + run: + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - r-base + - 'r-devtools >=1.13.0' + - 'r-igraph >=1.2.1' + - 'r-matrix >=1.2-12' + - 'r-stringr >=1.3.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package uses an innovative network-based approach that will enhance our ability to determine the identities of significant ions detected by LC-MS.' + diff --git a/recipes/bioconductor-metnet/build.sh b/recipes/bioconductor-metnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-metnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-metnet/meta.yaml b/recipes/bioconductor-metnet/meta.yaml new file mode 100644 index 0000000000000..ede817e93b557 --- /dev/null +++ b/recipes/bioconductor-metnet/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "MetNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f9840eca47a1f6485e581fbde8da864 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics (>= 0.24.0), BiocStyle (>= 2.6.1), igraph (>= 1.1.2), knitr (>= 1.11) +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - 'r-bnlearn >=4.3' + - 'r-mpmi >=0.42' + - 'r-parmigene >=1.0.2' + - 'r-ppcor >=1.1' + - 'r-rfpermute >=2.1.5' + - 'r-sna >=2.4' + - 'r-stabs >=0.6' + - 'r-wgcna >=1.61' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - 'r-bnlearn >=4.3' + - 'r-mpmi >=0.42' + - 'r-parmigene >=1.0.2' + - 'r-ppcor >=1.1' + - 'r-rfpermute >=2.1.5' + - 'r-sna >=2.4' + - 'r-stabs >=0.6' + - 'r-wgcna >=1.61' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'MetNet contains functionality to infer metabolic network topologies from quantitative data and high-resolution mass/charge information. Using statistical models (including correlation, mutual information, regression and Bayes statistics) and quantitative data (intensity values of features) adjacency matrices are inferred that can be combined to a consensus matrix. Mass differences calculated between mass/charge values of features will be matched against a data frame of supplied mass/charge differences referring to transformations of enzymatic activities. In a third step, the two matrices are combined to form a adjacency matrix inferred from both quantitative and structure information.' + diff --git a/recipes/bioconductor-mfa/build.sh b/recipes/bioconductor-mfa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mfa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mfa/meta.yaml b/recipes/bioconductor-mfa/meta.yaml new file mode 100644 index 0000000000000..c5c17d0c5df22 --- /dev/null +++ b/recipes/bioconductor-mfa/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.4.0" %} +{% set name = "mfa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5528451a5c29e77ff4cf810962a2f968 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, BiocStyle, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-coda + - r-dplyr + - r-ggmcmc + - r-ggplot2 + - r-magrittr + - r-mcmcglmm + - r-mcmcpack + - r-rcpp + - r-tibble + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-coda + - r-dplyr + - r-ggmcmc + - r-ggplot2 + - r-magrittr + - r-mcmcglmm + - r-mcmcpack + - r-rcpp + - r-tibble + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'MFA models genomic bifurcations using a Bayesian hierarchical mixture of factor analysers.' + diff --git a/recipes/bioconductor-mfuzz/build.sh b/recipes/bioconductor-mfuzz/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mfuzz/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mfuzz/meta.yaml b/recipes/bioconductor-mfuzz/meta.yaml new file mode 100644 index 0000000000000..fcc6a82d9e290 --- /dev/null +++ b/recipes/bioconductor-mfuzz/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "2.42.0" %} +{% set name = "Mfuzz" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e994e57b660e1e59335de41f82762d58 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: marray +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - r-base + - r-e1071 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - r-base + - r-e1071 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)' + diff --git a/recipes/bioconductor-mgfm/build.sh b/recipes/bioconductor-mgfm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mgfm/build.sh +++ b/recipes/bioconductor-mgfm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mgfm/meta.yaml b/recipes/bioconductor-mgfm/meta.yaml index 2bec5be092414..bc5a1c5f6c42d 100644 --- a/recipes/bioconductor-mgfm/meta.yaml +++ b/recipes/bioconductor-mgfm/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MGFM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2a7559087deeb218da2bf445cef955435d497fe0b66df8e1b14c963a7169ccf + md5: 4c546557bee46a59290c4900403f7edf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgu133a.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package is designed to detect marker genes from Microarray gene expression data sets' extra: identifiers: - biotools:mgfm - doi:10.1186/s12864-015-1785-9 + parent_recipe: + name: bioconductor-mgfm + path: recipes/bioconductor-mgfm + version: 1.14.0 + diff --git a/recipes/bioconductor-mgfr/build.sh b/recipes/bioconductor-mgfr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mgfr/build.sh +++ b/recipes/bioconductor-mgfr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mgfr/meta.yaml b/recipes/bioconductor-mgfr/meta.yaml index 3c110f8cbacec..c83898101b689 100644 --- a/recipes/bioconductor-mgfr/meta.yaml +++ b/recipes/bioconductor-mgfr/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "MGFR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c93e06fdf48156fc542ae73cc67305ab625eab81008b01c87cfe4a779196d4d9 + md5: 53e276e661120a9237e382c5da01d8d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package is designed to detect marker genes from RNA-seq data.' extra: identifiers: - biotools:mgfr - doi:10.1186/s12864-015-1785-9 + parent_recipe: + name: bioconductor-mgfr + path: recipes/bioconductor-mgfr + version: 1.6.0 + diff --git a/recipes/bioconductor-mgsa/build.sh b/recipes/bioconductor-mgsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mgsa/build.sh +++ b/recipes/bioconductor-mgsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mgsa/meta.yaml b/recipes/bioconductor-mgsa/meta.yaml index 7524f7bdb49a7..a1cba90c5f9cf 100644 --- a/recipes/bioconductor-mgsa/meta.yaml +++ b/recipes/bioconductor-mgsa/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "mgsa" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: fa5422aff3b0539b354139b8f3895127160a37a7c83b4940ed2a0001140fd86b + md5: 273187423f0ea752f7d0e31aa3def023 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: DBI, RSQLite, GO.db, testthat requirements: host: - r-base @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Model-based Gene Set Analysis (MGSA) is a Bayesian modeling approach for gene set enrichment. The package mgsa implements MGSA and tools to use MGSA together with the Gene Ontology.' extra: identifiers: - biotools:mgsa - doi:10.1093/nar/gkq045 + parent_recipe: + name: bioconductor-mgsa + path: recipes/bioconductor-mgsa + version: 1.28.0 + diff --git a/recipes/bioconductor-mgu74a.db/meta.yaml b/recipes/bioconductor-mgu74a.db/meta.yaml new file mode 100644 index 0000000000000..f09cf8dd554aa --- /dev/null +++ b/recipes/bioconductor-mgu74a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b746929f272a811061cf03040ec5ea3b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74a.db/post-link.sh b/recipes/bioconductor-mgu74a.db/post-link.sh new file mode 100644 index 0000000000000..7887cb4633b7e --- /dev/null +++ b/recipes/bioconductor-mgu74a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74a.db/bioconductor-mgu74a.db_3.2.3_src_all.tar.gz" +) +MD5="b746929f272a811061cf03040ec5ea3b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74a.db/pre-unlink.sh b/recipes/bioconductor-mgu74a.db/pre-unlink.sh new file mode 100644 index 0000000000000..a0703b9cf78ad --- /dev/null +++ b/recipes/bioconductor-mgu74a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74a.db diff --git a/recipes/bioconductor-mgu74acdf/meta.yaml b/recipes/bioconductor-mgu74acdf/meta.yaml new file mode 100644 index 0000000000000..3ecd4436473ac --- /dev/null +++ b/recipes/bioconductor-mgu74acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ed6e86398e51c7b0ddca4431797ecbc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74A.cdf file.' + diff --git a/recipes/bioconductor-mgu74acdf/post-link.sh b/recipes/bioconductor-mgu74acdf/post-link.sh new file mode 100644 index 0000000000000..9daecb6bb66d0 --- /dev/null +++ b/recipes/bioconductor-mgu74acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74acdf/bioconductor-mgu74acdf_2.18.0_src_all.tar.gz" +) +MD5="ed6e86398e51c7b0ddca4431797ecbc0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74acdf/pre-unlink.sh b/recipes/bioconductor-mgu74acdf/pre-unlink.sh new file mode 100644 index 0000000000000..8741bc0dcea92 --- /dev/null +++ b/recipes/bioconductor-mgu74acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74acdf diff --git a/recipes/bioconductor-mgu74aprobe/meta.yaml b/recipes/bioconductor-mgu74aprobe/meta.yaml new file mode 100644 index 0000000000000..292e9774d7f0e --- /dev/null +++ b/recipes/bioconductor-mgu74aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7fea6d44856203e6293e0cd9fe1ad066 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74A\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74aprobe/post-link.sh b/recipes/bioconductor-mgu74aprobe/post-link.sh new file mode 100644 index 0000000000000..c60592c1ac828 --- /dev/null +++ b/recipes/bioconductor-mgu74aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74aprobe/bioconductor-mgu74aprobe_2.18.0_src_all.tar.gz" +) +MD5="7fea6d44856203e6293e0cd9fe1ad066" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74aprobe/pre-unlink.sh b/recipes/bioconductor-mgu74aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..8571c2f6b653a --- /dev/null +++ b/recipes/bioconductor-mgu74aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74aprobe diff --git a/recipes/bioconductor-mgu74av2.db/meta.yaml b/recipes/bioconductor-mgu74av2.db/meta.yaml new file mode 100644 index 0000000000000..10a81e7eb53a4 --- /dev/null +++ b/recipes/bioconductor-mgu74av2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74av2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ca637dece483fe0a0f752e4fa013d389 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74av2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74av2.db/post-link.sh b/recipes/bioconductor-mgu74av2.db/post-link.sh new file mode 100644 index 0000000000000..c960acd2da7dc --- /dev/null +++ b/recipes/bioconductor-mgu74av2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74av2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74av2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2.db/bioconductor-mgu74av2.db_3.2.3_src_all.tar.gz" +) +MD5="ca637dece483fe0a0f752e4fa013d389" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74av2.db/pre-unlink.sh b/recipes/bioconductor-mgu74av2.db/pre-unlink.sh new file mode 100644 index 0000000000000..fd2f1996e3a5d --- /dev/null +++ b/recipes/bioconductor-mgu74av2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74av2.db diff --git a/recipes/bioconductor-mgu74av2cdf/meta.yaml b/recipes/bioconductor-mgu74av2cdf/meta.yaml new file mode 100644 index 0000000000000..1da559ec84bd7 --- /dev/null +++ b/recipes/bioconductor-mgu74av2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74av2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 35e2abb9fbfd68d90dc32a2faae00c95 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74Av2.CDF file.' + diff --git a/recipes/bioconductor-mgu74av2cdf/post-link.sh b/recipes/bioconductor-mgu74av2cdf/post-link.sh new file mode 100644 index 0000000000000..5983908152195 --- /dev/null +++ b/recipes/bioconductor-mgu74av2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74av2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74av2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2cdf/bioconductor-mgu74av2cdf_2.18.0_src_all.tar.gz" +) +MD5="35e2abb9fbfd68d90dc32a2faae00c95" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74av2cdf/pre-unlink.sh b/recipes/bioconductor-mgu74av2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..cfd76d6c42747 --- /dev/null +++ b/recipes/bioconductor-mgu74av2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74av2cdf diff --git a/recipes/bioconductor-mgu74av2probe/meta.yaml b/recipes/bioconductor-mgu74av2probe/meta.yaml new file mode 100644 index 0000000000000..c48e73cc91b2d --- /dev/null +++ b/recipes/bioconductor-mgu74av2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74av2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ac540b0e26b14a411740233b02d3e11c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Av2\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74av2probe/post-link.sh b/recipes/bioconductor-mgu74av2probe/post-link.sh new file mode 100644 index 0000000000000..22c3db98e7990 --- /dev/null +++ b/recipes/bioconductor-mgu74av2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74av2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74av2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74av2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74av2probe/bioconductor-mgu74av2probe_2.18.0_src_all.tar.gz" +) +MD5="ac540b0e26b14a411740233b02d3e11c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74av2probe/pre-unlink.sh b/recipes/bioconductor-mgu74av2probe/pre-unlink.sh new file mode 100644 index 0000000000000..271410c4b535f --- /dev/null +++ b/recipes/bioconductor-mgu74av2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74av2probe diff --git a/recipes/bioconductor-mgu74b.db/meta.yaml b/recipes/bioconductor-mgu74b.db/meta.yaml new file mode 100644 index 0000000000000..a6007d9bf3cc3 --- /dev/null +++ b/recipes/bioconductor-mgu74b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9d019b194a64ec8c915514019896708e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74b.db/post-link.sh b/recipes/bioconductor-mgu74b.db/post-link.sh new file mode 100644 index 0000000000000..a13a8bd413ad4 --- /dev/null +++ b/recipes/bioconductor-mgu74b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74b.db/bioconductor-mgu74b.db_3.2.3_src_all.tar.gz" +) +MD5="9d019b194a64ec8c915514019896708e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74b.db/pre-unlink.sh b/recipes/bioconductor-mgu74b.db/pre-unlink.sh new file mode 100644 index 0000000000000..7da0e67e2b238 --- /dev/null +++ b/recipes/bioconductor-mgu74b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74b.db diff --git a/recipes/bioconductor-mgu74bcdf/meta.yaml b/recipes/bioconductor-mgu74bcdf/meta.yaml new file mode 100644 index 0000000000000..1a0097b7b9ed7 --- /dev/null +++ b/recipes/bioconductor-mgu74bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a1f0f98f29d34a421622447252113e1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74B.cdf file.' + diff --git a/recipes/bioconductor-mgu74bcdf/post-link.sh b/recipes/bioconductor-mgu74bcdf/post-link.sh new file mode 100644 index 0000000000000..9e2adf9c0d53b --- /dev/null +++ b/recipes/bioconductor-mgu74bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bcdf/bioconductor-mgu74bcdf_2.18.0_src_all.tar.gz" +) +MD5="a1f0f98f29d34a421622447252113e1e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74bcdf/pre-unlink.sh b/recipes/bioconductor-mgu74bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..e6adb3bdb20ef --- /dev/null +++ b/recipes/bioconductor-mgu74bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74bcdf diff --git a/recipes/bioconductor-mgu74bprobe/meta.yaml b/recipes/bioconductor-mgu74bprobe/meta.yaml new file mode 100644 index 0000000000000..6925c6a876ab1 --- /dev/null +++ b/recipes/bioconductor-mgu74bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 224d606e6fc87592d387dbaabe5cd353 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74B\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74bprobe/post-link.sh b/recipes/bioconductor-mgu74bprobe/post-link.sh new file mode 100644 index 0000000000000..a3ea38f1a3258 --- /dev/null +++ b/recipes/bioconductor-mgu74bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bprobe/bioconductor-mgu74bprobe_2.18.0_src_all.tar.gz" +) +MD5="224d606e6fc87592d387dbaabe5cd353" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74bprobe/pre-unlink.sh b/recipes/bioconductor-mgu74bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..763fd49f6e4c3 --- /dev/null +++ b/recipes/bioconductor-mgu74bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74bprobe diff --git a/recipes/bioconductor-mgu74bv2.db/meta.yaml b/recipes/bioconductor-mgu74bv2.db/meta.yaml new file mode 100644 index 0000000000000..7dbbcdb391f34 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74bv2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dfc729955539aa0a2a852745a515d413 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74bv2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74bv2.db/post-link.sh b/recipes/bioconductor-mgu74bv2.db/post-link.sh new file mode 100644 index 0000000000000..edd912987907f --- /dev/null +++ b/recipes/bioconductor-mgu74bv2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74bv2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74bv2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2.db/bioconductor-mgu74bv2.db_3.2.3_src_all.tar.gz" +) +MD5="dfc729955539aa0a2a852745a515d413" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74bv2.db/pre-unlink.sh b/recipes/bioconductor-mgu74bv2.db/pre-unlink.sh new file mode 100644 index 0000000000000..7c107fa5eb6a6 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74bv2.db diff --git a/recipes/bioconductor-mgu74bv2cdf/meta.yaml b/recipes/bioconductor-mgu74bv2cdf/meta.yaml new file mode 100644 index 0000000000000..23ec9644f50d6 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74bv2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 45c48d11af03633dc10f8682b7ad74c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74Bv2.CDF file.' + diff --git a/recipes/bioconductor-mgu74bv2cdf/post-link.sh b/recipes/bioconductor-mgu74bv2cdf/post-link.sh new file mode 100644 index 0000000000000..0823bf2b39cef --- /dev/null +++ b/recipes/bioconductor-mgu74bv2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74bv2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74bv2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2cdf/bioconductor-mgu74bv2cdf_2.18.0_src_all.tar.gz" +) +MD5="45c48d11af03633dc10f8682b7ad74c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74bv2cdf/pre-unlink.sh b/recipes/bioconductor-mgu74bv2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..2a429d78ed297 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74bv2cdf diff --git a/recipes/bioconductor-mgu74bv2probe/meta.yaml b/recipes/bioconductor-mgu74bv2probe/meta.yaml new file mode 100644 index 0000000000000..ba67aa5ce8b20 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74bv2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f6a12f88ea3c43a3e885c7e9b3fd03d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Bv2\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74bv2probe/post-link.sh b/recipes/bioconductor-mgu74bv2probe/post-link.sh new file mode 100644 index 0000000000000..87d047de5a680 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74bv2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74bv2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74bv2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74bv2probe/bioconductor-mgu74bv2probe_2.18.0_src_all.tar.gz" +) +MD5="f6a12f88ea3c43a3e885c7e9b3fd03d2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74bv2probe/pre-unlink.sh b/recipes/bioconductor-mgu74bv2probe/pre-unlink.sh new file mode 100644 index 0000000000000..91d06cf4e45e6 --- /dev/null +++ b/recipes/bioconductor-mgu74bv2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74bv2probe diff --git a/recipes/bioconductor-mgu74c.db/meta.yaml b/recipes/bioconductor-mgu74c.db/meta.yaml new file mode 100644 index 0000000000000..5f0fd33f27739 --- /dev/null +++ b/recipes/bioconductor-mgu74c.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74c.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a92c9ac08ce2f543b016268948178776 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74c) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74c.db/post-link.sh b/recipes/bioconductor-mgu74c.db/post-link.sh new file mode 100644 index 0000000000000..a1e0e9d773cde --- /dev/null +++ b/recipes/bioconductor-mgu74c.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74c.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74c.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74c.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74c.db/bioconductor-mgu74c.db_3.2.3_src_all.tar.gz" +) +MD5="a92c9ac08ce2f543b016268948178776" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74c.db/pre-unlink.sh b/recipes/bioconductor-mgu74c.db/pre-unlink.sh new file mode 100644 index 0000000000000..aae9f5b2e2be9 --- /dev/null +++ b/recipes/bioconductor-mgu74c.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74c.db diff --git a/recipes/bioconductor-mgu74ccdf/meta.yaml b/recipes/bioconductor-mgu74ccdf/meta.yaml new file mode 100644 index 0000000000000..6f5a23a0712d9 --- /dev/null +++ b/recipes/bioconductor-mgu74ccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74ccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 172e626b0e3072edc65c4efff35fe998 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74C.cdf file.' + diff --git a/recipes/bioconductor-mgu74ccdf/post-link.sh b/recipes/bioconductor-mgu74ccdf/post-link.sh new file mode 100644 index 0000000000000..3ae3ca619dce0 --- /dev/null +++ b/recipes/bioconductor-mgu74ccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74ccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74ccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74ccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74ccdf/bioconductor-mgu74ccdf_2.18.0_src_all.tar.gz" +) +MD5="172e626b0e3072edc65c4efff35fe998" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74ccdf/pre-unlink.sh b/recipes/bioconductor-mgu74ccdf/pre-unlink.sh new file mode 100644 index 0000000000000..d9d4cfcbd14d3 --- /dev/null +++ b/recipes/bioconductor-mgu74ccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74ccdf diff --git a/recipes/bioconductor-mgu74cprobe/meta.yaml b/recipes/bioconductor-mgu74cprobe/meta.yaml new file mode 100644 index 0000000000000..283f87bcf6166 --- /dev/null +++ b/recipes/bioconductor-mgu74cprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74cprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 186992992708f0071fd552ef92b9e25c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74C\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74cprobe/post-link.sh b/recipes/bioconductor-mgu74cprobe/post-link.sh new file mode 100644 index 0000000000000..4c8a42f8041f8 --- /dev/null +++ b/recipes/bioconductor-mgu74cprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74cprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74cprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cprobe/bioconductor-mgu74cprobe_2.18.0_src_all.tar.gz" +) +MD5="186992992708f0071fd552ef92b9e25c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74cprobe/pre-unlink.sh b/recipes/bioconductor-mgu74cprobe/pre-unlink.sh new file mode 100644 index 0000000000000..1166654ff52af --- /dev/null +++ b/recipes/bioconductor-mgu74cprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74cprobe diff --git a/recipes/bioconductor-mgu74cv2.db/meta.yaml b/recipes/bioconductor-mgu74cv2.db/meta.yaml new file mode 100644 index 0000000000000..1dba9f6847fc9 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgu74cv2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3f9ebd44f6dc4b23c009afa95afeb638 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome U74v2 annotation data (chip mgu74cv2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgu74cv2.db/post-link.sh b/recipes/bioconductor-mgu74cv2.db/post-link.sh new file mode 100644 index 0000000000000..9d7c8fa665efd --- /dev/null +++ b/recipes/bioconductor-mgu74cv2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74cv2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74cv2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2.db/bioconductor-mgu74cv2.db_3.2.3_src_all.tar.gz" +) +MD5="3f9ebd44f6dc4b23c009afa95afeb638" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74cv2.db/pre-unlink.sh b/recipes/bioconductor-mgu74cv2.db/pre-unlink.sh new file mode 100644 index 0000000000000..1d94b92478c2c --- /dev/null +++ b/recipes/bioconductor-mgu74cv2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74cv2.db diff --git a/recipes/bioconductor-mgu74cv2cdf/meta.yaml b/recipes/bioconductor-mgu74cv2cdf/meta.yaml new file mode 100644 index 0000000000000..703b915762597 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74cv2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9ef62b4b28f97770859db24393a07ed5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MG_U74Cv2.CDF file.' + diff --git a/recipes/bioconductor-mgu74cv2cdf/post-link.sh b/recipes/bioconductor-mgu74cv2cdf/post-link.sh new file mode 100644 index 0000000000000..fcd77d0612e80 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74cv2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74cv2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2cdf/bioconductor-mgu74cv2cdf_2.18.0_src_all.tar.gz" +) +MD5="9ef62b4b28f97770859db24393a07ed5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74cv2cdf/pre-unlink.sh b/recipes/bioconductor-mgu74cv2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..99d35f15a9cc6 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74cv2cdf diff --git a/recipes/bioconductor-mgu74cv2probe/meta.yaml b/recipes/bioconductor-mgu74cv2probe/meta.yaml new file mode 100644 index 0000000000000..660e327c3edd9 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mgu74cv2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0373496c817a1c1a153114047cfa7c5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MG-U74Cv2\_probe\_tab.' + diff --git a/recipes/bioconductor-mgu74cv2probe/post-link.sh b/recipes/bioconductor-mgu74cv2probe/post-link.sh new file mode 100644 index 0000000000000..78d7874916b66 --- /dev/null +++ b/recipes/bioconductor-mgu74cv2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgu74cv2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgu74cv2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mgu74cv2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgu74cv2probe/bioconductor-mgu74cv2probe_2.18.0_src_all.tar.gz" +) +MD5="0373496c817a1c1a153114047cfa7c5b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgu74cv2probe/pre-unlink.sh b/recipes/bioconductor-mgu74cv2probe/pre-unlink.sh new file mode 100644 index 0000000000000..a3b27aa90dcae --- /dev/null +++ b/recipes/bioconductor-mgu74cv2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgu74cv2probe diff --git a/recipes/bioconductor-mguatlas5k.db/meta.yaml b/recipes/bioconductor-mguatlas5k.db/meta.yaml new file mode 100644 index 0000000000000..5cb50746b57e8 --- /dev/null +++ b/recipes/bioconductor-mguatlas5k.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mguatlas5k.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 826093fe7228c08962aff36ad89af28e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Clontech BD Atlas Long Oligos Mouse 5K annotation data (chip mguatlas5k) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mguatlas5k.db/post-link.sh b/recipes/bioconductor-mguatlas5k.db/post-link.sh new file mode 100644 index 0000000000000..173e8ca8ae172 --- /dev/null +++ b/recipes/bioconductor-mguatlas5k.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mguatlas5k.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mguatlas5k.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mguatlas5k.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mguatlas5k.db/bioconductor-mguatlas5k.db_3.2.3_src_all.tar.gz" +) +MD5="826093fe7228c08962aff36ad89af28e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mguatlas5k.db/pre-unlink.sh b/recipes/bioconductor-mguatlas5k.db/pre-unlink.sh new file mode 100644 index 0000000000000..37cf0c4859b78 --- /dev/null +++ b/recipes/bioconductor-mguatlas5k.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mguatlas5k.db diff --git a/recipes/bioconductor-mgug4104a.db/meta.yaml b/recipes/bioconductor-mgug4104a.db/meta.yaml new file mode 100644 index 0000000000000..6322154f7a890 --- /dev/null +++ b/recipes/bioconductor-mgug4104a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgug4104a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7b1cef094a226257cd657ed8d61e9ef1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent annotation data (chip mgug4104a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgug4104a.db/post-link.sh b/recipes/bioconductor-mgug4104a.db/post-link.sh new file mode 100644 index 0000000000000..0c221ff3dfd7f --- /dev/null +++ b/recipes/bioconductor-mgug4104a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgug4104a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4104a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgug4104a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4104a.db/bioconductor-mgug4104a.db_3.2.3_src_all.tar.gz" +) +MD5="7b1cef094a226257cd657ed8d61e9ef1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgug4104a.db/pre-unlink.sh b/recipes/bioconductor-mgug4104a.db/pre-unlink.sh new file mode 100644 index 0000000000000..f684fb135db00 --- /dev/null +++ b/recipes/bioconductor-mgug4104a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgug4104a.db diff --git a/recipes/bioconductor-mgug4120a.db/meta.yaml b/recipes/bioconductor-mgug4120a.db/meta.yaml new file mode 100644 index 0000000000000..26dbe381760c1 --- /dev/null +++ b/recipes/bioconductor-mgug4120a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgug4120a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bb57e8b2efe3d038ec2a0ace0313a4e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent annotation data (chip mgug4120a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgug4120a.db/post-link.sh b/recipes/bioconductor-mgug4120a.db/post-link.sh new file mode 100644 index 0000000000000..b77cb2f742364 --- /dev/null +++ b/recipes/bioconductor-mgug4120a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgug4120a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4120a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgug4120a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4120a.db/bioconductor-mgug4120a.db_3.2.3_src_all.tar.gz" +) +MD5="bb57e8b2efe3d038ec2a0ace0313a4e7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgug4120a.db/pre-unlink.sh b/recipes/bioconductor-mgug4120a.db/pre-unlink.sh new file mode 100644 index 0000000000000..bf04f94cec34a --- /dev/null +++ b/recipes/bioconductor-mgug4120a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgug4120a.db diff --git a/recipes/bioconductor-mgug4121a.db/meta.yaml b/recipes/bioconductor-mgug4121a.db/meta.yaml new file mode 100644 index 0000000000000..c7de07c755351 --- /dev/null +++ b/recipes/bioconductor-mgug4121a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mgug4121a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6b5cc321d5175356c383b91e30e120b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Mouse annotation data (chip mgug4121a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mgug4121a.db/post-link.sh b/recipes/bioconductor-mgug4121a.db/post-link.sh new file mode 100644 index 0000000000000..e9d5fb12fbfe8 --- /dev/null +++ b/recipes/bioconductor-mgug4121a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mgug4121a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4121a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mgug4121a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mgug4121a.db/bioconductor-mgug4121a.db_3.2.3_src_all.tar.gz" +) +MD5="6b5cc321d5175356c383b91e30e120b7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mgug4121a.db/pre-unlink.sh b/recipes/bioconductor-mgug4121a.db/pre-unlink.sh new file mode 100644 index 0000000000000..19f73ab217f10 --- /dev/null +++ b/recipes/bioconductor-mgug4121a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mgug4121a.db diff --git a/recipes/bioconductor-mgug4122a.db/meta.yaml b/recipes/bioconductor-mgug4122a.db/meta.yaml index 9f8ad8f6be1e7..97cb40089f656 100644 --- a/recipes/bioconductor-mgug4122a.db/meta.yaml +++ b/recipes/bioconductor-mgug4122a.db/meta.yaml @@ -1,37 +1,43 @@ {% set version = "3.2.3" %} {% set name = "mgug4122a.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bd57e228a20744ed325b970ddd5ca731ca45e957c39d72eebcd7f2d4b0cc9574 + md5: 5fcdce909ac1c0ccbf06bf6411f6fe52 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories' - + summary: 'Agilent "Mouse Genome, Whole" annotation data (chip mgug4122a) assembled using data from public repositories' +extra: + parent_recipe: + name: bioconductor-mgug4122a.db + path: recipes/bioconductor-mgug4122a.db + version: 3.2.3 diff --git a/recipes/bioconductor-mgug4122a.db/post-link.sh b/recipes/bioconductor-mgug4122a.db/post-link.sh index 3d8878f2bb00e..5cda8d3fe83dc 100644 --- a/recipes/bioconductor-mgug4122a.db/post-link.sh +++ b/recipes/bioconductor-mgug4122a.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="mgug4122a.db_3.2.3.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mgug4122a.db_3.2.3.tar.gz" "https://bioarchive.galaxyproject.org/mgug4122a.db_3.2.3.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mgug4122a.db/bioconductor-mgug4122a.db_3.2.3_src_all.tar.gz" diff --git a/recipes/bioconductor-mi16cod.db/meta.yaml b/recipes/bioconductor-mi16cod.db/meta.yaml new file mode 100644 index 0000000000000..54991a513c612 --- /dev/null +++ b/recipes/bioconductor-mi16cod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "mi16cod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f3a8e6f45ce5c298c1b1c5b32bf2630c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Mouse Inflammation 16 Bioarray annotation data (chip mi16cod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mi16cod.db/post-link.sh b/recipes/bioconductor-mi16cod.db/post-link.sh new file mode 100644 index 0000000000000..03e21373676a1 --- /dev/null +++ b/recipes/bioconductor-mi16cod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mi16cod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mi16cod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/mi16cod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mi16cod.db/bioconductor-mi16cod.db_3.4.0_src_all.tar.gz" +) +MD5="f3a8e6f45ce5c298c1b1c5b32bf2630c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mi16cod.db/pre-unlink.sh b/recipes/bioconductor-mi16cod.db/pre-unlink.sh new file mode 100644 index 0000000000000..fed43f12980cb --- /dev/null +++ b/recipes/bioconductor-mi16cod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mi16cod.db diff --git a/recipes/bioconductor-michip/build.sh b/recipes/bioconductor-michip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-michip/build.sh +++ b/recipes/bioconductor-michip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-michip/meta.yaml b/recipes/bioconductor-michip/meta.yaml index f45f2768bc45b..95776537fb8ba 100644 --- a/recipes/bioconductor-michip/meta.yaml +++ b/recipes/bioconductor-michip/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "MiChip" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 69eb53f00ca96f769a54ba865d8b984179e7cb365a19b21b5adcf1dc73ca6594 + md5: b64b0ae539c74dcf5d71610ffce198a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.' + summary: 'This package takes the MiChip miRNA microarray .grp scanner output files and parses these out, providing summary and plotting functions to analyse MiChip hybridizations. A set of hybridizations is packaged into an ExpressionSet allowing it to be used by other BioConductor packages.' extra: identifiers: - biotools:michip - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-michip + path: recipes/bioconductor-michip + version: 1.34.0 + diff --git a/recipes/bioconductor-microbiome/build.sh b/recipes/bioconductor-microbiome/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-microbiome/build.sh +++ b/recipes/bioconductor-microbiome/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-microbiome/meta.yaml b/recipes/bioconductor-microbiome/meta.yaml index c7552d3f1e6e5..fd773cb792e8f 100644 --- a/recipes/bioconductor-microbiome/meta.yaml +++ b/recipes/bioconductor-microbiome/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.2" %} {% set name = "microbiome" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 59d98634f9b71ec447995e8f2bcb77d654dae598843e9c467e5f087135e7b8e0 + md5: faf9cbb6d7ae71b815ead3c8448cde2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, Cairo, knitcitations, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-base - r-dplyr - r-ggplot2 @@ -26,7 +28,7 @@ requirements: - r-tidyr - r-vegan run: - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-base - r-dplyr - r-ggplot2 @@ -37,8 +39,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Utilities for microbiome analysis.' - +extra: + parent_recipe: + name: bioconductor-microbiome + path: recipes/bioconductor-microbiome + version: 1.2.1 diff --git a/recipes/bioconductor-microrna/build.sh b/recipes/bioconductor-microrna/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-microrna/build.sh +++ b/recipes/bioconductor-microrna/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-microrna/meta.yaml b/recipes/bioconductor-microrna/meta.yaml index 402534456689d..229f8a5129c78 100644 --- a/recipes/bioconductor-microrna/meta.yaml +++ b/recipes/bioconductor-microrna/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "microRNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3a9b7411555aa850b571a082425ac3717485621e0b2fa0d83ced75cfe054c5a8 + md5: 2ee23e69a38f498c578d6721d97dc985 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base build: - {{ compiler('c') }} @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Different data resources for microRNAs and some functions for manipulating them.' extra: identifiers: - biotools:microrna - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-microrna + path: recipes/bioconductor-microrna + version: 1.38.0 + diff --git a/recipes/bioconductor-micrornaome/meta.yaml b/recipes/bioconductor-micrornaome/meta.yaml new file mode 100644 index 0000000000000..01b5708939cb8 --- /dev/null +++ b/recipes/bioconductor-micrornaome/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.4.0" %} +{% set name = "microRNAome" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bae32fb7fe64c2d23b0ac8d5d5574a1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides a SummarizedExperiment object of read counts for microRNAs across tissues, cell-types, and cancer cell-lines. The read count matrix was prepared and provided by the author of the study: Towards the human cellular microRNAome.' + diff --git a/recipes/bioconductor-micrornaome/post-link.sh b/recipes/bioconductor-micrornaome/post-link.sh new file mode 100644 index 0000000000000..a5169ee2ac333 --- /dev/null +++ b/recipes/bioconductor-micrornaome/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="microRNAome_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/microRNAome_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/microRNAome_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-micrornaome/bioconductor-micrornaome_1.4.0_src_all.tar.gz" +) +MD5="bae32fb7fe64c2d23b0ac8d5d5574a1a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-micrornaome/pre-unlink.sh b/recipes/bioconductor-micrornaome/pre-unlink.sh new file mode 100644 index 0000000000000..66ddca5fc647e --- /dev/null +++ b/recipes/bioconductor-micrornaome/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ microRNAome diff --git a/recipes/bioconductor-migsa/build.sh b/recipes/bioconductor-migsa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-migsa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-migsa/meta.yaml b/recipes/bioconductor-migsa/meta.yaml new file mode 100644 index 0000000000000..87409dc9776d6 --- /dev/null +++ b/recipes/bioconductor-migsa/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.6.0" %} +{% set name = "MIGSA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0db3f4f96d22c45fbc237fdeeb59aa5e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: breastCancerMAINZ, breastCancerNKI, breastCancerTRANSBIG, breastCancerUNT, breastCancerUPP, breastCancerVDX, mGSZ, pbcmc, MIGSAdata +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-data.table + - r-futile.logger + - r-ggdendro + - r-ggplot2 + - r-ismev + - r-matrixstats + - r-reshape2 + - r-rjsonio + - r-vegan + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-data.table + - r-futile.logger + - r-ggdendro + - r-ggplot2 + - r-ismev + - r-matrixstats + - r-reshape2 + - r-rjsonio + - r-vegan +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Massive and Integrative Gene Set Analysis. The MIGSA package allows to perform a massive and integrative gene set analysis over several expression and gene sets simultaneously. It provides a common gene expression analytic framework that grants a comprehensive and coherent analysis. Only a minimal user parameter setting is required to perform both singular and gene set enrichment analyses in an integrative manner by means of the best available methods, i.e. dEnricher and mGSZ respectively. The greatest strengths of this big omics data tool are the availability of several functions to explore, analyze and visualize its results in order to facilitate the data mining task over huge information sources. MIGSA package also provides several functions that allow to easily load the most updated gene sets from several repositories.' + diff --git a/recipes/bioconductor-migsadata/meta.yaml b/recipes/bioconductor-migsadata/meta.yaml new file mode 100644 index 0000000000000..5b30220f65294 --- /dev/null +++ b/recipes/bioconductor-migsadata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.6.0" %} +{% set name = "MIGSAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a9d6b8af543c349a1955dc93934b487b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'MIGSA vignette data. The MIGSAdata package provides several data objects needed by MIGSA package to correctly generate its vignette, and follow it step by step.' + diff --git a/recipes/bioconductor-migsadata/post-link.sh b/recipes/bioconductor-migsadata/post-link.sh new file mode 100644 index 0000000000000..23938e3617496 --- /dev/null +++ b/recipes/bioconductor-migsadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MIGSAdata_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MIGSAdata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/MIGSAdata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-migsadata/bioconductor-migsadata_1.6.0_src_all.tar.gz" +) +MD5="a9d6b8af543c349a1955dc93934b487b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-migsadata/pre-unlink.sh b/recipes/bioconductor-migsadata/pre-unlink.sh new file mode 100644 index 0000000000000..68d877b94e349 --- /dev/null +++ b/recipes/bioconductor-migsadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MIGSAdata diff --git a/recipes/bioconductor-mimager/build.sh b/recipes/bioconductor-mimager/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mimager/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mimager/meta.yaml b/recipes/bioconductor-mimager/meta.yaml new file mode 100644 index 0000000000000..0c06e3eb66f8b --- /dev/null +++ b/recipes/bioconductor-mimager/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "mimager" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 15abbaac41f80515ccbc4fda98e409a9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat, lintr, Matrix, abind, affydata, hgu95av2cdf, oligoData, pd.hugene.1.0.st.v1 +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - r-gtable + - r-scales + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - r-gtable + - r-scales +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Easily visualize and inspect microarrays for spatial artifacts.' + diff --git a/recipes/bioconductor-mimosa/build.sh b/recipes/bioconductor-mimosa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mimosa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mimosa/meta.yaml b/recipes/bioconductor-mimosa/meta.yaml new file mode 100644 index 0000000000000..4b76fecc1eb38 --- /dev/null +++ b/recipes/bioconductor-mimosa/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.20.0" %} +{% set name = "MIMOSA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a35da9493c017fdc67cdb503fec4ffb0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: parallel, knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-coda + - r-data.table + - r-formula + - r-ggplot2 + - r-mass + - r-mcmcpack + - r-modeest + - r-plyr + - r-pracma + - r-rcpp + - r-rcpparmadillo + - r-reshape + - r-scales + - r-testthat + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-coda + - r-data.table + - r-formula + - r-ggplot2 + - r-mass + - r-mcmcpack + - r-modeest + - r-plyr + - r-pracma + - r-rcpp + - r-rcpparmadillo + - r-reshape + - r-scales + - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Modeling count data using Dirichlet-multinomial and beta-binomial mixtures with applications to single-cell assays.' + diff --git a/recipes/bioconductor-mineica/build.sh b/recipes/bioconductor-mineica/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mineica/build.sh +++ b/recipes/bioconductor-mineica/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mineica/conda_build_config.yaml b/recipes/bioconductor-mineica/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mineica/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mineica/meta.yaml b/recipes/bioconductor-mineica/meta.yaml index a11a9243ae579..0c89b46c5febd 100644 --- a/recipes/bioconductor-mineica/meta.yaml +++ b/recipes/bioconductor-mineica/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "MineICA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e009aafcc3e787349413f1405e4d7efd00e0e9357910fdca01ea7b035753c9b3 + md5: 0580f82c0a418930e9246cacb625dc93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, GOstats, cluster, hgu133a.db, mclust, igraph, breastCancerMAINZ, breastCancerTRANSBIG, breastCancerUPP, breastCancerVDX requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-lumihumanall.db >=1.22.0,<1.24.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-cluster - r-colorspace @@ -46,17 +48,17 @@ requirements: - r-scales - r-xtable run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-lumihumanall.db >=1.22.0,<1.24.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-lumihumanall.db >=1.22.0,<1.23.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-cluster - r-colorspace @@ -77,10 +79,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The goal of MineICA is to perform Independent Component Analysis (ICA) on multiple transcriptome datasets, integrating additional data (e.g molecular, clinical and pathological). This Integrative ICA helps the biological interpretation of the components by studying their association with variables (e.g sample annotations) and gene sets, and enables the comparison of components from different datasets using correlation-based graph.' extra: identifiers: - biotools:mineica - doi:10.1155/2014/213656 + parent_recipe: + name: bioconductor-mineica + path: recipes/bioconductor-mineica + version: 1.20.0 + diff --git a/recipes/bioconductor-minet/build.sh b/recipes/bioconductor-minet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-minet/build.sh +++ b/recipes/bioconductor-minet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-minet/meta.yaml b/recipes/bioconductor-minet/meta.yaml index ff49d3c766fb4..68e2b5a5dc65b 100644 --- a/recipes/bioconductor-minet/meta.yaml +++ b/recipes/bioconductor-minet/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "3.38.0" %} +{% set version = "3.40.0" %} {% set name = "minet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f96653b88e780c232e1fa2baa67efe62e7a2642e0ffbe3cf77aef9239ca07e93 + md5: cfe31fbcec7dfc321436f468487dd842 build: number: 0 rpaths: @@ -31,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package implements various algorithms for inferring mutual information networks from data.' extra: identifiers: - biotools:minet - doi:10.1186/1471-2105-9-461 + parent_recipe: + name: bioconductor-minet + path: recipes/bioconductor-minet + version: 3.38.0 + diff --git a/recipes/bioconductor-minfi/build.sh b/recipes/bioconductor-minfi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-minfi/build.sh +++ b/recipes/bioconductor-minfi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-minfi/meta.yaml b/recipes/bioconductor-minfi/meta.yaml index ec36df4909fba..9bd56a0386347 100644 --- a/recipes/bioconductor-minfi/meta.yaml +++ b/recipes/bioconductor-minfi/meta.yaml @@ -1,42 +1,44 @@ -{% set version = "1.26.2" %} +{% set version = "1.28.0" %} {% set name = "minfi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e0567ac79a10eff553198943eed842a1000cefc18df03d30201a9bbdbf50d9ff + md5: 5db8544bddf740588efc96a00e7c1b7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: IlluminaHumanMethylation450kmanifest (>= 0.2.0), IlluminaHumanMethylation450kanno.ilmn12.hg19 (>= 0.2.1), minfiData (>= 0.18.0), minfiDataEPIC, FlowSorted.Blood.450k (>= 1.0.1), RUnit, digest, BiocStyle, knitr, rmarkdown, tools requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bumphunter >=1.22.0,<1.24.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-beanplot - r-data.table @@ -49,25 +51,25 @@ requirements: - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bumphunter >=1.22.0,<1.24.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-hdf5array >=1.8.1,<1.10.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bumphunter >=1.24.0,<1.25.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-beanplot - r-data.table @@ -83,9 +85,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to analyze & visualize Illumina Infinium methylation arrays.' extra: identifiers: - biotools:minfi + parent_recipe: + name: bioconductor-minfi + path: recipes/bioconductor-minfi + version: 1.26.2 + diff --git a/recipes/bioconductor-minfidata/meta.yaml b/recipes/bioconductor-minfidata/meta.yaml new file mode 100644 index 0000000000000..7606836242755 --- /dev/null +++ b/recipes/bioconductor-minfidata/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.28.0" %} +{% set name = "minfiData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40cafa6a33fdc318ced42d538a27b98d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Data from 6 samples across 2 groups from 450k methylation arrays.' + diff --git a/recipes/bioconductor-minfidata/post-link.sh b/recipes/bioconductor-minfidata/post-link.sh new file mode 100644 index 0000000000000..ce5ceda20246c --- /dev/null +++ b/recipes/bioconductor-minfidata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="minfiData_0.28.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minfiData_0.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/minfiData_0.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minfidata/bioconductor-minfidata_0.28.0_src_all.tar.gz" +) +MD5="40cafa6a33fdc318ced42d538a27b98d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-minfidata/pre-unlink.sh b/recipes/bioconductor-minfidata/pre-unlink.sh new file mode 100644 index 0000000000000..0da96d87dcd2c --- /dev/null +++ b/recipes/bioconductor-minfidata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ minfiData diff --git a/recipes/bioconductor-minfidataepic/meta.yaml b/recipes/bioconductor-minfidataepic/meta.yaml new file mode 100644 index 0000000000000..dd3c96c94c9c8 --- /dev/null +++ b/recipes/bioconductor-minfidataepic/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.8.0" %} +{% set name = "minfiDataEPIC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 92cb1d44c458f6d61d7893e7288a1589 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Data from 3 technical replicates of the cell line GM12878 from the EPIC methylation array.' + diff --git a/recipes/bioconductor-minfidataepic/post-link.sh b/recipes/bioconductor-minfidataepic/post-link.sh new file mode 100644 index 0000000000000..09f6fe0407137 --- /dev/null +++ b/recipes/bioconductor-minfidataepic/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="minfiDataEPIC_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minfiDataEPIC_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/minfiDataEPIC_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minfidataepic/bioconductor-minfidataepic_1.8.0_src_all.tar.gz" +) +MD5="92cb1d44c458f6d61d7893e7288a1589" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-minfidataepic/pre-unlink.sh b/recipes/bioconductor-minfidataepic/pre-unlink.sh new file mode 100644 index 0000000000000..7fff8b65d2789 --- /dev/null +++ b/recipes/bioconductor-minfidataepic/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ minfiDataEPIC diff --git a/recipes/bioconductor-minimumdistance/build.sh b/recipes/bioconductor-minimumdistance/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-minimumdistance/build.sh +++ b/recipes/bioconductor-minimumdistance/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-minimumdistance/conda_build_config.yaml b/recipes/bioconductor-minimumdistance/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-minimumdistance/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-minimumdistance/meta.yaml b/recipes/bioconductor-minimumdistance/meta.yaml index 2d199601fdeb9..0de5857ad22dc 100644 --- a/recipes/bioconductor-minimumdistance/meta.yaml +++ b/recipes/bioconductor-minimumdistance/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "MinimumDistance" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c14a2d2ccbc66010d589b8ee0b276917cd5e1ed653eb22a85acbac5c8835adb8 + md5: 94c0e99960d55c5416e88f76a65bc021 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: human610quadv1bCrlmm (>= 1.0.3), BSgenome.Hsapiens.UCSC.hg18, BSgenome.Hsapiens.UCSC.hg19, SNPchip, RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-vanillaice >=1.42.4,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vanillaice >=1.44.0,<1.45.0' - r-base - r-data.table - r-ff @@ -35,16 +37,16 @@ requirements: - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-vanillaice >=1.42.4,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vanillaice >=1.44.0,<1.45.0' - r-base - r-data.table - r-ff @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of de novo copy number variants in trios from high-dimensional genotyping platforms.' extra: identifiers: - biotools:minimumdistance - doi:10.1186/1471-2105-13-330 + parent_recipe: + name: bioconductor-minimumdistance + path: recipes/bioconductor-minimumdistance + version: 1.24.1 + diff --git a/recipes/bioconductor-minionsummarydata/meta.yaml b/recipes/bioconductor-minionsummarydata/meta.yaml new file mode 100644 index 0000000000000..531cbdd60deda --- /dev/null +++ b/recipes/bioconductor-minionsummarydata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "minionSummaryData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4e3db62e383ae1e28af148fadaf23a40 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Summarised MinION sequencing data for Salmonella Typhi published by Ashton et al. in 2015. Three replicate runs are each provided as Fast5Summary objects.' + diff --git a/recipes/bioconductor-minionsummarydata/post-link.sh b/recipes/bioconductor-minionsummarydata/post-link.sh new file mode 100644 index 0000000000000..55c4b8fb3b46a --- /dev/null +++ b/recipes/bioconductor-minionsummarydata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="minionSummaryData_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/minionSummaryData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/minionSummaryData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-minionsummarydata/bioconductor-minionsummarydata_1.12.0_src_all.tar.gz" +) +MD5="4e3db62e383ae1e28af148fadaf23a40" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-minionsummarydata/pre-unlink.sh b/recipes/bioconductor-minionsummarydata/pre-unlink.sh new file mode 100644 index 0000000000000..2ae1628e3256a --- /dev/null +++ b/recipes/bioconductor-minionsummarydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ minionSummaryData diff --git a/recipes/bioconductor-mipp/build.sh b/recipes/bioconductor-mipp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mipp/build.sh +++ b/recipes/bioconductor-mipp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mipp/meta.yaml b/recipes/bioconductor-mipp/meta.yaml index b16fd404c7d04..aadf3a03ca62b 100644 --- a/recipes/bioconductor-mipp/meta.yaml +++ b/recipes/bioconductor-mipp/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "MiPP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 450c675a8ef7acc06876ae79e56b87e67f8dbdbfc22f7e3d44f3cb40e1de8f7c + md5: 44dbca699e0c65714e8fa3c1375205c3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 - r-mass @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package finds optimal sets of genes that seperate samples into two or more classes.' extra: identifiers: - biotools:mipp - doi:10.1093/bioinformatics/bti1020 + parent_recipe: + name: bioconductor-mipp + path: recipes/bioconductor-mipp + version: 1.52.0 + diff --git a/recipes/bioconductor-mira/build.sh b/recipes/bioconductor-mira/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mira/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mira/meta.yaml b/recipes/bioconductor-mira/meta.yaml new file mode 100644 index 0000000000000..e017ad3664d4e --- /dev/null +++ b/recipes/bioconductor-mira/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.4.0" %} +{% set name = "MIRA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 02bb707ed5364f77a096150ec6735ae0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, parallel, testthat, BiocStyle, rmarkdown, AnnotationHub, LOLA +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-ggplot2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MIRA measures the degree of "dip" in methylation level surrounding a regulatory site of interest, such as a transcription factor binding site, for instances of that type of site across the genome which can then be used to infer regulatory activity.' + diff --git a/recipes/bioconductor-mirage/build.sh b/recipes/bioconductor-mirage/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirage/build.sh +++ b/recipes/bioconductor-mirage/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirage/meta.yaml b/recipes/bioconductor-mirage/meta.yaml index 79478da4951e0..f0b1eccb07a9a 100644 --- a/recipes/bioconductor-mirage/meta.yaml +++ b/recipes/bioconductor-mirage/meta.yaml @@ -1,41 +1,50 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "MiRaGE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 661e3447c487e305d9f645aebfa69b166082c3c87ed38b17995c4f8473c45900 + md5: cee716133c5fdbfb9d5019da05677e3a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: seqinr (>= 3.0.7), biomaRt (>= 2.19.1), GenomicFeatures (>= 1.15.4), Biostrings (>= 2.31.3), BSgenome.Hsapiens.UCSC.hg19, BSgenome.Mmusculus.UCSC.mm10, miRNATarget, humanStemCell, IRanges, GenomicRanges (>= 1.8.3), BSgenome, beadarrayExampleData requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'The package contains functions for inferece of target gene regulation by miRNA, based on only target gene expression profile.' extra: identifiers: - biotools:mirage + parent_recipe: + name: bioconductor-mirage + path: recipes/bioconductor-mirage + version: 1.22.0 + diff --git a/recipes/bioconductor-mirbase.db/meta.yaml b/recipes/bioconductor-mirbase.db/meta.yaml new file mode 100644 index 0000000000000..e8ec09b37e9ad --- /dev/null +++ b/recipes/bioconductor-mirbase.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "mirbase.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 316bc12cee8c2dd9240b7fc30cd1619e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'miRBase: the microRNA database assembled using data from miRBase (http://www.mirbase.org/).' + diff --git a/recipes/bioconductor-mirbase.db/post-link.sh b/recipes/bioconductor-mirbase.db/post-link.sh new file mode 100644 index 0000000000000..5ce988916ffd8 --- /dev/null +++ b/recipes/bioconductor-mirbase.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mirbase.db_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirbase.db_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/mirbase.db_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirbase.db/bioconductor-mirbase.db_1.2.0_src_all.tar.gz" +) +MD5="316bc12cee8c2dd9240b7fc30cd1619e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirbase.db/pre-unlink.sh b/recipes/bioconductor-mirbase.db/pre-unlink.sh new file mode 100644 index 0000000000000..7c051e2ccb74e --- /dev/null +++ b/recipes/bioconductor-mirbase.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mirbase.db diff --git a/recipes/bioconductor-mirbaseconverter/build.sh b/recipes/bioconductor-mirbaseconverter/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirbaseconverter/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirbaseconverter/meta.yaml b/recipes/bioconductor-mirbaseconverter/meta.yaml new file mode 100644 index 0000000000000..687cd5ff7311e --- /dev/null +++ b/recipes/bioconductor-mirbaseconverter/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "miRBaseConverter" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4333ef90ec81266289f19a0857a614a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, RUnit, knitr, rtracklayer, utils +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A comprehensive tool for converting and retrieving the miRNA Name, Accession, Sequence, Version, History and Family information in different miRBase versions. It can process a huge number of miRNAs in a short time without other depends.' + diff --git a/recipes/bioconductor-mirbaseversions.db/meta.yaml b/recipes/bioconductor-mirbaseversions.db/meta.yaml index d5c28935320ac..49eb5c6abd5cb 100644 --- a/recipes/bioconductor-mirbaseversions.db/meta.yaml +++ b/recipes/bioconductor-mirbaseversions.db/meta.yaml @@ -1,30 +1,32 @@ {% set version = "1.1.0" %} {% set name = "miRBaseVersions.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1cc65f746c705d061aa6f5172563389d5abe412dd446c5cd1b456afa1218c026 + md5: 9944ab7a474f84a40100c56298f9cb77 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, annotate requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - r-gtools - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - r-gtools @@ -34,8 +36,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Annotation package containing all available miRNA names from 22 versions (data from http://www.mirbase.org/).' - +extra: + parent_recipe: + name: bioconductor-mirbaseversions.db + path: recipes/bioconductor-mirbaseversions.db + version: 1.1.0 diff --git a/recipes/bioconductor-mirbaseversions.db/post-link.sh b/recipes/bioconductor-mirbaseversions.db/post-link.sh index df3d08cff07d2..f32dff43924f9 100644 --- a/recipes/bioconductor-mirbaseversions.db/post-link.sh +++ b/recipes/bioconductor-mirbaseversions.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="miRBaseVersions.db_1.1.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/miRBaseVersions.db_1.1.0.tar.gz" "https://bioarchive.galaxyproject.org/miRBaseVersions.db_1.1.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirbaseversions.db/bioconductor-mirbaseversions.db_1.1.0_src_all.tar.gz" ) MD5="9944ab7a474f84a40100c56298f9cb77" diff --git a/recipes/bioconductor-mircomp/build.sh b/recipes/bioconductor-mircomp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mircomp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mircomp/meta.yaml b/recipes/bioconductor-mircomp/meta.yaml new file mode 100644 index 0000000000000..1d8f4b5109300 --- /dev/null +++ b/recipes/bioconductor-mircomp/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.12.0" %} +{% set name = "miRcomp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 776c9e34a4c9d963f2588068c8438170 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics, shiny +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mircompdata >=1.12.0,<1.13.0' + - r-base + - r-kernsmooth + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-mircompdata >=1.12.0,<1.13.0' + - r-base + - r-kernsmooth +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'Based on a large miRNA dilution study, this package provides tools to read in the raw amplification data and use these data to assess the performance of methods that estimate expression from the amplification curves.' + diff --git a/recipes/bioconductor-mircompdata/meta.yaml b/recipes/bioconductor-mircompdata/meta.yaml new file mode 100644 index 0000000000000..64b451416c3cb --- /dev/null +++ b/recipes/bioconductor-mircompdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.12.0" %} +{% set name = "miRcompData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2b86aeb9ff05f956dbaa0f7dd132cbc4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'Raw amplification data from a large microRNA mixture / dilution study. These data are used by the miRcomp package to assess the performance of methods that estimate expression from the amplification curves.' + diff --git a/recipes/bioconductor-mircompdata/post-link.sh b/recipes/bioconductor-mircompdata/post-link.sh new file mode 100644 index 0000000000000..8fa5ee554c358 --- /dev/null +++ b/recipes/bioconductor-mircompdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="miRcompData_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/miRcompData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/miRcompData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mircompdata/bioconductor-mircompdata_1.12.0_src_all.tar.gz" +) +MD5="2b86aeb9ff05f956dbaa0f7dd132cbc4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mircompdata/pre-unlink.sh b/recipes/bioconductor-mircompdata/pre-unlink.sh new file mode 100644 index 0000000000000..36321cfb31b38 --- /dev/null +++ b/recipes/bioconductor-mircompdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ miRcompData diff --git a/recipes/bioconductor-mirintegrator/build.sh b/recipes/bioconductor-mirintegrator/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirintegrator/build.sh +++ b/recipes/bioconductor-mirintegrator/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirintegrator/meta.yaml b/recipes/bioconductor-mirintegrator/meta.yaml index 9578399f6a617..aa899e50b4945 100644 --- a/recipes/bioconductor-mirintegrator/meta.yaml +++ b/recipes/bioconductor-mirintegrator/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "mirIntegrator" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 69f2b51176831ce0ce2640c98c26d17520eb0c9d11838fef666218d35e8bf11b + md5: c89d486120b4e814ee43c8268a64e7d8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rontotools >=2.8.0,<2.10.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rontotools >=2.10.0,<2.11.0' - r-base - r-ggplot2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rontotools >=2.8.0,<2.10.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rontotools >=2.10.0,<2.11.0' - r-base - r-ggplot2 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'Tools for augmenting signaling pathways to perform pathway analysis of microRNA and mRNA expression levels.' extra: identifiers: - biotools:mirintegrator - doi:10.1038/srep29251 + parent_recipe: + name: bioconductor-mirintegrator + path: recipes/bioconductor-mirintegrator + version: 1.10.0 + diff --git a/recipes/bioconductor-mirlab/build.sh b/recipes/bioconductor-mirlab/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirlab/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirlab/meta.yaml b/recipes/bioconductor-mirlab/meta.yaml new file mode 100644 index 0000000000000..58d4f2db1e5e1 --- /dev/null +++ b/recipes/bioconductor-mirlab/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.12.0" %} +{% set name = "miRLAB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0ff8f05e5b21897eb8a29bf4f4b93ea9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr,BiocGenerics, AnnotationDbi,RUnit +requirements: + host: + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-ctc >=1.56.0,<1.57.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-roleswitch >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - r-base + - r-dplyr + - r-energy + - r-entropy + - r-glmnet + - r-gplots + - r-heatmap.plus + - r-hmisc + - r-httr + - r-invariantcausalprediction + - r-pcalg + - r-rcurl + - r-stringr + run: + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-ctc >=1.56.0,<1.57.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-roleswitch >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - r-base + - r-dplyr + - r-energy + - r-entropy + - r-glmnet + - r-gplots + - r-heatmap.plus + - r-hmisc + - r-httr + - r-invariantcausalprediction + - r-pcalg + - r-rcurl + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.' + diff --git a/recipes/bioconductor-mirmine/build.sh b/recipes/bioconductor-mirmine/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirmine/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirmine/meta.yaml b/recipes/bioconductor-mirmine/meta.yaml new file mode 100644 index 0000000000000..dc58d6835d768 --- /dev/null +++ b/recipes/bioconductor-mirmine/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "miRmine" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2936f1b79cedb5ec7b30eda3374a3b1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, DESeq2 +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'miRmine database is a collection of expression profiles from different publicly available miRNA-seq datasets, Panwar et al (2017) miRmine: A Database of Human miRNA Expression, prepared with this data package as RangedSummarizedExperiment.' + diff --git a/recipes/bioconductor-mirna102xgaincdf/meta.yaml b/recipes/bioconductor-mirna102xgaincdf/meta.yaml new file mode 100644 index 0000000000000..d9f6796e420db --- /dev/null +++ b/recipes/bioconductor-mirna102xgaincdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mirna102xgaincdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9091a45c2ac15c2de0263743ab334f97 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the miRNA-1_0_2Xgain.CDF file.' + diff --git a/recipes/bioconductor-mirna102xgaincdf/post-link.sh b/recipes/bioconductor-mirna102xgaincdf/post-link.sh new file mode 100644 index 0000000000000..9c75a47fbcade --- /dev/null +++ b/recipes/bioconductor-mirna102xgaincdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mirna102xgaincdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna102xgaincdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mirna102xgaincdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna102xgaincdf/bioconductor-mirna102xgaincdf_2.18.0_src_all.tar.gz" +) +MD5="9091a45c2ac15c2de0263743ab334f97" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirna102xgaincdf/pre-unlink.sh b/recipes/bioconductor-mirna102xgaincdf/pre-unlink.sh new file mode 100644 index 0000000000000..beee70cd2998e --- /dev/null +++ b/recipes/bioconductor-mirna102xgaincdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mirna102xgaincdf diff --git a/recipes/bioconductor-mirna10cdf/meta.yaml b/recipes/bioconductor-mirna10cdf/meta.yaml new file mode 100644 index 0000000000000..e1fa03d3d447d --- /dev/null +++ b/recipes/bioconductor-mirna10cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mirna10cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 814da2a2e298e132f4db0b2e8ab814be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the miRNA-1_0.CDF file.' + diff --git a/recipes/bioconductor-mirna10cdf/post-link.sh b/recipes/bioconductor-mirna10cdf/post-link.sh new file mode 100644 index 0000000000000..8d9e0e7c09aa0 --- /dev/null +++ b/recipes/bioconductor-mirna10cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mirna10cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna10cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mirna10cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna10cdf/bioconductor-mirna10cdf_2.18.0_src_all.tar.gz" +) +MD5="814da2a2e298e132f4db0b2e8ab814be" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirna10cdf/pre-unlink.sh b/recipes/bioconductor-mirna10cdf/pre-unlink.sh new file mode 100644 index 0000000000000..f90b09376f239 --- /dev/null +++ b/recipes/bioconductor-mirna10cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mirna10cdf diff --git a/recipes/bioconductor-mirna10probe/meta.yaml b/recipes/bioconductor-mirna10probe/meta.yaml new file mode 100644 index 0000000000000..34b2628d554fd --- /dev/null +++ b/recipes/bioconductor-mirna10probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mirna10probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8bfa6cdfeee1c563b4881214bd5d4ce1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was miRNA-1\_0\_probe\_tab.' + diff --git a/recipes/bioconductor-mirna10probe/post-link.sh b/recipes/bioconductor-mirna10probe/post-link.sh new file mode 100644 index 0000000000000..b03f1e170b613 --- /dev/null +++ b/recipes/bioconductor-mirna10probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mirna10probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna10probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mirna10probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna10probe/bioconductor-mirna10probe_2.18.0_src_all.tar.gz" +) +MD5="8bfa6cdfeee1c563b4881214bd5d4ce1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirna10probe/pre-unlink.sh b/recipes/bioconductor-mirna10probe/pre-unlink.sh new file mode 100644 index 0000000000000..46f1cd5c40798 --- /dev/null +++ b/recipes/bioconductor-mirna10probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mirna10probe diff --git a/recipes/bioconductor-mirna20cdf/meta.yaml b/recipes/bioconductor-mirna20cdf/meta.yaml new file mode 100644 index 0000000000000..29c93823b7725 --- /dev/null +++ b/recipes/bioconductor-mirna20cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mirna20cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 56f7807673ff108427ae7f6bdf85ae1c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the miRNA-2_0.cdf file.' + diff --git a/recipes/bioconductor-mirna20cdf/post-link.sh b/recipes/bioconductor-mirna20cdf/post-link.sh new file mode 100644 index 0000000000000..0fc5c0a174ec0 --- /dev/null +++ b/recipes/bioconductor-mirna20cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mirna20cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mirna20cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mirna20cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirna20cdf/bioconductor-mirna20cdf_2.18.0_src_all.tar.gz" +) +MD5="56f7807673ff108427ae7f6bdf85ae1c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirna20cdf/pre-unlink.sh b/recipes/bioconductor-mirna20cdf/pre-unlink.sh new file mode 100644 index 0000000000000..352f082d49a5f --- /dev/null +++ b/recipes/bioconductor-mirna20cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mirna20cdf diff --git a/recipes/bioconductor-mirnameconverter/build.sh b/recipes/bioconductor-mirnameconverter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirnameconverter/build.sh +++ b/recipes/bioconductor-mirnameconverter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirnameconverter/meta.yaml b/recipes/bioconductor-mirnameconverter/meta.yaml index 3a0529f45cf85..2daa44a0437d3 100644 --- a/recipes/bioconductor-mirnameconverter/meta.yaml +++ b/recipes/bioconductor-mirnameconverter/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "miRNAmeConverter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 30ad6cc9cc62c47ddfc87f0888b9c0de72f0a1ca48442a61da957967c276fa82 + md5: fe9206b632ea3f12bd7d4d20e7d65db6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: methods, testthat, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi - r-reshape2 run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirbaseversions.db >=1.1.0,<1.3.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirbaseversions.db >=1.1.0,<1.2.0' - r-base - r-dbi - r-reshape2 @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Translating mature miRNA names to different miRBase versions, sequence retrieval, checking names for validity and detecting miRBase version of a given set of names (data from http://www.mirbase.org/).' extra: identifiers: - biotools:mirnameconverter + parent_recipe: + name: bioconductor-mirnameconverter + path: recipes/bioconductor-mirnameconverter + version: 1.8.0 + diff --git a/recipes/bioconductor-mirnapath/build.sh b/recipes/bioconductor-mirnapath/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirnapath/build.sh +++ b/recipes/bioconductor-mirnapath/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirnapath/meta.yaml b/recipes/bioconductor-mirnapath/meta.yaml index f73457de51ea0..f4aa2c6204f77 100644 --- a/recipes/bioconductor-mirnapath/meta.yaml +++ b/recipes/bioconductor-mirnapath/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "miRNApath" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 67b80c37e539794715f2d5a2052555a5aa61f1bdc214286f122ff6bf01135b73 + md5: a7abdc36034d7ef47f5946a42bf72ff6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,9 +26,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2.1 summary: 'This package provides pathway enrichment techniques for miRNA expression data. Specifically, the set of methods handles the many-to-many relationship between miRNAs and the multiple genes they are predicted to target (and thus affect.) It also handles the gene-to-pathway relationships separately. Both steps are designed to preserve the additive effects of miRNAs on genes, many miRNAs affecting one gene, one miRNA affecting multiple genes, or many miRNAs affecting many genes.' extra: identifiers: - biotools:mirnapath + parent_recipe: + name: bioconductor-mirnapath + path: recipes/bioconductor-mirnapath + version: 1.40.0 + diff --git a/recipes/bioconductor-mirnatap.db/meta.yaml b/recipes/bioconductor-mirnatap.db/meta.yaml index 92b1ff74a75a3..665720bb1672c 100644 --- a/recipes/bioconductor-mirnatap.db/meta.yaml +++ b/recipes/bioconductor-mirnatap.db/meta.yaml @@ -1,31 +1,32 @@ {% set version = "0.99.10" %} {% set name = "miRNAtap.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 43e735987bae9aa68b6e7544c5d1d87ebf7edcc075427114508eb8b47c7d91c8 + md5: 48010280b68d6f1ddbff3b374132ce0a build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirnatap >=1.14.0,<1.16.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirnatap >=1.16.0,<1.17.0' - r-base - r-dbi - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirnatap >=1.14.0,<1.16.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirnatap >=1.16.0,<1.17.0' - r-base - r-dbi - r-rsqlite @@ -34,8 +35,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: GPL-2 summary: 'This package holds the database for miRNAtap.' - +extra: + parent_recipe: + name: bioconductor-mirnatap.db + path: recipes/bioconductor-mirnatap.db + version: 0.99.10 diff --git a/recipes/bioconductor-mirnatap.db/post-link.sh b/recipes/bioconductor-mirnatap.db/post-link.sh index 645cf3dbbd1af..d36d6707719bc 100644 --- a/recipes/bioconductor-mirnatap.db/post-link.sh +++ b/recipes/bioconductor-mirnatap.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="miRNAtap.db_0.99.10.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/miRNAtap.db_0.99.10.tar.gz" "https://bioarchive.galaxyproject.org/miRNAtap.db_0.99.10.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-mirnatap.db/bioconductor-mirnatap.db_0.99.10_src_all.tar.gz" diff --git a/recipes/bioconductor-mirnatap/build.sh b/recipes/bioconductor-mirnatap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirnatap/build.sh +++ b/recipes/bioconductor-mirnatap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirnatap/meta.yaml b/recipes/bioconductor-mirnatap/meta.yaml index f21e0a79d998d..61ff7b16f064a 100644 --- a/recipes/bioconductor-mirnatap/meta.yaml +++ b/recipes/bioconductor-mirnatap/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "miRNAtap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cf5dbfa8557d27d2ccd51953f14457a394d0af6e92dd577097e10ccbb70a648d + md5: a56e2fa7cabbdeba36042c08fab11890 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: topGO, org.Hs.eg.db, miRNAtap.db, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - r-plyr @@ -26,7 +28,7 @@ requirements: - r-sqldf - r-stringr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - r-plyr @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package facilitates implementation of workflows requiring miRNA predictions, it allows to integrate ranked miRNA target predictions from multiple sources available online and aggregate them with various methods which improves quality of predictions above any of the single sources. Currently predictions are available for Homo sapiens, Mus musculus and Rattus norvegicus (the last one through homology translation).' extra: identifiers: - biotools:mirnatap - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mirnatap + path: recipes/bioconductor-mirnatap + version: 1.14.0 + diff --git a/recipes/bioconductor-mirnatarget/meta.yaml b/recipes/bioconductor-mirnatarget/meta.yaml new file mode 100644 index 0000000000000..79661ab1d6df8 --- /dev/null +++ b/recipes/bioconductor-mirnatarget/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "miRNATarget" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ccb859ec474b6235e9d5deb41c955dda +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'gene target tabale of miRNA for human/mouse used for MiRaGE package' + diff --git a/recipes/bioconductor-mirnatarget/post-link.sh b/recipes/bioconductor-mirnatarget/post-link.sh new file mode 100644 index 0000000000000..f32cfd16b0c1b --- /dev/null +++ b/recipes/bioconductor-mirnatarget/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="miRNATarget_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/miRNATarget_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/miRNATarget_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mirnatarget/bioconductor-mirnatarget_1.20.0_src_all.tar.gz" +) +MD5="ccb859ec474b6235e9d5deb41c955dda" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mirnatarget/pre-unlink.sh b/recipes/bioconductor-mirnatarget/pre-unlink.sh new file mode 100644 index 0000000000000..2452bc6494930 --- /dev/null +++ b/recipes/bioconductor-mirnatarget/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ miRNATarget diff --git a/recipes/bioconductor-mirsm/build.sh b/recipes/bioconductor-mirsm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirsm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirsm/meta.yaml b/recipes/bioconductor-mirsm/meta.yaml new file mode 100644 index 0000000000000..bcbc13eb3f5f0 --- /dev/null +++ b/recipes/bioconductor-mirsm/meta.yaml @@ -0,0 +1,82 @@ +{% set version = "1.0.0" %} +{% set name = "miRSM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3a0717a35ca8d1c1edde44aaee7a27c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db +requirements: + host: + - 'bioconductor-bicare >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fabia >=2.28.0,<2.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-ibbig >=1.26.0,<1.27.0' + - 'bioconductor-mirsponge >=1.8.0,<1.9.0' + - 'bioconductor-rqubic >=1.28.0,<1.29.0' + - 'bioconductor-runibic >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bibitr + - r-biclust + - r-dynamictreecut + - r-flashclust + - r-gfa + - r-igraph + - r-isa2 + - r-linkcomm + - r-mcl + - r-nmf + - r-pma + - r-rcpp + - r-s4vd + - r-wgcna + run: + - 'bioconductor-bicare >=1.40.0,<1.41.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fabia >=2.28.0,<2.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-ibbig >=1.26.0,<1.27.0' + - 'bioconductor-mirsponge >=1.8.0,<1.9.0' + - 'bioconductor-rqubic >=1.28.0,<1.29.0' + - 'bioconductor-runibic >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bibitr + - r-biclust + - r-dynamictreecut + - r-flashclust + - r-gfa + - r-igraph + - r-isa2 + - r-linkcomm + - r-mcl + - r-nmf + - r-pma + - r-rcpp + - r-s4vd + - r-wgcna + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The package aims to identify miRNA sponge modules by integrating expression data and miRNA-target binding information. It provides several functions to study miRNA sponge modules, including popular methods for inferring gene modules (candidate miRNA sponge modules), and a function to identify miRNA sponge modules, as well as a function to conduct functional analysis of miRNA sponge modules.' + diff --git a/recipes/bioconductor-mirsponge/build.sh b/recipes/bioconductor-mirsponge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mirsponge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirsponge/meta.yaml b/recipes/bioconductor-mirsponge/meta.yaml new file mode 100644 index 0000000000000..190bc851a3d6c --- /dev/null +++ b/recipes/bioconductor-mirsponge/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.8.0" %} +{% set name = "miRsponge" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 559435233adf8708b41cebf0fbb786e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, testthat, org.Hs.eg.db +requirements: + host: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - r-base + - r-corpcor + - r-igraph + - r-linkcomm + - r-mcl + - r-rcpp + - r-survival + - r-varhandle + run: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-reactomepa >=1.26.0,<1.27.0' + - r-base + - r-corpcor + - r-igraph + - r-linkcomm + - r-mcl + - r-rcpp + - r-survival + - r-varhandle + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides several functions to study miRNA sponge (also called ceRNA or miRNA decoy), including popular methods for identifying miRNA sponge interactions, and the integrative method to integrate miRNA sponge interactions from different methods, as well as the functions to validate miRNA sponge interactions, and infer miRNA sponge modules, conduct enrichment analysis of modules, and conduct survival analysis of modules.' + diff --git a/recipes/bioconductor-mirsynergy/build.sh b/recipes/bioconductor-mirsynergy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mirsynergy/build.sh +++ b/recipes/bioconductor-mirsynergy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mirsynergy/meta.yaml b/recipes/bioconductor-mirsynergy/meta.yaml index 3ef6b70625724..084d3d8cfab10 100644 --- a/recipes/bioconductor-mirsynergy/meta.yaml +++ b/recipes/bioconductor-mirsynergy/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Mirsynergy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f33a4dda5b24aeb2b6c3d391df0722c5a4faee12f342848d94b2207626d13df9 + md5: 59cb823d731e6970bc39bbee925bb6f3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: glmnet, RUnit, BiocGenerics, knitr requirements: host: - r-base @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Detect synergistic miRNA regulatory modules by overlapping neighbourhood expansion.' extra: identifiers: - biotools:mirsynergy + parent_recipe: + name: bioconductor-mirsynergy + path: recipes/bioconductor-mirsynergy + version: 1.16.0 + diff --git a/recipes/bioconductor-missmethyl/build.sh b/recipes/bioconductor-missmethyl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-missmethyl/build.sh +++ b/recipes/bioconductor-missmethyl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-missmethyl/meta.yaml b/recipes/bioconductor-missmethyl/meta.yaml index 3da59f67e8313..cc1174d6ce723 100644 --- a/recipes/bioconductor-missmethyl/meta.yaml +++ b/recipes/bioconductor-missmethyl/meta.yaml @@ -1,49 +1,51 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "missMethyl" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3ac149ded3ef2eb2b1cbdec20706e11dfb2d45ef2eb3201dcd8f6570b0659afc + md5: d18a07d4783273dabcefecbb86ceee77 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: minfiData, BiocStyle, knitr, rmarkdown, edgeR, tweeDEseqCountData requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.5.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-biasedurn - r-ruv - r-statmod - r-stringr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' - - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.5.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b4.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' - r-base - r-biasedurn - r-ruv @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Normalisation and testing for differential variability and differential methylation for data from Illumina''s Infinium HumanMethylation450 array. The normalisation procedure is subset-quantile within-array normalisation (SWAN), which allows Infinium I and II type probes on a single array to be normalised together. The test for differential variability is based on an empirical Bayes version of Levene''s test. Differential methylation testing is performed using RUV, which can adjust for systematic errors of unknown origin in high-dimensional data by using negative control probes. Gene ontology analysis is performed by taking into account the number of probes per gene on the array.' extra: identifiers: - biotools:missmethyl + parent_recipe: + name: bioconductor-missmethyl + path: recipes/bioconductor-missmethyl + version: 1.14.0 + diff --git a/recipes/bioconductor-missrows/build.sh b/recipes/bioconductor-missrows/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-missrows/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-missrows/meta.yaml b/recipes/bioconductor-missrows/meta.yaml new file mode 100644 index 0000000000000..4cad6bee28a77 --- /dev/null +++ b/recipes/bioconductor-missrows/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "missRows" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ffdf5f3c103e7749bacded4b44aa7762 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gtools + - r-plyr + run: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - r-gtools + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The missRows package implements the MI-MFA method to deal with missing individuals (''biological units'') in multi-omics data integration. The MI-MFA method generates multiple imputed datasets from a Multiple Factor Analysis model, then the yield results are combined in a single consensus solution. The package provides functions for estimating coordinates of individuals and variables, imputing missing individuals, and various diagnostic plots to inspect the pattern of missingness and visualize the uncertainty due to missing values.' + diff --git a/recipes/bioconductor-mitoode/build.sh b/recipes/bioconductor-mitoode/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mitoode/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mitoode/meta.yaml b/recipes/bioconductor-mitoode/meta.yaml new file mode 100644 index 0000000000000..f0edd2e70633f --- /dev/null +++ b/recipes/bioconductor-mitoode/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.20.0" %} +{% set name = "mitoODE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4c6d2041e91f3a5d445ebacc7fdd5178 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# SystemRequirements: +requirements: + host: + - 'bioconductor-mitoodedata >=1.18.0,<1.19.0' + - r-base + - r-kernsmooth + - r-mass + - r-minpack.lm + run: + - 'bioconductor-mitoodedata >=1.18.0,<1.19.0' + - r-base + - r-kernsmooth + - r-mass + - r-minpack.lm + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'The package contains the methods to fit a cell-cycle model on cell count data and the code to reproduce the results shown in our paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" by Pau, G., Walter, T., Neumann, B., Heriche, J.-K., Ellenberg, J., & Huber, W., BMC Bioinformatics (2013), 14(1), 308. doi:10.1186/1471-2105-14-308' + diff --git a/recipes/bioconductor-mitoodedata/meta.yaml b/recipes/bioconductor-mitoodedata/meta.yaml new file mode 100644 index 0000000000000..e193b03e3dfb8 --- /dev/null +++ b/recipes/bioconductor-mitoodedata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "mitoODEdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2b4cf1081b1509c750a63a16a9ec3fc9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# SystemRequirements: +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package contains the experimental data (assay annotation, siRNA annotation, time-lapse cell counts) associated to the paper "Dynamical modelling of phenotypes in a genome-wide RNAi live-cell imaging assay" (submitted). The data ultimately come from the Mitocheck assay reported in "Phenotypic profiling of the human genome by time-lapse microscopy reveals cell division genes" (Neumann, Walter et al, Nature 2010).' + diff --git a/recipes/bioconductor-mitoodedata/post-link.sh b/recipes/bioconductor-mitoodedata/post-link.sh new file mode 100644 index 0000000000000..f0449371816fa --- /dev/null +++ b/recipes/bioconductor-mitoodedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mitoODEdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mitoODEdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mitoODEdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mitoodedata/bioconductor-mitoodedata_1.18.0_src_all.tar.gz" +) +MD5="2b4cf1081b1509c750a63a16a9ec3fc9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mitoodedata/pre-unlink.sh b/recipes/bioconductor-mitoodedata/pre-unlink.sh new file mode 100644 index 0000000000000..31a3618a21b7f --- /dev/null +++ b/recipes/bioconductor-mitoodedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mitoODEdata diff --git a/recipes/bioconductor-mixomics/build.sh b/recipes/bioconductor-mixomics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mixomics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mixomics/meta.yaml b/recipes/bioconductor-mixomics/meta.yaml new file mode 100644 index 0000000000000..4cc1941eb6133 --- /dev/null +++ b/recipes/bioconductor-mixomics/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "6.6.0" %} +{% set name = "mixOmics" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 08f6fa61be551b5de5f510f6dd1a171b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, rgl +requirements: + host: + - r-base + - r-corpcor + - r-dplyr + - r-ellipse + - r-ggplot2 + - r-gridextra + - r-igraph + - r-lattice + - r-mass + - r-matrixstats + - r-rarpack + - r-rcolorbrewer + - r-reshape2 + - r-tidyr + run: + - r-base + - r-corpcor + - r-dplyr + - r-ellipse + - r-ggplot2 + - r-gridextra + - r-igraph + - r-lattice + - r-mass + - r-matrixstats + - r-rarpack + - r-rcolorbrewer + - r-reshape2 + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Multivariate methods are well suited to large omics data sets where the number of variables (e.g. genes, proteins, metabolites) is much larger than the number of samples (patients, cells, mice). They have the appealing properties of reducing the dimension of the data by using instrumental variables (components), which are defined as combinations of all variables. Those components are then used to produce useful graphical outputs that enable better understanding of the relationships and correlation structures between the different data sets that are integrated. mixOmics offers a wide range of multivariate methods for the exploration and integration of biological datasets with a particular focus on variable selection. The package proposes several sparse multivariate models we have developed to identify the key variables that are highly correlated, and/or explain the biological outcome of interest. The data that can be analysed with mixOmics may come from high throughput sequencing technologies, such as omics data (transcriptomics, metabolomics, proteomics, metagenomics etc) but also beyond the realm of omics (e.g. spectral imaging). The methods implemented in mixOmics can also handle missing values without having to delete entire rows with missing data. A non exhaustive list of methods include variants of generalised Canonical Correlation Analysis, sparse Partial Least Squares and sparse Discriminant Analysis. Recently we implemented integrative methods to combine multiple data sets: N-integration with variants of Generalised Canonical Correlation Analysis and P-integration with variants of multi-group Partial Least Squares.' + diff --git a/recipes/bioconductor-mlinterfaces/build.sh b/recipes/bioconductor-mlinterfaces/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mlinterfaces/build.sh +++ b/recipes/bioconductor-mlinterfaces/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mlinterfaces/conda_build_config.yaml b/recipes/bioconductor-mlinterfaces/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mlinterfaces/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mlinterfaces/meta.yaml b/recipes/bioconductor-mlinterfaces/meta.yaml index 506ad63596abc..a117b2c56bd5e 100644 --- a/recipes/bioconductor-mlinterfaces/meta.yaml +++ b/recipes/bioconductor-mlinterfaces/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.60.1" %} +{% set version = "1.62.0" %} {% set name = "MLInterfaces" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ac720b4aaf59b61becb23423b108863a85e404b9d42c33e47275fd0eddf22dd + md5: 0375d370e1cd5ad27b392bf8528efa93 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: class, e1071, ipred, randomForest, gpls, pamr, nnet, ALL, hgu95av2.db, som, hu6800.db, lattice, caret (>= 5.07), golubEsets, ada, keggorthology, kernlab, mboost, party requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base - r-cluster - r-fpc @@ -39,10 +41,10 @@ requirements: - r-shiny - 'r-threejs >=0.2.2' run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base - r-cluster - r-fpc @@ -63,10 +65,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package provides uniform interfaces to machine learning code for data in R and Bioconductor containers.' extra: identifiers: - biotools:mlinterfaces - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mlinterfaces + path: recipes/bioconductor-mlinterfaces + version: 1.60.1 + diff --git a/recipes/bioconductor-mlp/build.sh b/recipes/bioconductor-mlp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mlp/build.sh +++ b/recipes/bioconductor-mlp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mlp/conda_build_config.yaml b/recipes/bioconductor-mlp/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mlp/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mlp/meta.yaml b/recipes/bioconductor-mlp/meta.yaml index 4afc56e334fcc..374c9aac26989 100644 --- a/recipes/bioconductor-mlp/meta.yaml +++ b/recipes/bioconductor-mlp/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "MLP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a288ebcf30964f9a87e593a6b7240284d8d4924eebec4bf1f9899709eb9965e8 + md5: aa60c8428853779c635788ea6e600255 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GO.db, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, org.Cf.eg.db, KEGG.db, annotate, Rgraphviz, GOstats, limma, mouse4302.db, reactome.db requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-gdata - r-gmodels @@ -27,8 +29,8 @@ requirements: - r-gtools - r-plotrix run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-gdata - r-gmodels @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Mean Log P Analysis' extra: identifiers: - biotools:mlp - doi:10.1007/978-3-642-24007-2_12 + parent_recipe: + name: bioconductor-mlp + path: recipes/bioconductor-mlp + version: 1.28.0 + diff --git a/recipes/bioconductor-mlseq/build.sh b/recipes/bioconductor-mlseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mlseq/build.sh +++ b/recipes/bioconductor-mlseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mlseq/meta.yaml b/recipes/bioconductor-mlseq/meta.yaml index f4969f9760259..1eb504281fd97 100644 --- a/recipes/bioconductor-mlseq/meta.yaml +++ b/recipes/bioconductor-mlseq/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.20.3" %} +{% set version = "2.0.0" %} {% set name = "MLSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 09663f7b24051519e3f587c95a35122a4f571907ec1a93db0b40d9b7e119f26d + md5: 8f9f9f5111af5496b8c8f3cb0ea5f8db build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat, BiocStyle, VennDiagram, pamr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-sseq >=1.18.0,<1.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sseq >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-caret - r-foreach @@ -31,12 +33,12 @@ requirements: - r-plyr - r-xtable run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-sseq >=1.18.0,<1.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sseq >=1.20.0,<1.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-caret - r-foreach @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'This package applies several machine learning methods, including SVM, bagSVM, Random Forest and CART to RNA-Seq data.' extra: identifiers: - biotools:mlseq - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mlseq + path: recipes/bioconductor-mlseq + version: 1.20.3 + diff --git a/recipes/bioconductor-mm24kresogen.db/meta.yaml b/recipes/bioconductor-mm24kresogen.db/meta.yaml new file mode 100644 index 0000000000000..1cdea13147bc5 --- /dev/null +++ b/recipes/bioconductor-mm24kresogen.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "2.5.0" %} +{% set name = "mm24kresogen.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 437f5d4bc225ee500af1ecc2d4da472b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'RNG_MRC Mouse Pangenomic 24k Set annotation data (chip mm24kresogen) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mm24kresogen.db/post-link.sh b/recipes/bioconductor-mm24kresogen.db/post-link.sh new file mode 100644 index 0000000000000..14d210937114d --- /dev/null +++ b/recipes/bioconductor-mm24kresogen.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mm24kresogen.db_2.5.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mm24kresogen.db_2.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/mm24kresogen.db_2.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mm24kresogen.db/bioconductor-mm24kresogen.db_2.5.0_src_all.tar.gz" +) +MD5="437f5d4bc225ee500af1ecc2d4da472b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mm24kresogen.db/pre-unlink.sh b/recipes/bioconductor-mm24kresogen.db/pre-unlink.sh new file mode 100644 index 0000000000000..3176c6e804e1a --- /dev/null +++ b/recipes/bioconductor-mm24kresogen.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mm24kresogen.db diff --git a/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml new file mode 100644 index 0000000000000..3bfeff3e4e5ca --- /dev/null +++ b/recipes/bioconductor-mmagilentdesign026655.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "MmAgilentDesign026655.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7ef619bd2c74f22ea4f3c2b2c4131fe9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Chips that use Agilent design number 026655 annotation data (chip MmAgilentDesign026655) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh b/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh new file mode 100644 index 0000000000000..adc9172431c2d --- /dev/null +++ b/recipes/bioconductor-mmagilentdesign026655.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MmAgilentDesign026655.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MmAgilentDesign026655.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/MmAgilentDesign026655.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mmagilentdesign026655.db/bioconductor-mmagilentdesign026655.db_3.2.3_src_all.tar.gz" +) +MD5="7ef619bd2c74f22ea4f3c2b2c4131fe9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mmagilentdesign026655.db/pre-unlink.sh b/recipes/bioconductor-mmagilentdesign026655.db/pre-unlink.sh new file mode 100644 index 0000000000000..a26b55578ab26 --- /dev/null +++ b/recipes/bioconductor-mmagilentdesign026655.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MmAgilentDesign026655.db diff --git a/recipes/bioconductor-mmdiff/build.sh b/recipes/bioconductor-mmdiff/build.sh index 0d6a53f143312..c532a7c91a328 100644 --- a/recipes/bioconductor-mmdiff/build.sh +++ b/recipes/bioconductor-mmdiff/build.sh @@ -13,4 +13,4 @@ $R CMD INSTALL --build . # http://docs.continuum.io/conda/build.html # for a list of environment variables that are set during the build # process. -# +# diff --git a/recipes/bioconductor-mmdiff/conda_build_config.yaml b/recipes/bioconductor-mmdiff/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-mmdiff/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-mmdiff2/build.sh b/recipes/bioconductor-mmdiff2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mmdiff2/build.sh +++ b/recipes/bioconductor-mmdiff2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mmdiff2/meta.yaml b/recipes/bioconductor-mmdiff2/meta.yaml index e5c6257b40cbf..cbd878d02bfb4 100644 --- a/recipes/bioconductor-mmdiff2/meta.yaml +++ b/recipes/bioconductor-mmdiff2/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MMDiff2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0f5051f1460df312c86a4841c4b49723659e891f68bafce67a4cbbfeaef87379 + md5: e13ca07c7dea4123eb3cb08be914edef build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MMDiffBamSubset, MotifDb, knitr, BiocStyle, BSgenome.Mmusculus.UCSC.mm9 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-locfit - r-rcolorbrewer - r-shiny run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-locfit @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package detects statistically significant differences between read enrichment profiles in different ChIP-Seq samples. To take advantage of shape differences it uses Kernel methods (Maximum Mean Discrepancy, MMD).' extra: identifiers: - biotools:mmdiff2 - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mmdiff2 + path: recipes/bioconductor-mmdiff2 + version: 1.8.0 + diff --git a/recipes/bioconductor-mmdiffbamsubset/meta.yaml b/recipes/bioconductor-mmdiffbamsubset/meta.yaml new file mode 100644 index 0000000000000..d443a483a323b --- /dev/null +++ b/recipes/bioconductor-mmdiffbamsubset/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "MMDiffBamSubset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 28e6a879bd736040d44de460c7e582aa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MMDiff2 +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Subset of BAM files, including WT_2.bam, Null_2.bam, Resc_2.bam, Input.bam from the "Cfp1" experiment (see Clouaire et al., Genes Dev. 2012). Data is available under ArrayExpress accession numbers E-ERAD-79. Additionally, corresponding subset of peaks called by MACS' + diff --git a/recipes/bioconductor-mmdiffbamsubset/post-link.sh b/recipes/bioconductor-mmdiffbamsubset/post-link.sh new file mode 100644 index 0000000000000..3360054b8f984 --- /dev/null +++ b/recipes/bioconductor-mmdiffbamsubset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MMDiffBamSubset_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MMDiffBamSubset_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/MMDiffBamSubset_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mmdiffbamsubset/bioconductor-mmdiffbamsubset_1.18.0_src_all.tar.gz" +) +MD5="28e6a879bd736040d44de460c7e582aa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mmdiffbamsubset/pre-unlink.sh b/recipes/bioconductor-mmdiffbamsubset/pre-unlink.sh new file mode 100644 index 0000000000000..08f5a6847c893 --- /dev/null +++ b/recipes/bioconductor-mmdiffbamsubset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MMDiffBamSubset diff --git a/recipes/bioconductor-mmpalatemirna/build.sh b/recipes/bioconductor-mmpalatemirna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mmpalatemirna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mmpalatemirna/meta.yaml b/recipes/bioconductor-mmpalatemirna/meta.yaml new file mode 100644 index 0000000000000..31bafecf016bd --- /dev/null +++ b/recipes/bioconductor-mmpalatemirna/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.32.0" %} +{% set name = "MmPalateMiRNA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f4d32e709429b59908cea3fd1ef9e70b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GOstats, graph, Category, org.Mm.eg.db, microRNA, targetscan.Mm.eg.db, RSQLite, DBI, AnnotationDbi, clValid, class, cluster, multtest, RColorBrewer, latticeExtra +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-lattice + - r-statmod + - r-xtable + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-lattice + - r-statmod + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'R package compendium for the analysis of murine palate miRNA two-color expression data.' + diff --git a/recipes/bioconductor-moda/build.sh b/recipes/bioconductor-moda/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-moda/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-moda/meta.yaml b/recipes/bioconductor-moda/meta.yaml new file mode 100644 index 0000000000000..5887d637af86d --- /dev/null +++ b/recipes/bioconductor-moda/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.8.0" %} +{% set name = "MODA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 50ed2605dabd7656e45804206fcafc6f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-amountain >=1.8.0,<1.9.0' + - r-base + - r-cluster + - r-dynamictreecut + - r-igraph + - r-rcolorbrewer + - r-wgcna + run: + - 'bioconductor-amountain >=1.8.0,<1.9.0' + - r-base + - r-cluster + - r-dynamictreecut + - r-igraph + - r-rcolorbrewer + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'MODA can be used to estimate and construct condition-specific gene co-expression networks, and identify differentially expressed subnetworks as conserved or condition specific modules which are potentially associated with relevant biological processes.' + diff --git a/recipes/bioconductor-moe430a.db/meta.yaml b/recipes/bioconductor-moe430a.db/meta.yaml new file mode 100644 index 0000000000000..ed01ed0a31a51 --- /dev/null +++ b/recipes/bioconductor-moe430a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "moe430a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c95b12e1954943ccc347ae57794e1c19 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Mouse Expression Set 430 annotation data (chip moe430a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-moe430a.db/post-link.sh b/recipes/bioconductor-moe430a.db/post-link.sh new file mode 100644 index 0000000000000..0ff71a18492aa --- /dev/null +++ b/recipes/bioconductor-moe430a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/moe430a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430a.db/bioconductor-moe430a.db_3.2.3_src_all.tar.gz" +) +MD5="c95b12e1954943ccc347ae57794e1c19" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430a.db/pre-unlink.sh b/recipes/bioconductor-moe430a.db/pre-unlink.sh new file mode 100644 index 0000000000000..ccfc5eb5180e6 --- /dev/null +++ b/recipes/bioconductor-moe430a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430a.db diff --git a/recipes/bioconductor-moe430acdf/meta.yaml b/recipes/bioconductor-moe430acdf/meta.yaml new file mode 100644 index 0000000000000..2e131e4862958 --- /dev/null +++ b/recipes/bioconductor-moe430acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "moe430acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b03f1295fc483f0d782a4615e8ca0137 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MOE430A.CDF file.' + diff --git a/recipes/bioconductor-moe430acdf/post-link.sh b/recipes/bioconductor-moe430acdf/post-link.sh new file mode 100644 index 0000000000000..ae6a77da243fc --- /dev/null +++ b/recipes/bioconductor-moe430acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/moe430acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430acdf/bioconductor-moe430acdf_2.18.0_src_all.tar.gz" +) +MD5="b03f1295fc483f0d782a4615e8ca0137" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430acdf/pre-unlink.sh b/recipes/bioconductor-moe430acdf/pre-unlink.sh new file mode 100644 index 0000000000000..bbdc7985dc1eb --- /dev/null +++ b/recipes/bioconductor-moe430acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430acdf diff --git a/recipes/bioconductor-moe430aprobe/meta.yaml b/recipes/bioconductor-moe430aprobe/meta.yaml new file mode 100644 index 0000000000000..0bd56d3d6aae8 --- /dev/null +++ b/recipes/bioconductor-moe430aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "moe430aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0aa83189d04599a65211d1a2f0a51c8f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430A\_probe\_tab.' + diff --git a/recipes/bioconductor-moe430aprobe/post-link.sh b/recipes/bioconductor-moe430aprobe/post-link.sh new file mode 100644 index 0000000000000..2a7c1d83f6cea --- /dev/null +++ b/recipes/bioconductor-moe430aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/moe430aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430aprobe/bioconductor-moe430aprobe_2.18.0_src_all.tar.gz" +) +MD5="0aa83189d04599a65211d1a2f0a51c8f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430aprobe/pre-unlink.sh b/recipes/bioconductor-moe430aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3ae970b1c69f1 --- /dev/null +++ b/recipes/bioconductor-moe430aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430aprobe diff --git a/recipes/bioconductor-moe430b.db/meta.yaml b/recipes/bioconductor-moe430b.db/meta.yaml new file mode 100644 index 0000000000000..575c14639750e --- /dev/null +++ b/recipes/bioconductor-moe430b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "moe430b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 74027eafdb3815a8310e84ade3a43dff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Mouse Expression Set 430 annotation data (chip moe430b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-moe430b.db/post-link.sh b/recipes/bioconductor-moe430b.db/post-link.sh new file mode 100644 index 0000000000000..857b193382bc6 --- /dev/null +++ b/recipes/bioconductor-moe430b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/moe430b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430b.db/bioconductor-moe430b.db_3.2.3_src_all.tar.gz" +) +MD5="74027eafdb3815a8310e84ade3a43dff" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430b.db/pre-unlink.sh b/recipes/bioconductor-moe430b.db/pre-unlink.sh new file mode 100644 index 0000000000000..bbbbe918b9a1b --- /dev/null +++ b/recipes/bioconductor-moe430b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430b.db diff --git a/recipes/bioconductor-moe430bcdf/meta.yaml b/recipes/bioconductor-moe430bcdf/meta.yaml new file mode 100644 index 0000000000000..8e7aa427baa3a --- /dev/null +++ b/recipes/bioconductor-moe430bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "moe430bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b7112dcf8ccfe4e079ca67ff62046f2e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MOE430B.CDF file.' + diff --git a/recipes/bioconductor-moe430bcdf/post-link.sh b/recipes/bioconductor-moe430bcdf/post-link.sh new file mode 100644 index 0000000000000..0d9bdc8c844e1 --- /dev/null +++ b/recipes/bioconductor-moe430bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/moe430bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430bcdf/bioconductor-moe430bcdf_2.18.0_src_all.tar.gz" +) +MD5="b7112dcf8ccfe4e079ca67ff62046f2e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430bcdf/pre-unlink.sh b/recipes/bioconductor-moe430bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..068514d3efc20 --- /dev/null +++ b/recipes/bioconductor-moe430bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430bcdf diff --git a/recipes/bioconductor-moe430bprobe/meta.yaml b/recipes/bioconductor-moe430bprobe/meta.yaml new file mode 100644 index 0000000000000..27b9532b1d2ac --- /dev/null +++ b/recipes/bioconductor-moe430bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "moe430bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1368e6f4225babe7a693ccd39a3a436a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MOE430B\_probe\_tab.' + diff --git a/recipes/bioconductor-moe430bprobe/post-link.sh b/recipes/bioconductor-moe430bprobe/post-link.sh new file mode 100644 index 0000000000000..957490e625ae2 --- /dev/null +++ b/recipes/bioconductor-moe430bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moe430bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moe430bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/moe430bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moe430bprobe/bioconductor-moe430bprobe_2.18.0_src_all.tar.gz" +) +MD5="1368e6f4225babe7a693ccd39a3a436a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moe430bprobe/pre-unlink.sh b/recipes/bioconductor-moe430bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..60c4aaa21f0ee --- /dev/null +++ b/recipes/bioconductor-moe430bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moe430bprobe diff --git a/recipes/bioconductor-moex10stprobeset.db/meta.yaml b/recipes/bioconductor-moex10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..0a52728df75ea --- /dev/null +++ b/recipes/bioconductor-moex10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "moex10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1464d765c3db1bf50a6eb115ae30c74c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix moex10 annotation data (chip moex10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-moex10stprobeset.db/post-link.sh b/recipes/bioconductor-moex10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..a366f8d83335d --- /dev/null +++ b/recipes/bioconductor-moex10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moex10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moex10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/moex10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moex10stprobeset.db/bioconductor-moex10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="1464d765c3db1bf50a6eb115ae30c74c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moex10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-moex10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..6683b21fa3d6e --- /dev/null +++ b/recipes/bioconductor-moex10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moex10stprobeset.db diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..17be4537c0851 --- /dev/null +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "moex10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 67253f6ab5cb335049139951ca8064bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix moex10 annotation data (chip moex10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..b9289050a3fee --- /dev/null +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="moex10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/moex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/moex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moex10sttranscriptcluster.db/bioconductor-moex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="67253f6ab5cb335049139951ca8064bd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moex10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-moex10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..f78feaa358532 --- /dev/null +++ b/recipes/bioconductor-moex10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ moex10sttranscriptcluster.db diff --git a/recipes/bioconductor-moexexonprobesetlocation/meta.yaml b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml new file mode 100644 index 0000000000000..f8fca38a14224 --- /dev/null +++ b/recipes/bioconductor-moexexonprobesetlocation/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.15.0" %} +{% set name = "MoExExonProbesetLocation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 07eea205fce2a8cf4585fa7e71fb0057 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' + diff --git a/recipes/bioconductor-moexexonprobesetlocation/post-link.sh b/recipes/bioconductor-moexexonprobesetlocation/post-link.sh new file mode 100644 index 0000000000000..b38f5a397f078 --- /dev/null +++ b/recipes/bioconductor-moexexonprobesetlocation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MoExExonProbesetLocation_1.15.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/MoExExonProbesetLocation_1.15.0.tar.gz" + "https://bioarchive.galaxyproject.org/MoExExonProbesetLocation_1.15.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-moexexonprobesetlocation/bioconductor-moexexonprobesetlocation_1.15.0_src_all.tar.gz" +) +MD5="07eea205fce2a8cf4585fa7e71fb0057" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-moexexonprobesetlocation/pre-unlink.sh b/recipes/bioconductor-moexexonprobesetlocation/pre-unlink.sh new file mode 100644 index 0000000000000..c65de5315bab9 --- /dev/null +++ b/recipes/bioconductor-moexexonprobesetlocation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MoExExonProbesetLocation diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml new file mode 100644 index 0000000000000..3c5009663dbb5 --- /dev/null +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.1.0" %} +{% set name = "mogene.1.0.st.v1frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b46f76903d0f19b85e8fa30347813ff5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.13.0.' + diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh new file mode 100644 index 0000000000000..3684e28ad6c61 --- /dev/null +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene.1.0.st.v1frmavecs_1.1.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene.1.0.st.v1frmavecs/bioconductor-mogene.1.0.st.v1frmavecs_1.1.0_src_all.tar.gz" +) +MD5="b46f76903d0f19b85e8fa30347813ff5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene.1.0.st.v1frmavecs/pre-unlink.sh b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..33b6561ca8df9 --- /dev/null +++ b/recipes/bioconductor-mogene.1.0.st.v1frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene.1.0.st.v1frmavecs diff --git a/recipes/bioconductor-mogene10stprobeset.db/meta.yaml b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..274bc5a722cbb --- /dev/null +++ b/recipes/bioconductor-mogene10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f4859f71d1314d19ead1c4fe20c04e4b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene10 annotation data (chip mogene10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene10stprobeset.db/post-link.sh b/recipes/bioconductor-mogene10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..7650d00d4447c --- /dev/null +++ b/recipes/bioconductor-mogene10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stprobeset.db/bioconductor-mogene10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="f4859f71d1314d19ead1c4fe20c04e4b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-mogene10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..534eb0fe35277 --- /dev/null +++ b/recipes/bioconductor-mogene10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene10stprobeset.db diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..ef1707ed6fefa --- /dev/null +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 84966d4986d62c859f61f2725c7b20ea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene10 annotation data (chip mogene10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..c340dda60bcae --- /dev/null +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10sttranscriptcluster.db/bioconductor-mogene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="84966d4986d62c859f61f2725c7b20ea" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-mogene10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..2437b4530bf0f --- /dev/null +++ b/recipes/bioconductor-mogene10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene10sttranscriptcluster.db diff --git a/recipes/bioconductor-mogene10stv1cdf/meta.yaml b/recipes/bioconductor-mogene10stv1cdf/meta.yaml new file mode 100644 index 0000000000000..43e697ef43c98 --- /dev/null +++ b/recipes/bioconductor-mogene10stv1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mogene10stv1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9c0271f5d6493290fc47f041a8c3f925 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the MoGene-1_0-st-v1.cdf file.' + diff --git a/recipes/bioconductor-mogene10stv1cdf/post-link.sh b/recipes/bioconductor-mogene10stv1cdf/post-link.sh new file mode 100644 index 0000000000000..2c36e501df7a3 --- /dev/null +++ b/recipes/bioconductor-mogene10stv1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene10stv1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stv1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene10stv1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1cdf/bioconductor-mogene10stv1cdf_2.18.0_src_all.tar.gz" +) +MD5="9c0271f5d6493290fc47f041a8c3f925" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene10stv1cdf/pre-unlink.sh b/recipes/bioconductor-mogene10stv1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..e4c137519e02f --- /dev/null +++ b/recipes/bioconductor-mogene10stv1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene10stv1cdf diff --git a/recipes/bioconductor-mogene10stv1probe/meta.yaml b/recipes/bioconductor-mogene10stv1probe/meta.yaml new file mode 100644 index 0000000000000..a659c360b2d4b --- /dev/null +++ b/recipes/bioconductor-mogene10stv1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mogene10stv1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 63cba1e2a0edee9f201267057fddb0fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was MoGene-1\_0-st-v1\_probe\_tab.' + diff --git a/recipes/bioconductor-mogene10stv1probe/post-link.sh b/recipes/bioconductor-mogene10stv1probe/post-link.sh new file mode 100644 index 0000000000000..1c02997b9e805 --- /dev/null +++ b/recipes/bioconductor-mogene10stv1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene10stv1probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene10stv1probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene10stv1probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene10stv1probe/bioconductor-mogene10stv1probe_2.18.0_src_all.tar.gz" +) +MD5="63cba1e2a0edee9f201267057fddb0fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene10stv1probe/pre-unlink.sh b/recipes/bioconductor-mogene10stv1probe/pre-unlink.sh new file mode 100644 index 0000000000000..001c01893968d --- /dev/null +++ b/recipes/bioconductor-mogene10stv1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene10stv1probe diff --git a/recipes/bioconductor-mogene11stprobeset.db/meta.yaml b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..a4e13d1307583 --- /dev/null +++ b/recipes/bioconductor-mogene11stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene11stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9bfdd5ede041282555dca8a6a75e7579 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene11 annotation data (chip mogene11stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene11stprobeset.db/post-link.sh b/recipes/bioconductor-mogene11stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..62866bb96ceea --- /dev/null +++ b/recipes/bioconductor-mogene11stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene11stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene11stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene11stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene11stprobeset.db/bioconductor-mogene11stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="9bfdd5ede041282555dca8a6a75e7579" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene11stprobeset.db/pre-unlink.sh b/recipes/bioconductor-mogene11stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..835a23ae0a32b --- /dev/null +++ b/recipes/bioconductor-mogene11stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene11stprobeset.db diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..c9d8a7ff8a892 --- /dev/null +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene11sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a3bc3ed82534b5a53bdba583f7a403c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene11 annotation data (chip mogene11sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..a55407be9622c --- /dev/null +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene11sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene11sttranscriptcluster.db/bioconductor-mogene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="a3bc3ed82534b5a53bdba583f7a403c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene11sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-mogene11sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..68142c0075878 --- /dev/null +++ b/recipes/bioconductor-mogene11sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene11sttranscriptcluster.db diff --git a/recipes/bioconductor-mogene20stprobeset.db/meta.yaml b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..5ce6158da6890 --- /dev/null +++ b/recipes/bioconductor-mogene20stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene20stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 228a1172930e05806cd8b184b326b556 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene20 annotation data (chip mogene20stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene20stprobeset.db/post-link.sh b/recipes/bioconductor-mogene20stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..6c3efd4b63b04 --- /dev/null +++ b/recipes/bioconductor-mogene20stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene20stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene20stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene20stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene20stprobeset.db/bioconductor-mogene20stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="228a1172930e05806cd8b184b326b556" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene20stprobeset.db/pre-unlink.sh b/recipes/bioconductor-mogene20stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..f56dfc5fe01b8 --- /dev/null +++ b/recipes/bioconductor-mogene20stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene20stprobeset.db diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..bfaa41e68fb94 --- /dev/null +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene20sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c3c6f08d15d9cd3fe850860de0a06213 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene20 annotation data (chip mogene20sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..8187d6f49d1c4 --- /dev/null +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene20sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene20sttranscriptcluster.db/bioconductor-mogene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="c3c6f08d15d9cd3fe850860de0a06213" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene20sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-mogene20sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..de07c11e555e7 --- /dev/null +++ b/recipes/bioconductor-mogene20sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene20sttranscriptcluster.db diff --git a/recipes/bioconductor-mogene21stprobeset.db/meta.yaml b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..b7cd40fd39b23 --- /dev/null +++ b/recipes/bioconductor-mogene21stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene21stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 34c2b435725e7dcd29c3d921453216dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene21 annotation data (chip mogene21stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene21stprobeset.db/post-link.sh b/recipes/bioconductor-mogene21stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..6896396fde4d0 --- /dev/null +++ b/recipes/bioconductor-mogene21stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene21stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene21stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene21stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene21stprobeset.db/bioconductor-mogene21stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="34c2b435725e7dcd29c3d921453216dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene21stprobeset.db/pre-unlink.sh b/recipes/bioconductor-mogene21stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..f0c7b2d679696 --- /dev/null +++ b/recipes/bioconductor-mogene21stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene21stprobeset.db diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..bafcec46d09d4 --- /dev/null +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mogene21sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0f131b607470652724d7b22ae2af1c7a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mogene21 annotation data (chip mogene21sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..d9c50941f8116 --- /dev/null +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mogene21sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mogene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mogene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mogene21sttranscriptcluster.db/bioconductor-mogene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="0f131b607470652724d7b22ae2af1c7a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mogene21sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-mogene21sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..28c5623c01b0b --- /dev/null +++ b/recipes/bioconductor-mogene21sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mogene21sttranscriptcluster.db diff --git a/recipes/bioconductor-mogsa/build.sh b/recipes/bioconductor-mogsa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mogsa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mogsa/meta.yaml b/recipes/bioconductor-mogsa/meta.yaml new file mode 100644 index 0000000000000..47d3e696737a6 --- /dev/null +++ b/recipes/bioconductor-mogsa/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.16.0" %} +{% set name = "mogsa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8cf09a49ac7d52e667f40ab2e5d2922c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-cluster + - r-corpcor + - r-gplots + - r-svd + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-cluster + - r-corpcor + - r-gplots + - r-svd +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provide a method for doing gene set analysis based on multiple omics data.' + diff --git a/recipes/bioconductor-monocle/build.sh b/recipes/bioconductor-monocle/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-monocle/build.sh +++ b/recipes/bioconductor-monocle/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-monocle/meta.yaml b/recipes/bioconductor-monocle/meta.yaml index 92186068fe13d..5a08fe6b87657 100644 --- a/recipes/bioconductor-monocle/meta.yaml +++ b/recipes/bioconductor-monocle/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "monocle" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 55c6863b78832d61487e63981c4afbe49c523f7d5799043dfb2349637e69be32 + md5: bc85ee520d81832a181fe01680558997 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: destiny, Hmisc, knitr, Seurat, scater, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-hsmmsinglecell >=0.114.0,<0.116.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-hsmmsinglecell >=1.2.0,<1.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-cluster - r-combinat @@ -47,14 +48,14 @@ requirements: - r-slam - r-stringr - r-tibble - - 'r-vgam >=1.0-1' + - 'r-vgam >=1.0-6' - r-viridis run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-hsmmsinglecell >=0.114.0,<0.116.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-hsmmsinglecell >=1.2.0,<1.3.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-cluster - r-combinat @@ -79,7 +80,7 @@ requirements: - r-slam - r-stringr - r-tibble - - 'r-vgam >=1.0-1' + - 'r-vgam >=1.0-6' - r-viridis build: - {{ compiler('c') }} @@ -89,9 +90,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Monocle performs differential expression and time-series analysis for single-cell expression experiments. It orders individual cells according to progress through a biological process, without knowing ahead of time which genes define progress through that process. Monocle also performs differential expression analysis, clustering, visualization, and other useful tasks on single cell expression data. It is designed to work with RNA-Seq and qPCR data, but could be used with other types as well.' extra: identifiers: - biotools:monocle + parent_recipe: + name: bioconductor-monocle + path: recipes/bioconductor-monocle + version: 2.8.0 + diff --git a/recipes/bioconductor-moonlightr/build.sh b/recipes/bioconductor-moonlightr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-moonlightr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-moonlightr/meta.yaml b/recipes/bioconductor-moonlightr/meta.yaml new file mode 100644 index 0000000000000..1d0fcdc6c1dce --- /dev/null +++ b/recipes/bioconductor-moonlightr/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.8.0" %} +{% set name = "MoonlightR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ee7e9a7914dd2f526db0f189785be525 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, png +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - r-base + - r-circlize + - r-doparallel + - r-foreach + - r-gplots + - r-hiver + - r-parmigene + - r-randomforest + - r-rcolorbrewer + - r-rismed + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - r-base + - r-circlize + - r-doparallel + - r-foreach + - r-gplots + - r-hiver + - r-parmigene + - r-randomforest + - r-rcolorbrewer + - r-rismed +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Motivation: The understanding of cancer mechanism requires the identification of genes playing a role in the development of the pathology and the characterization of their role (notably oncogenes and tumor suppressors). Results: We present an R/bioconductor package called MoonlightR which returns a list of candidate driver genes for specific cancer types on the basis of TCGA expression data. The method first infers gene regulatory networks and then carries out a functional enrichment analysis (FEA) (implementing an upstream regulator analysis, URA) to score the importance of well-known biological processes with respect to the studied cancer type. Eventually, by means of random forests, MoonlightR predicts two specific roles for the candidate driver genes: i) tumor suppressor genes (TSGs) and ii) oncogenes (OCGs). As a consequence, this methodology does not only identify genes playing a dual role (e.g. TSG in one cancer type and OCG in another) but also helps in elucidating the biological processes underlying their specific roles. In particular, MoonlightR can be used to discover OCGs and TSGs in the same cancer type. This may help in answering the question whether some genes change role between early stages (I, II) and late stages (III, IV) in breast cancer. In the future, this analysis could be useful to determine the causes of different resistances to chemotherapeutic treatments.' + diff --git a/recipes/bioconductor-mops/build.sh b/recipes/bioconductor-mops/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mops/build.sh +++ b/recipes/bioconductor-mops/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mops/meta.yaml b/recipes/bioconductor-mops/meta.yaml index 36df584fcdcad..6d6543867a486 100644 --- a/recipes/bioconductor-mops/meta.yaml +++ b/recipes/bioconductor-mops/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "MoPS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c6755294077ca4882ff1888801a67d964f73f2de263d038db2fdd7631445b26f + md5: 45c3777290bc95c462428fcc28aa18e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identification and characterization of periodic fluctuations in time-series data.' extra: identifiers: - biotools:mops - doi:10.1002/msb.134886 + parent_recipe: + name: bioconductor-mops + path: recipes/bioconductor-mops + version: 1.14.0 + diff --git a/recipes/bioconductor-mosaics/build.sh b/recipes/bioconductor-mosaics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mosaics/build.sh +++ b/recipes/bioconductor-mosaics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mosaics/meta.yaml b/recipes/bioconductor-mosaics/meta.yaml index 606425c54e40e..07bf38ea897aa 100644 --- a/recipes/bioconductor-mosaics/meta.yaml +++ b/recipes/bioconductor-mosaics/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "mosaics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 92790b8e556304e5292db09054e392754b28692eb01daf923515848feeb1ae61 + md5: 9e40d17d91730001365219582cd223fc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: mosaicsExample +# SystemRequirements: Perl requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - r-mass - r-rcpp run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - r-mass @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides functions for fitting MOSAiCS and MOSAiCS-HMM, a statistical framework to analyze one-sample or two-sample ChIP-seq data of transcription factor binding and histone modification.' extra: identifiers: - biotools:mosaics - doi:10.1198/jasa.2011.ap09706 + parent_recipe: + name: bioconductor-mosaics + path: recipes/bioconductor-mosaics + version: 2.18.0 + diff --git a/recipes/bioconductor-mosaicsexample/meta.yaml b/recipes/bioconductor-mosaicsexample/meta.yaml new file mode 100644 index 0000000000000..e737ef7933a2c --- /dev/null +++ b/recipes/bioconductor-mosaicsexample/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "mosaicsExample" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5f16c9ddafc0db17641a7c8dde96a62b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data for the mosaics package, consisting of (1) chromosome 22 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding and H3K4me3 modification in MCF7 cell line from ENCODE database (HG19) and (2) chromosome 21 ChIP and control sample data from a ChIP-seq experiment of STAT1 binding, with mappability, GC content, and sequence ambiguity scores of human genome HG18.' + diff --git a/recipes/bioconductor-mosaicsexample/post-link.sh b/recipes/bioconductor-mosaicsexample/post-link.sh new file mode 100644 index 0000000000000..96ba22aba647f --- /dev/null +++ b/recipes/bioconductor-mosaicsexample/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mosaicsExample_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mosaicsExample_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/mosaicsExample_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mosaicsexample/bioconductor-mosaicsexample_1.20.0_src_all.tar.gz" +) +MD5="5f16c9ddafc0db17641a7c8dde96a62b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mosaicsexample/pre-unlink.sh b/recipes/bioconductor-mosaicsexample/pre-unlink.sh new file mode 100644 index 0000000000000..86c51b70dbeb7 --- /dev/null +++ b/recipes/bioconductor-mosaicsexample/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mosaicsExample diff --git a/recipes/bioconductor-motifbreakr/build.sh b/recipes/bioconductor-motifbreakr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motifbreakr/build.sh +++ b/recipes/bioconductor-motifbreakr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifbreakr/meta.yaml b/recipes/bioconductor-motifbreakr/meta.yaml index 9632b3fdec70b..9729c1ac90b37 100644 --- a/recipes/bioconductor-motifbreakr/meta.yaml +++ b/recipes/bioconductor-motifbreakr/meta.yaml @@ -1,55 +1,57 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "motifbreakR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9bee8e72857e467d0f39b1baff54bad69e8e53615156b25b489dbcf0f1695c99 + md5: f4acb1d102a78b4ca2bb951366e5cace build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP.20120608, SNPlocs.Hsapiens.dbSNP142.GRCh37, knitr, rmarkdown, BSgenome.Drerio.UCSC.danRer7, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-motifdb >=1.22.0,<1.24.0' - - 'bioconductor-motifstack >=1.24.1,<1.26.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-grimport - r-matrixstats - r-stringr - r-tfmpvalue run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-motifdb >=1.22.0,<1.24.0' - - 'bioconductor-motifstack >=1.24.1,<1.26.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-motifstack >=1.26.0,<1.27.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-grimport - r-matrixstats @@ -59,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'We introduce motifbreakR, which allows the biologist to judge in the first place whether the sequence surrounding the polymorphism is a good match, and in the second place how much information is gained or lost in one allele of the polymorphism relative to another. MotifbreakR is both flexible and extensible over previous offerings; giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum probability matrix, 2) log-probabilities, and 3) weighted by relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor (currently there are 22).' extra: identifiers: - biotools:motifbreakr + parent_recipe: + name: bioconductor-motifbreakr + path: recipes/bioconductor-motifbreakr + version: 1.10.0 + diff --git a/recipes/bioconductor-motifcounter/build.sh b/recipes/bioconductor-motifcounter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motifcounter/build.sh +++ b/recipes/bioconductor-motifcounter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifcounter/meta.yaml b/recipes/bioconductor-motifcounter/meta.yaml index 851ddd0a8de38..af9aa8709b4f9 100644 --- a/recipes/bioconductor-motifcounter/meta.yaml +++ b/recipes/bioconductor-motifcounter/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "motifcounter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 789db94396699281cf357a9d3f09ac3ab9ba02ba8a100a95cc996aa489de532c + md5: 17980f892c118972ea93583cd449328d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown, testthat, MotifDb, seqLogo, prettydoc requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base build: - {{ compiler('c') }} @@ -30,8 +31,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: '''motifcounter'' provides functionality to compute the statistics related with motif matching and counting of motif matches in DNA sequences. As an input, ''motifcounter'' requires a motif in terms of a position frequency matrix (PFM). Furthermore, a set of DNA sequences is required to estimated a higher-order background model (BGM). The package provides functions to investigate the the per-position and per strand log-likelihood scores between the PFM and the BGM across a given sequence of set of sequences. Furthermore, the package facilitates motif matching based on an automatically derived score threshold. To this end the distribution of scores is efficiently determined and the score threshold is chosen for a user-prescribed significance level. This allows to control for the false positive rate. Moreover, ''motifcounter'' implements a motif match enrichment test based on two the number of motif matches that are expected in random DNA sequences. Motif enrichment is facilitated by either a compound Poisson approximation or a combinatorial approximation of the motif match counts. Both models take higher-order background models, the motif''s self-similarity, and hits on both DNA strands into account. The package is in particular useful for long motifs and/or relaxed choices of score thresholds, because the implemented algorithms efficiently bypass the need for enumerating a (potentially huge) set of DNA words that can give rise to a motif match.' - + summary: '''motifcounter'' provides motif matching, motif counting and motif enrichment functionality based on position frequency matrices. The main features of the packages include the utilization of higher-order background models and accounting for self-overlapping motif matches when determining motif enrichment. The background model allows to capture dinucleotide (or higher-order nucleotide) composition adequately which may reduced model biases and misleading results compared to using simple GC background models. When conducting a motif enrichment analysis based on the motif match count, the package relies on a compound Poisson distribution or alternatively a combinatorial model. These distribution account for self-overlapping motif structures as exemplified by repeat-like or palindromic motifs, and allow to determine the p-value and fold-enrichment for a set of observed motif matches.' +extra: + parent_recipe: + name: bioconductor-motifcounter + path: recipes/bioconductor-motifcounter + version: 1.4.0 diff --git a/recipes/bioconductor-motifdb/build.sh b/recipes/bioconductor-motifdb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motifdb/build.sh +++ b/recipes/bioconductor-motifdb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifdb/meta.yaml b/recipes/bioconductor-motifdb/meta.yaml index 24ff4da86f3f9..42049622bdd72 100644 --- a/recipes/bioconductor-motifdb/meta.yaml +++ b/recipes/bioconductor-motifdb/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.1" %} {% set name = "MotifDb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 79db31ce111250bb16bb78434632833cc369b6e0c65b7d37fc1f2b8e63b2ac60 + md5: 0e4f0a765443f27fa97aa8c26ba18331 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-splitstackshape run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-splitstackshape test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | file LICENSE' - summary: 'More than 9000 annotated position frequency matrices from 14 public sources, for multiple organisms.' + summary: 'More than 9900 annotated position frequency matrices from 14 public sources, for multiple organisms.' extra: identifiers: - biotools:motifdb - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-motifdb + path: recipes/bioconductor-motifdb + version: 1.22.0 + diff --git a/recipes/bioconductor-motifmatchr/build.sh b/recipes/bioconductor-motifmatchr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-motifmatchr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifmatchr/meta.yaml b/recipes/bioconductor-motifmatchr/meta.yaml new file mode 100644 index 0000000000000..dd72988110474 --- /dev/null +++ b/recipes/bioconductor-motifmatchr/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.0" %} +{% set name = "motifmatchr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 81b108d831a4e6084991dadd868f779a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - r-matrix + - r-rcpp + - r-rcpparmadillo + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - r-matrix + - r-rcpp + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'Quickly find motif matches for many motifs and many sequences. Wraps C++ code from the MOODS motif calling library, which was developed by Pasi Rastas, Janne Korhonen, and Petri Martinmäki.' + diff --git a/recipes/bioconductor-motifrg/build.sh b/recipes/bioconductor-motifrg/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motifrg/build.sh +++ b/recipes/bioconductor-motifrg/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifrg/meta.yaml b/recipes/bioconductor-motifrg/meta.yaml index 0e0487a5afce8..b28b0e488463f 100644 --- a/recipes/bioconductor-motifrg/meta.yaml +++ b/recipes/bioconductor-motifrg/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "motifRG" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3760c720798edbeae5ba2387bc293a1f949281f0c9bcd5a0c25f343f5bf4b057 + md5: 6e6636d8724438f812dd372a28196722 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for discriminative motif discovery using regression methods' extra: identifiers: - biotools:motifrg - doi:10.1093/bioinformatics/btt615 + parent_recipe: + name: bioconductor-motifrg + path: recipes/bioconductor-motifrg + version: 1.24.0 + diff --git a/recipes/bioconductor-motifstack/build.sh b/recipes/bioconductor-motifstack/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motifstack/build.sh +++ b/recipes/bioconductor-motifstack/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motifstack/meta.yaml b/recipes/bioconductor-motifstack/meta.yaml index fd75642a2f759..7c2de50c34f71 100644 --- a/recipes/bioconductor-motifstack/meta.yaml +++ b/recipes/bioconductor-motifstack/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "motifStack" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 24e32273232a69e8ac054d45022907aabfb84b7168f9beb49b3d732567cf72a5 + md5: 1ae29bba676e9d9f4d6c43430266946d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, MotifDb, RColorBrewer, BiocStyle, knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-motiv >=1.36.0,<1.38.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-motiv >=1.38.0,<1.39.0' - r-ade4 - r-base - r-grimport @@ -27,8 +29,8 @@ requirements: - r-scales - r-xml run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-motiv >=1.36.0,<1.38.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-motiv >=1.38.0,<1.39.0' - r-ade4 - r-base - r-grimport @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The motifStack package is designed for graphic representation of multiple motifs with different similarity scores. It works with both DNA/RNA sequence motif and amino acid sequence motif. In addition, it provides the flexibility for users to customize the graphic parameters such as the font type and symbol colors.' extra: identifiers: - biotools:motifstack - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-motifstack + path: recipes/bioconductor-motifstack + version: 1.24.1 + diff --git a/recipes/bioconductor-motiv/build.sh b/recipes/bioconductor-motiv/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-motiv/build.sh +++ b/recipes/bioconductor-motiv/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-motiv/meta.yaml b/recipes/bioconductor-motiv/meta.yaml index 3abde93d6a4bf..fc64a5b274446 100644 --- a/recipes/bioconductor-motiv/meta.yaml +++ b/recipes/bioconductor-motiv/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "MotIV" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da12f8071ef2e9bb2dd5dea46073e22b4981dbc2f1913a41774f2325580eb68f + md5: 513e9e6da9a911fc4d5b23c48b06c5d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: rtracklayer +# SystemRequirements: GNU Scientific Library >= 1.6 (http://www.gnu.org/software/gsl/) requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgadem >=2.28.0,<2.30.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgadem >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - - openblas run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgadem >=2.28.0,<2.30.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgadem >=2.30.0,<2.31.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -44,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package makes use of STAMP for comparing a set of motifs to a given database (e.g. JASPAR). It can also be used to visualize motifs, motif distributions, modules and filter motifs.' extra: identifiers: - biotools:motiv - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-motiv + path: recipes/bioconductor-motiv + version: 1.36.0 + diff --git a/recipes/bioconductor-mouse.db0/meta.yaml b/recipes/bioconductor-mouse.db0/meta.yaml new file mode 100644 index 0000000000000..57be6bab80414 --- /dev/null +++ b/recipes/bioconductor-mouse.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "mouse.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 01237a7808395a578f72063603b6db98 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for mouse, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-mouse.db0/post-link.sh b/recipes/bioconductor-mouse.db0/post-link.sh new file mode 100644 index 0000000000000..e2584ea7c7c19 --- /dev/null +++ b/recipes/bioconductor-mouse.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/mouse.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse.db0/bioconductor-mouse.db0_3.7.1_src_all.tar.gz" +) +MD5="01237a7808395a578f72063603b6db98" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse.db0/pre-unlink.sh b/recipes/bioconductor-mouse.db0/pre-unlink.sh new file mode 100644 index 0000000000000..aa660c7140be8 --- /dev/null +++ b/recipes/bioconductor-mouse.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse.db0 diff --git a/recipes/bioconductor-mouse4302.db/meta.yaml b/recipes/bioconductor-mouse4302.db/meta.yaml new file mode 100644 index 0000000000000..f0709c398fa4e --- /dev/null +++ b/recipes/bioconductor-mouse4302.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mouse4302.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f959fad0072a265d04a8851db1deed74 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Mouse Genome 430 2.0 Array annotation data (chip mouse4302) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mouse4302.db/post-link.sh b/recipes/bioconductor-mouse4302.db/post-link.sh new file mode 100644 index 0000000000000..0852b25a0754a --- /dev/null +++ b/recipes/bioconductor-mouse4302.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse4302.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302.db/bioconductor-mouse4302.db_3.2.3_src_all.tar.gz" +) +MD5="f959fad0072a265d04a8851db1deed74" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse4302.db/pre-unlink.sh b/recipes/bioconductor-mouse4302.db/pre-unlink.sh new file mode 100644 index 0000000000000..c84688462d7a5 --- /dev/null +++ b/recipes/bioconductor-mouse4302.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse4302.db diff --git a/recipes/bioconductor-mouse4302barcodevecs/meta.yaml b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml new file mode 100644 index 0000000000000..93d3882df8639 --- /dev/null +++ b/recipes/bioconductor-mouse4302barcodevecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "mouse4302barcodevecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 01aade84e4b3b235cfe37e825c8fe171 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Data used by the barcode package for microarrays of type mouse4302.' + diff --git a/recipes/bioconductor-mouse4302barcodevecs/post-link.sh b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh new file mode 100644 index 0000000000000..e80b116aeb639 --- /dev/null +++ b/recipes/bioconductor-mouse4302barcodevecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse4302barcodevecs_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mouse4302barcodevecs_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302barcodevecs_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302barcodevecs/bioconductor-mouse4302barcodevecs_1.20.0_src_all.tar.gz" +) +MD5="01aade84e4b3b235cfe37e825c8fe171" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse4302barcodevecs/pre-unlink.sh b/recipes/bioconductor-mouse4302barcodevecs/pre-unlink.sh new file mode 100644 index 0000000000000..596fc9cc382cb --- /dev/null +++ b/recipes/bioconductor-mouse4302barcodevecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse4302barcodevecs diff --git a/recipes/bioconductor-mouse4302cdf/meta.yaml b/recipes/bioconductor-mouse4302cdf/meta.yaml new file mode 100644 index 0000000000000..fcee012a14516 --- /dev/null +++ b/recipes/bioconductor-mouse4302cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mouse4302cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bda3463613f958de35c58777db05cec2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mouse430_2.cdf file.' + diff --git a/recipes/bioconductor-mouse4302cdf/post-link.sh b/recipes/bioconductor-mouse4302cdf/post-link.sh new file mode 100644 index 0000000000000..99eeee2fd894e --- /dev/null +++ b/recipes/bioconductor-mouse4302cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse4302cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302cdf/bioconductor-mouse4302cdf_2.18.0_src_all.tar.gz" +) +MD5="bda3463613f958de35c58777db05cec2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse4302cdf/pre-unlink.sh b/recipes/bioconductor-mouse4302cdf/pre-unlink.sh new file mode 100644 index 0000000000000..89d6d49ebc0b6 --- /dev/null +++ b/recipes/bioconductor-mouse4302cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse4302cdf diff --git a/recipes/bioconductor-mouse4302frmavecs/meta.yaml b/recipes/bioconductor-mouse4302frmavecs/meta.yaml new file mode 100644 index 0000000000000..d835d5bdc5f64 --- /dev/null +++ b/recipes/bioconductor-mouse4302frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.5.0" %} +{% set name = "mouse4302frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ec144b381abbe54d696356c1c124e372 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-mouse4302frmavecs/post-link.sh b/recipes/bioconductor-mouse4302frmavecs/post-link.sh new file mode 100644 index 0000000000000..863d0f7c6916d --- /dev/null +++ b/recipes/bioconductor-mouse4302frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse4302frmavecs_1.5.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302frmavecs_1.5.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302frmavecs_1.5.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302frmavecs/bioconductor-mouse4302frmavecs_1.5.0_src_all.tar.gz" +) +MD5="ec144b381abbe54d696356c1c124e372" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse4302frmavecs/pre-unlink.sh b/recipes/bioconductor-mouse4302frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..bb09cab8956e0 --- /dev/null +++ b/recipes/bioconductor-mouse4302frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse4302frmavecs diff --git a/recipes/bioconductor-mouse4302probe/meta.yaml b/recipes/bioconductor-mouse4302probe/meta.yaml new file mode 100644 index 0000000000000..39d73c6a03754 --- /dev/null +++ b/recipes/bioconductor-mouse4302probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mouse4302probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7116787a7db241a545e79e419a8cfa0d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-mouse4302probe/post-link.sh b/recipes/bioconductor-mouse4302probe/post-link.sh new file mode 100644 index 0000000000000..bd069e23bc491 --- /dev/null +++ b/recipes/bioconductor-mouse4302probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse4302probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse4302probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse4302probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse4302probe/bioconductor-mouse4302probe_2.18.0_src_all.tar.gz" +) +MD5="7116787a7db241a545e79e419a8cfa0d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse4302probe/pre-unlink.sh b/recipes/bioconductor-mouse4302probe/pre-unlink.sh new file mode 100644 index 0000000000000..52a8f68c9fc66 --- /dev/null +++ b/recipes/bioconductor-mouse4302probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse4302probe diff --git a/recipes/bioconductor-mouse430a2.db/meta.yaml b/recipes/bioconductor-mouse430a2.db/meta.yaml new file mode 100644 index 0000000000000..7640d865e93f7 --- /dev/null +++ b/recipes/bioconductor-mouse430a2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mouse430a2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4700ba9bf151277334af4fef9020a197 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Mouse Genome 430A 2.0 Array annotation data (chip mouse430a2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mouse430a2.db/post-link.sh b/recipes/bioconductor-mouse430a2.db/post-link.sh new file mode 100644 index 0000000000000..73befef803f09 --- /dev/null +++ b/recipes/bioconductor-mouse430a2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse430a2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mouse430a2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2.db/bioconductor-mouse430a2.db_3.2.3_src_all.tar.gz" +) +MD5="4700ba9bf151277334af4fef9020a197" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse430a2.db/pre-unlink.sh b/recipes/bioconductor-mouse430a2.db/pre-unlink.sh new file mode 100644 index 0000000000000..a8e444bc78628 --- /dev/null +++ b/recipes/bioconductor-mouse430a2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse430a2.db diff --git a/recipes/bioconductor-mouse430a2cdf/meta.yaml b/recipes/bioconductor-mouse430a2cdf/meta.yaml new file mode 100644 index 0000000000000..6a80d567e9a3c --- /dev/null +++ b/recipes/bioconductor-mouse430a2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mouse430a2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1114c0415d1200bc21ad205e0830b075 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mouse430A_2.cdf file.' + diff --git a/recipes/bioconductor-mouse430a2cdf/post-link.sh b/recipes/bioconductor-mouse430a2cdf/post-link.sh new file mode 100644 index 0000000000000..7378333ea0cf3 --- /dev/null +++ b/recipes/bioconductor-mouse430a2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse430a2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse430a2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2cdf/bioconductor-mouse430a2cdf_2.18.0_src_all.tar.gz" +) +MD5="1114c0415d1200bc21ad205e0830b075" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse430a2cdf/pre-unlink.sh b/recipes/bioconductor-mouse430a2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..ec4f7aca7df47 --- /dev/null +++ b/recipes/bioconductor-mouse430a2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse430a2cdf diff --git a/recipes/bioconductor-mouse430a2frmavecs/meta.yaml b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml new file mode 100644 index 0000000000000..d42e4af88070d --- /dev/null +++ b/recipes/bioconductor-mouse430a2frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.3.0" %} +{% set name = "mouse430a2frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3bcb8de9182bbb8de5d560748eafa0cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-mouse430a2frmavecs/post-link.sh b/recipes/bioconductor-mouse430a2frmavecs/post-link.sh new file mode 100644 index 0000000000000..e64b1d7800a14 --- /dev/null +++ b/recipes/bioconductor-mouse430a2frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse430a2frmavecs_1.3.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2frmavecs_1.3.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse430a2frmavecs_1.3.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2frmavecs/bioconductor-mouse430a2frmavecs_1.3.0_src_all.tar.gz" +) +MD5="3bcb8de9182bbb8de5d560748eafa0cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse430a2frmavecs/pre-unlink.sh b/recipes/bioconductor-mouse430a2frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..09f91aed58695 --- /dev/null +++ b/recipes/bioconductor-mouse430a2frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse430a2frmavecs diff --git a/recipes/bioconductor-mouse430a2probe/meta.yaml b/recipes/bioconductor-mouse430a2probe/meta.yaml new file mode 100644 index 0000000000000..43d2d0da46697 --- /dev/null +++ b/recipes/bioconductor-mouse430a2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mouse430a2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bb3c34477d4fcf03a539772011118795 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mouse430A\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-mouse430a2probe/post-link.sh b/recipes/bioconductor-mouse430a2probe/post-link.sh new file mode 100644 index 0000000000000..e61da4a643010 --- /dev/null +++ b/recipes/bioconductor-mouse430a2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouse430a2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouse430a2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mouse430a2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mouse430a2probe/bioconductor-mouse430a2probe_2.18.0_src_all.tar.gz" +) +MD5="bb3c34477d4fcf03a539772011118795" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mouse430a2probe/pre-unlink.sh b/recipes/bioconductor-mouse430a2probe/pre-unlink.sh new file mode 100644 index 0000000000000..cfcde008b5cf3 --- /dev/null +++ b/recipes/bioconductor-mouse430a2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouse430a2probe diff --git a/recipes/bioconductor-mousechrloc/meta.yaml b/recipes/bioconductor-mousechrloc/meta.yaml new file mode 100644 index 0000000000000..cc36c7e3cd185 --- /dev/null +++ b/recipes/bioconductor-mousechrloc/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.1.6" %} +{% set name = "mouseCHRLOC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0b81d7391e628cc355af4de3c5585a5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'Annotation data file for mouseCHRLOC assembled using data from public data repositories' + diff --git a/recipes/bioconductor-mousechrloc/post-link.sh b/recipes/bioconductor-mousechrloc/post-link.sh new file mode 100644 index 0000000000000..28548d0e18029 --- /dev/null +++ b/recipes/bioconductor-mousechrloc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mouseCHRLOC_2.1.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mouseCHRLOC_2.1.6.tar.gz" + "https://bioarchive.galaxyproject.org/mouseCHRLOC_2.1.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mousechrloc/bioconductor-mousechrloc_2.1.6_src_all.tar.gz" +) +MD5="0b81d7391e628cc355af4de3c5585a5f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mousechrloc/pre-unlink.sh b/recipes/bioconductor-mousechrloc/pre-unlink.sh new file mode 100644 index 0000000000000..240c99004f948 --- /dev/null +++ b/recipes/bioconductor-mousechrloc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mouseCHRLOC diff --git a/recipes/bioconductor-mpedbarray.db/meta.yaml b/recipes/bioconductor-mpedbarray.db/meta.yaml new file mode 100644 index 0000000000000..118d221526daa --- /dev/null +++ b/recipes/bioconductor-mpedbarray.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mpedbarray.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7bcd1fee1554b6f8844c9bf30b7db4ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Nelson Lab mpedbarray Annotation Data (mpedbarray) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mpedbarray.db/post-link.sh b/recipes/bioconductor-mpedbarray.db/post-link.sh new file mode 100644 index 0000000000000..bf5ef0a66b6d2 --- /dev/null +++ b/recipes/bioconductor-mpedbarray.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mpedbarray.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mpedbarray.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mpedbarray.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mpedbarray.db/bioconductor-mpedbarray.db_3.2.3_src_all.tar.gz" +) +MD5="7bcd1fee1554b6f8844c9bf30b7db4ef" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mpedbarray.db/pre-unlink.sh b/recipes/bioconductor-mpedbarray.db/pre-unlink.sh new file mode 100644 index 0000000000000..575f88faa5fd6 --- /dev/null +++ b/recipes/bioconductor-mpedbarray.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mpedbarray.db diff --git a/recipes/bioconductor-mpfe/build.sh b/recipes/bioconductor-mpfe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mpfe/build.sh +++ b/recipes/bioconductor-mpfe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mpfe/meta.yaml b/recipes/bioconductor-mpfe/meta.yaml index 7360be8d20d64..102cd3d3f6feb 100644 --- a/recipes/bioconductor-mpfe/meta.yaml +++ b/recipes/bioconductor-mpfe/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "MPFE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d9c09c28caa072cd8c879f24f642bf05a5987a193fa2efa869ed6cbe78e782d0 + md5: 92ff1513ce4265b001b14cf66c945c7d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Estimate distribution of methylation patterns from a table of counts from a bisulphite sequencing experiment given a non-conversion rate and read error rate.' extra: identifiers: - biotools:mpfe - doi:10.1186/s12859-015-0600-6 + parent_recipe: + name: bioconductor-mpfe + path: recipes/bioconductor-mpfe + version: 1.16.0 + diff --git a/recipes/bioconductor-mpra/build.sh b/recipes/bioconductor-mpra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mpra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mpra/meta.yaml b/recipes/bioconductor-mpra/meta.yaml new file mode 100644 index 0000000000000..2f7a95ec0896e --- /dev/null +++ b/recipes/bioconductor-mpra/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.1" %} +{% set name = "mpra" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b0422b285ab02e09f2f90544ce57a1d9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-scales + - r-statmod + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-scales + - r-statmod +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools for data management, count preprocessing, and differential analysis in massively parallel report assays (MPRA).' + diff --git a/recipes/bioconductor-mpranalyze/build.sh b/recipes/bioconductor-mpranalyze/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mpranalyze/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mpranalyze/meta.yaml b/recipes/bioconductor-mpranalyze/meta.yaml new file mode 100644 index 0000000000000..4d498fb3e69d8 --- /dev/null +++ b/recipes/bioconductor-mpranalyze/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "MPRAnalyze" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 541246cf352908065896374ab33e6957 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-progress + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-progress +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'MPRAnalyze provides statistical framework for the analysis of data generated by Massively Parallel Reporter Assays (MPRAs), used to directly measure enhancer activity. MPRAnalyze can be used for quantification of enhancer activity, classification of active enhancers and comparative analyses of enhancer activity between conditions. MPRAnalyze construct a nested pair of generalized linear models (GLMs) to relate the DNA and RNA observations, easily adjustable to various experimental designs and conditions, and provides a set of rigorous statistical testig schemes.' + diff --git a/recipes/bioconductor-msa/build.sh b/recipes/bioconductor-msa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msa/meta.yaml b/recipes/bioconductor-msa/meta.yaml new file mode 100644 index 0000000000000..ea34c454942a7 --- /dev/null +++ b/recipes/bioconductor-msa/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.14.0" %} +{% set name = "msa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 65b7ca9155681b6bb247565c249918e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: Biobase, knitr, seqinr, ape, phangorn +# SystemRequirements: GNU make +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-rcpp >=0.11.1' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-rcpp >=0.11.1' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The ''msa'' package provides a unified R/Bioconductor interface to the multiple sequence alignment algorithms ClustalW, ClustalOmega, and Muscle. All three algorithms are integrated in the package, therefore, they do not depend on any external software tools and are available for all major platforms. The multiple sequence alignment algorithms are complemented by a function for pretty-printing multiple sequence alignments using the LaTeX package TeXshade.' + diff --git a/recipes/bioconductor-msd16s/meta.yaml b/recipes/bioconductor-msd16s/meta.yaml new file mode 100644 index 0000000000000..4a5078a3b2e1e --- /dev/null +++ b/recipes/bioconductor-msd16s/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "msd16s" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1c717466a3154de3717810a24aa2620f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-metagenomeseq >=1.24.0,<1.25.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gut 16S sequencing expression data from 992 healthy and moderate-to-severe diarrhetic samples used in ''Diarrhea in young children from low-income countries leads to large-scale alterations in intestinal microbiota composition''.' + diff --git a/recipes/bioconductor-msd16s/post-link.sh b/recipes/bioconductor-msd16s/post-link.sh new file mode 100644 index 0000000000000..39eb513b68779 --- /dev/null +++ b/recipes/bioconductor-msd16s/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="msd16s_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msd16s_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/msd16s_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msd16s/bioconductor-msd16s_1.2.0_src_all.tar.gz" +) +MD5="1c717466a3154de3717810a24aa2620f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-msd16s/pre-unlink.sh b/recipes/bioconductor-msd16s/pre-unlink.sh new file mode 100644 index 0000000000000..50cf35decb769 --- /dev/null +++ b/recipes/bioconductor-msd16s/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ msd16s diff --git a/recipes/bioconductor-msdata/meta.yaml b/recipes/bioconductor-msdata/meta.yaml new file mode 100644 index 0000000000000..d11ca6817686d --- /dev/null +++ b/recipes/bioconductor-msdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.22.0" %} +{% set name = "msdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a0a63e124df97fca391c7ae458439dad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xcms, mzR, MSnbase +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Ion Trap positive ionization mode data in mzData file format. Subset from 500-850 m/z and 1190-1310 seconds, incl. MS2 and MS3, intensity threshold 100.000. Extracts from FTICR Apex III, m/z 400-450. Subset of UPLC - Bruker micrOTOFq data, both mzData, mzML and mz5. LC-MSMS and MRM files from proteomics experiments. PSI mzIdentML example files for various search engines.' + diff --git a/recipes/bioconductor-msdata/post-link.sh b/recipes/bioconductor-msdata/post-link.sh new file mode 100644 index 0000000000000..544240642a162 --- /dev/null +++ b/recipes/bioconductor-msdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="msdata_0.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msdata_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/msdata_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msdata/bioconductor-msdata_0.22.0_src_all.tar.gz" +) +MD5="a0a63e124df97fca391c7ae458439dad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-msdata/pre-unlink.sh b/recipes/bioconductor-msdata/pre-unlink.sh new file mode 100644 index 0000000000000..391dd0af8415c --- /dev/null +++ b/recipes/bioconductor-msdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ msdata diff --git a/recipes/bioconductor-msgbsr/build.sh b/recipes/bioconductor-msgbsr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msgbsr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msgbsr/meta.yaml b/recipes/bioconductor-msgbsr/meta.yaml new file mode 100644 index 0000000000000..471765203c1f7 --- /dev/null +++ b/recipes/bioconductor-msgbsr/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.6.0" %} +{% set name = "msgbsR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b9c5908b8e17e076243823c0f265940e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: roxygen2, BSgenome.Rnorvegicus.UCSC.rn6 +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-easyrnaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-plyr + - r-r.utils + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-easyrnaseq >=2.18.0,<2.19.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-plyr + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Pipeline for the anaysis of a MS-GBS experiment.' + diff --git a/recipes/bioconductor-msgfgui/build.sh b/recipes/bioconductor-msgfgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msgfgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msgfgui/meta.yaml b/recipes/bioconductor-msgfgui/meta.yaml new file mode 100644 index 0000000000000..5909154e234c1 --- /dev/null +++ b/recipes/bioconductor-msgfgui/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.16.0" %} +{% set name = "MSGFgui" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 173259cc9698ddb9281a13f6d166c34b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - 'bioconductor-msgfplus >=1.16.0,<1.17.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - r-base + - r-shiny + - 'r-shinyfiles >=0.4.0' + - r-xlsx + run: + - 'bioconductor-msgfplus >=1.16.0,<1.17.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - r-base + - r-shiny + - 'r-shinyfiles >=0.4.0' + - r-xlsx +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package makes it possible to perform analyses using the MSGFplus package in a GUI environment. Furthermore it enables the user to investigate the results using interactive plots, summary statistics and filtering. Lastly it exposes the current results to another R session so the user can seamlessly integrate the gui into other workflows.' + diff --git a/recipes/bioconductor-msgfplus/build.sh b/recipes/bioconductor-msgfplus/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msgfplus/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msgfplus/meta.yaml b/recipes/bioconductor-msgfplus/meta.yaml new file mode 100644 index 0000000000000..1ebd9b5870008 --- /dev/null +++ b/recipes/bioconductor-msgfplus/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.16.0" %} +{% set name = "MSGFplus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 811c35791c188ed3c1a1eb9ad740e2b6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gWidgets, knitr, testthat +# SystemRequirements: Java (>= 1.7) +requirements: + host: + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - r-base + run: + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package contains function to perform peptide identification using the MS-GF+ algorithm. The package contains functionality for building up a parameter set both in code and through a simple GUI, as well as running the algorithm in batches, potentially asynchronously.' + diff --git a/recipes/bioconductor-msmseda/build.sh b/recipes/bioconductor-msmseda/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msmseda/build.sh +++ b/recipes/bioconductor-msmseda/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msmseda/meta.yaml b/recipes/bioconductor-msmseda/meta.yaml index c7a190c92f246..95d7bb4568111 100644 --- a/recipes/bioconductor-msmseda/meta.yaml +++ b/recipes/bioconductor-msmseda/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "msmsEDA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 025ba8acc9cc34ce841340b66f4171742423bc86d72acc8117c9816a0918344a + md5: ee7217c0d5ab5172234cf644ff61dad4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' - r-base - r-gplots - r-mass - r-rcolorbrewer run: - - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' - r-base - r-gplots - r-mass @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Exploratory data analysis to assess the quality of a set of LC-MS/MS experiments, and visualize de influence of the involved factors.' extra: identifiers: - biotools:msmseda - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-msmseda + path: recipes/bioconductor-msmseda + version: 1.18.0 + diff --git a/recipes/bioconductor-msmstests/build.sh b/recipes/bioconductor-msmstests/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msmstests/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msmstests/meta.yaml b/recipes/bioconductor-msmstests/meta.yaml new file mode 100644 index 0000000000000..a54c3b279c35d --- /dev/null +++ b/recipes/bioconductor-msmstests/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.20.0" %} +{% set name = "msmsTests" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8c55c20520bf995d48fb4e17dcd448a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-msmseda >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + run: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-msmseda >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Statistical tests for label-free LC-MS/MS data by spectral counts, to discover differentially expressed proteins between two biological conditions. Three tests are available: Poisson GLM regression, quasi-likelihood GLM regression, and the negative binomial of the edgeR package.The three models admit blocking factors to control for nuissance variables.To assure a good level of reproducibility a post-test filter is available, where we may set the minimum effect size considered biologicaly relevant, and the minimum expression of the most abundant condition.' + diff --git a/recipes/bioconductor-msnbase/build.sh b/recipes/bioconductor-msnbase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msnbase/build.sh +++ b/recipes/bioconductor-msnbase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msnbase/conda_build_config.yaml b/recipes/bioconductor-msnbase/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-msnbase/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-msnbase/meta.yaml b/recipes/bioconductor-msnbase/meta.yaml index 97d2e3c6c63a8..1a8219c6bf0fe 100644 --- a/recipes/bioconductor-msnbase/meta.yaml +++ b/recipes/bioconductor-msnbase/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "2.6.4" %} +{% set version = "2.8.2" %} {% set name = "MSnbase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 35872e6a5057deb33ff46bb544c0c15c781f6ae15f3551b437b6b41c166a3bb2 + md5: 3e31a586f6f980ae2c81d55cf4ba5288 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, pryr, gridExtra, microbenchmark, zoo, knitr (>= 1.1.0), rols, Rdisop, pRoloc, pRolocdata (>= 1.7.1), msdata (>= 0.19.3), roxygen2, rgl, rpx, AnnotationHub, BiocStyle (>= 2.5.19), rmarkdown, imputeLCMD, norm, gplots, shiny, magrittr, SummarizedExperiment requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-digest - r-ggplot2 @@ -42,19 +43,19 @@ requirements: - r-scales - r-xml run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-digest - r-ggplot2 @@ -73,9 +74,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MSnbase provides infrastructure for manipulation, processing and visualisation of mass spectrometry and proteomics data, ranging from raw to quantitative and annotated data.' extra: identifiers: - biotools:msnbase + parent_recipe: + name: bioconductor-msnbase + path: recipes/bioconductor-msnbase + version: 2.6.4 + diff --git a/recipes/bioconductor-msnid/build.sh b/recipes/bioconductor-msnid/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-msnid/build.sh +++ b/recipes/bioconductor-msnid/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msnid/meta.yaml b/recipes/bioconductor-msnid/meta.yaml index 5a361b3fa9be4..6f4d0c82cc893 100644 --- a/recipes/bioconductor-msnid/meta.yaml +++ b/recipes/bioconductor-msnid/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.1" %} {% set name = "MSnID" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 27503867660c54d397ff1b29972185e7ba1a3317e4014f7e24201012212b589c + md5: 6ed6ba769c2e517b3bda627fa3f759ee build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, msmsTests, ggplot2, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - r-base - r-data.table - r-doparallel @@ -33,11 +34,11 @@ requirements: - r-rcpp - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - r-base - r-data.table - r-doparallel @@ -54,10 +55,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Extracts MS/MS ID data from mzIdentML (leveraging mzID package) or text files. After collating the search results from multiple datasets it assesses their identification quality and optimize filtering criteria to achieve the maximum number of identifications while not exceeding a specified false discovery rate. Also contains a number of utilities to explore the MS/MS results and assess missed and irregular enzymatic cleavages, mass measurement accuracy, etc.' extra: identifiers: - biotools:msnid - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-msnid + path: recipes/bioconductor-msnid + version: 1.14.0 + diff --git a/recipes/bioconductor-mspurity/build.sh b/recipes/bioconductor-mspurity/build.sh index da43ce2168312..c1d13421f5f1e 100755 --- a/recipes/bioconductor-mspurity/build.sh +++ b/recipes/bioconductor-mspurity/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mspurity/meta.yaml b/recipes/bioconductor-mspurity/meta.yaml index 0904084cbc4d3..8e0100e630cda 100644 --- a/recipes/bioconductor-mspurity/meta.yaml +++ b/recipes/bioconductor-mspurity/meta.yaml @@ -1,24 +1,25 @@ -{% set version = "1.6.2" %} +{% set version = "1.8.0" %} {% set name = "msPurity" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ebea0db0b8717636f27bd00504abe0432c64106dc6ecbdbeeab6f79d6c36fee9 + md5: 3074b76fb2b1feb6057eefb1f0d08375 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, xcms, BiocStyle, knitr, rmarkdown, msPurityData, CAMERA requirements: host: - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base - r-dbi - r-dosnow @@ -31,7 +32,7 @@ requirements: - r-rsqlite - r-stringr run: - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base - r-dbi - r-dosnow @@ -50,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Assess the contribution of the targeted precursor in fragmentation acquired or anticipated isolation windows using a metric called "precursor purity". Also provides simple processing steps (averaging, filtering, blank subtraction, etc) for DI-MS data. Works for both LC-MS(/MS) and DI-MS(/MS) data. Spectral matching of fragmentation spectra can also be run against a SQLite database of library spectra.' extra: identifiers: - biotools:mspurity - doi:10.1021/acs.analchem.6b04358 + parent_recipe: + name: bioconductor-mspurity + path: recipes/bioconductor-mspurity + version: 1.6.2 + diff --git a/recipes/bioconductor-mspuritydata/meta.yaml b/recipes/bioconductor-mspuritydata/meta.yaml index 76e46174a4827..99058fedf2f10 100644 --- a/recipes/bioconductor-mspuritydata/meta.yaml +++ b/recipes/bioconductor-mspuritydata/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "msPurityData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c871a3b116f0944716620d15c5f36509ebfcc09564d0d64ea4a9a88afb27e179 + md5: 4425b2e32df130a6cdd51cf1647ed17a build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Fragmentation spectral libraries and data to test the msPurity package' - +extra: + parent_recipe: + name: bioconductor-mspuritydata + path: recipes/bioconductor-mspuritydata + version: 1.8.0 diff --git a/recipes/bioconductor-mspuritydata/post-link.sh b/recipes/bioconductor-mspuritydata/post-link.sh index eabf608499ab0..ca72bc030662a 100644 --- a/recipes/bioconductor-mspuritydata/post-link.sh +++ b/recipes/bioconductor-mspuritydata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="msPurityData_1.8.0.tar.gz" +FN="msPurityData_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/msPurityData_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/msPurityData_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msPurityData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/msPurityData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mspuritydata/bioconductor-mspuritydata_1.10.0_src_all.tar.gz" ) -MD5="fc31af64f42480bbd8b90bc3a3e087db" +MD5="4425b2e32df130a6cdd51cf1647ed17a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-msqc1/meta.yaml b/recipes/bioconductor-msqc1/meta.yaml new file mode 100644 index 0000000000000..fc57bba2f17f8 --- /dev/null +++ b/recipes/bioconductor-msqc1/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "msqc1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9c2ac1fa46c8e7b1baa7e503c5c8d3b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat, specL +requirements: + host: + - r-base + - r-lattice + run: + - r-base + - r-lattice + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'The data set contains an eight technical replicate data set and a three replicate dilution series of the MS Qual/Quant QC Mix standard sample (Sigma-Aldrich, Buchs, Switzerland) measured on five different mass spec platforms at the Functional Genomics Center Zurich.' + diff --git a/recipes/bioconductor-msqc1/post-link.sh b/recipes/bioconductor-msqc1/post-link.sh new file mode 100644 index 0000000000000..f3bb24d3734dc --- /dev/null +++ b/recipes/bioconductor-msqc1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="msqc1_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/msqc1_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/msqc1_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msqc1/bioconductor-msqc1_1.10.0_src_all.tar.gz" +) +MD5="9c2ac1fa46c8e7b1baa7e503c5c8d3b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-msqc1/pre-unlink.sh b/recipes/bioconductor-msqc1/pre-unlink.sh new file mode 100644 index 0000000000000..7b9b2f5073479 --- /dev/null +++ b/recipes/bioconductor-msqc1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ msqc1 diff --git a/recipes/bioconductor-msstats/build.sh b/recipes/bioconductor-msstats/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstats/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstats/meta.yaml b/recipes/bioconductor-msstats/meta.yaml new file mode 100644 index 0000000000000..a46693bc2ab27 --- /dev/null +++ b/recipes/bioconductor-msstats/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "3.14.0" %} +{% set name = "MSstats" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f739e109c0b98bb138dea3f20f6a609a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, MSstatsBioData +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-data.table + - r-dosnow + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggrepel + - r-gplots + - r-lme4 + - r-mass + - r-minpack.lm + - r-randomforest + - r-reshape2 + - r-snow + - r-stringr + - r-survival + - r-tidyr + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-base + - r-data.table + - r-dosnow + - r-dplyr + - r-foreach + - r-ggplot2 + - r-ggrepel + - r-gplots + - r-lme4 + - r-mass + - r-minpack.lm + - r-randomforest + - r-reshape2 + - r-snow + - r-stringr + - r-survival + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A set of tools for statistical relative protein significance analysis in DDA, SRM and DIA experiments.' + diff --git a/recipes/bioconductor-msstatsbiodata/meta.yaml b/recipes/bioconductor-msstatsbiodata/meta.yaml new file mode 100644 index 0000000000000..19f9ff21fbc5e --- /dev/null +++ b/recipes/bioconductor-msstatsbiodata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.4.0" %} +{% set name = "MSstatsBioData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d6b9978157012351f0fea33b1c678296 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, MSstats +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides the peak intensity data for detecting differentially abundant proteins in seven published biological investigations.' + diff --git a/recipes/bioconductor-msstatsbiodata/post-link.sh b/recipes/bioconductor-msstatsbiodata/post-link.sh new file mode 100644 index 0000000000000..86d438d785dd8 --- /dev/null +++ b/recipes/bioconductor-msstatsbiodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MSstatsBioData_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MSstatsBioData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/MSstatsBioData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-msstatsbiodata/bioconductor-msstatsbiodata_1.4.0_src_all.tar.gz" +) +MD5="d6b9978157012351f0fea33b1c678296" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-msstatsbiodata/pre-unlink.sh b/recipes/bioconductor-msstatsbiodata/pre-unlink.sh new file mode 100644 index 0000000000000..1e9c43b41009a --- /dev/null +++ b/recipes/bioconductor-msstatsbiodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MSstatsBioData diff --git a/recipes/bioconductor-msstatsqc/build.sh b/recipes/bioconductor-msstatsqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstatsqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsqc/meta.yaml b/recipes/bioconductor-msstatsqc/meta.yaml new file mode 100644 index 0000000000000..52ff707603309 --- /dev/null +++ b/recipes/bioconductor-msstatsqc/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "2.0.0" %} +{% set name = "MSstatsQC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d3f5863b2c83aaaecca2b1dd008c864 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr,rmarkdown, testthat, RforProteomics +requirements: + host: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qcmetrics >=1.20.0,<1.21.0' + - r-base + - r-dplyr + - r-ggextra + - r-ggplot2 + - r-plotly + - r-recordlinkage + run: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qcmetrics >=1.20.0,<1.21.0' + - r-base + - r-dplyr + - r-ggextra + - r-ggplot2 + - r-plotly + - r-recordlinkage +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'MSstatsQC is an R package which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.' + diff --git a/recipes/bioconductor-msstatsqcgui/build.sh b/recipes/bioconductor-msstatsqcgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstatsqcgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatsqcgui/meta.yaml b/recipes/bioconductor-msstatsqcgui/meta.yaml new file mode 100644 index 0000000000000..e30ba0c42a098 --- /dev/null +++ b/recipes/bioconductor-msstatsqcgui/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.2.0" %} +{% set name = "MSstatsQCgui" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d6fca497c46ca3dca3cc597ac2dcb1b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-msstatsqc >=2.0.0,<2.1.0' + - r-base + - r-dplyr + - r-ggextra + - r-gridextra + - r-plotly + - r-recordlinkage + - r-shiny + run: + - 'bioconductor-msstatsqc >=2.0.0,<2.1.0' + - r-base + - r-dplyr + - r-ggextra + - r-gridextra + - r-plotly + - r-recordlinkage + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic License 2.0' + summary: 'MSstatsQCgui is a Shiny app which provides longitudinal system suitability monitoring and quality control tools for proteomic experiments.' + diff --git a/recipes/bioconductor-msstatstmt/build.sh b/recipes/bioconductor-msstatstmt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-msstatstmt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-msstatstmt/meta.yaml b/recipes/bioconductor-msstatstmt/meta.yaml new file mode 100644 index 0000000000000..315ad8242a2dc --- /dev/null +++ b/recipes/bioconductor-msstatstmt/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "MSstatsTMT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: da5a08e2095cbf8073f533411e583450 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msstats >=3.14.0,<3.15.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-lme4 + - r-matrixstats + - r-nlme + - r-reshape2 + - r-tidyr + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msstats >=3.14.0,<3.15.0' + - r-base + - r-data.table + - r-dplyr + - r-ggplot2 + - r-lme4 + - r-matrixstats + - r-nlme + - r-reshape2 + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools for protein significance analysis in shotgun mass spectrometry-based proteomic experiments with tandem mass tag (TMT) labeling.' + diff --git a/recipes/bioconductor-mta10probeset.db/meta.yaml b/recipes/bioconductor-mta10probeset.db/meta.yaml new file mode 100644 index 0000000000000..c699afe260d7c --- /dev/null +++ b/recipes/bioconductor-mta10probeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mta10probeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 80ca03d68b6c9dd51d50122039b2d8ba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mta10 annotation data (chip mta10probeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mta10probeset.db/post-link.sh b/recipes/bioconductor-mta10probeset.db/post-link.sh new file mode 100644 index 0000000000000..d673a9f5c5012 --- /dev/null +++ b/recipes/bioconductor-mta10probeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mta10probeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mta10probeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mta10probeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mta10probeset.db/bioconductor-mta10probeset.db_8.7.0_src_all.tar.gz" +) +MD5="80ca03d68b6c9dd51d50122039b2d8ba" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mta10probeset.db/pre-unlink.sh b/recipes/bioconductor-mta10probeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..75d24dcecd377 --- /dev/null +++ b/recipes/bioconductor-mta10probeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mta10probeset.db diff --git a/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..688f5e77a0d88 --- /dev/null +++ b/recipes/bioconductor-mta10transcriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "mta10transcriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 04cb3bf18fafd5bef3c4444d32df8bd0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix mta10 annotation data (chip mta10transcriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh b/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..a96d57ac4a345 --- /dev/null +++ b/recipes/bioconductor-mta10transcriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mta10transcriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mta10transcriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/mta10transcriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mta10transcriptcluster.db/bioconductor-mta10transcriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="04cb3bf18fafd5bef3c4444d32df8bd0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mta10transcriptcluster.db/pre-unlink.sh b/recipes/bioconductor-mta10transcriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..d7cf2c439f596 --- /dev/null +++ b/recipes/bioconductor-mta10transcriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mta10transcriptcluster.db diff --git a/recipes/bioconductor-mtbls2/meta.yaml b/recipes/bioconductor-mtbls2/meta.yaml new file mode 100644 index 0000000000000..13fb95a1f81be --- /dev/null +++ b/recipes/bioconductor-mtbls2/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "mtbls2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d5fee1a7b0b6c8511edb2f540f59997d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xcms (>= 3.0.0), CAMERA, Risa (>= 1.0.0), knitr, Heatplus, pcaMethods, sp +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: CC0 + summary: 'Indole-3-acetaldoxime (IAOx) represents an early intermediate of the biosynthesis of a variety of indolic secondary metabolites including the phytoanticipin indol-3-ylmethyl glucosinolate and the phytoalexin camalexin (3-thiazol-2''-yl-indole). Arabidopsis thaliana cyp79B2 cyp79B3 double knockout plants are completely impaired in the conversion of tryptophan to indole-3-acetaldoxime and do not accumulate IAOx-derived metabolites any longer. Consequently, comparative analysis of wild-type and cyp79B2 cyp79B3 plant lines has the potential to explore the complete range of IAOx-derived indolic secondary metabolites.' + diff --git a/recipes/bioconductor-mtbls2/post-link.sh b/recipes/bioconductor-mtbls2/post-link.sh new file mode 100644 index 0000000000000..465aa5074d393 --- /dev/null +++ b/recipes/bioconductor-mtbls2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mtbls2_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mtbls2_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/mtbls2_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mtbls2/bioconductor-mtbls2_1.12.0_src_all.tar.gz" +) +MD5="d5fee1a7b0b6c8511edb2f540f59997d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mtbls2/pre-unlink.sh b/recipes/bioconductor-mtbls2/pre-unlink.sh new file mode 100644 index 0000000000000..0a1dd496fe5f1 --- /dev/null +++ b/recipes/bioconductor-mtbls2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mtbls2 diff --git a/recipes/bioconductor-mtseeker/build.sh b/recipes/bioconductor-mtseeker/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-mtseeker/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mtseeker/meta.yaml b/recipes/bioconductor-mtseeker/meta.yaml new file mode 100644 index 0000000000000..4069c6a2952d9 --- /dev/null +++ b/recipes/bioconductor-mtseeker/meta.yaml @@ -0,0 +1,73 @@ +{% set version = "1.0.6" %} +{% set name = "MTseeker" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 32712fee3db29edecc7b398e555850f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MTseekerData, BiocStyle, rmarkdown, ggthemes, ggplot2, pkgdown, knitr, rsvg +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gmapr >=1.24.0,<1.25.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - r-base + - r-circlize + - r-jsonlite + - r-viridis + - r-xml2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gmapr >=1.24.0,<1.25.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-varianttools >=1.24.0,<1.25.0' + - r-base + - r-circlize + - r-jsonlite + - r-viridis + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Variant analysis tools for mitochondrial genetics.' + diff --git a/recipes/bioconductor-mtseekerdata/meta.yaml b/recipes/bioconductor-mtseekerdata/meta.yaml new file mode 100644 index 0000000000000..45d42b269e65d --- /dev/null +++ b/recipes/bioconductor-mtseekerdata/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.0.0" %} +{% set name = "MTseekerData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f5271cbb8d617a4fb35b794def24e72a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gmapR, xml2, rtracklayer +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mtseeker >=1.0.0,<1.1.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-mtseeker >=1.0.0,<1.1.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides examples for the MTseeker package vignette.' + diff --git a/recipes/bioconductor-mtseekerdata/post-link.sh b/recipes/bioconductor-mtseekerdata/post-link.sh new file mode 100644 index 0000000000000..0321a9ba5bcfc --- /dev/null +++ b/recipes/bioconductor-mtseekerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MTseekerData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MTseekerData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/MTseekerData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mtseekerdata/bioconductor-mtseekerdata_1.0.0_src_all.tar.gz" +) +MD5="f5271cbb8d617a4fb35b794def24e72a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mtseekerdata/pre-unlink.sh b/recipes/bioconductor-mtseekerdata/pre-unlink.sh new file mode 100644 index 0000000000000..d0e5e6e8746ed --- /dev/null +++ b/recipes/bioconductor-mtseekerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MTseekerData diff --git a/recipes/bioconductor-mu11ksuba.db/meta.yaml b/recipes/bioconductor-mu11ksuba.db/meta.yaml new file mode 100644 index 0000000000000..b71bc9de7e322 --- /dev/null +++ b/recipes/bioconductor-mu11ksuba.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mu11ksuba.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2ed9098b7efa45430488d4c9f8df0750 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine 11K Set annotation data (chip mu11ksuba) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu11ksuba.db/post-link.sh b/recipes/bioconductor-mu11ksuba.db/post-link.sh new file mode 100644 index 0000000000000..bb44543ae3955 --- /dev/null +++ b/recipes/bioconductor-mu11ksuba.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksuba.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksuba.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksuba.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksuba.db/bioconductor-mu11ksuba.db_3.2.3_src_all.tar.gz" +) +MD5="2ed9098b7efa45430488d4c9f8df0750" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksuba.db/pre-unlink.sh b/recipes/bioconductor-mu11ksuba.db/pre-unlink.sh new file mode 100644 index 0000000000000..44523c458e882 --- /dev/null +++ b/recipes/bioconductor-mu11ksuba.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksuba.db diff --git a/recipes/bioconductor-mu11ksubacdf/meta.yaml b/recipes/bioconductor-mu11ksubacdf/meta.yaml new file mode 100644 index 0000000000000..6ccda93ce9b3b --- /dev/null +++ b/recipes/bioconductor-mu11ksubacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu11ksubacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 52fb8ac56435775022fb62f40efafd22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu11KsubA.CDF file.' + diff --git a/recipes/bioconductor-mu11ksubacdf/post-link.sh b/recipes/bioconductor-mu11ksubacdf/post-link.sh new file mode 100644 index 0000000000000..40a8fa1b958a1 --- /dev/null +++ b/recipes/bioconductor-mu11ksubacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksubacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksubacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubacdf/bioconductor-mu11ksubacdf_2.18.0_src_all.tar.gz" +) +MD5="52fb8ac56435775022fb62f40efafd22" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksubacdf/pre-unlink.sh b/recipes/bioconductor-mu11ksubacdf/pre-unlink.sh new file mode 100644 index 0000000000000..a4300be17e42f --- /dev/null +++ b/recipes/bioconductor-mu11ksubacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksubacdf diff --git a/recipes/bioconductor-mu11ksubaprobe/meta.yaml b/recipes/bioconductor-mu11ksubaprobe/meta.yaml new file mode 100644 index 0000000000000..abbadff19ee6c --- /dev/null +++ b/recipes/bioconductor-mu11ksubaprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu11ksubaprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 813cd0750cca6ff0cfb696b83286177e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubA\_probe\_tab.' + diff --git a/recipes/bioconductor-mu11ksubaprobe/post-link.sh b/recipes/bioconductor-mu11ksubaprobe/post-link.sh new file mode 100644 index 0000000000000..52dbdf4d29ecc --- /dev/null +++ b/recipes/bioconductor-mu11ksubaprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksubaprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubaprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksubaprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubaprobe/bioconductor-mu11ksubaprobe_2.18.0_src_all.tar.gz" +) +MD5="813cd0750cca6ff0cfb696b83286177e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksubaprobe/pre-unlink.sh b/recipes/bioconductor-mu11ksubaprobe/pre-unlink.sh new file mode 100644 index 0000000000000..902774ee1b05a --- /dev/null +++ b/recipes/bioconductor-mu11ksubaprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksubaprobe diff --git a/recipes/bioconductor-mu11ksubb.db/meta.yaml b/recipes/bioconductor-mu11ksubb.db/meta.yaml new file mode 100644 index 0000000000000..0db8583818e79 --- /dev/null +++ b/recipes/bioconductor-mu11ksubb.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mu11ksubb.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 44bde347574efd353ae89f41c06ccf76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine 11K Set annotation data (chip mu11ksubb) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu11ksubb.db/post-link.sh b/recipes/bioconductor-mu11ksubb.db/post-link.sh new file mode 100644 index 0000000000000..c01b37610c145 --- /dev/null +++ b/recipes/bioconductor-mu11ksubb.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksubb.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubb.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksubb.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubb.db/bioconductor-mu11ksubb.db_3.2.3_src_all.tar.gz" +) +MD5="44bde347574efd353ae89f41c06ccf76" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksubb.db/pre-unlink.sh b/recipes/bioconductor-mu11ksubb.db/pre-unlink.sh new file mode 100644 index 0000000000000..bc884c03d8c16 --- /dev/null +++ b/recipes/bioconductor-mu11ksubb.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksubb.db diff --git a/recipes/bioconductor-mu11ksubbcdf/meta.yaml b/recipes/bioconductor-mu11ksubbcdf/meta.yaml new file mode 100644 index 0000000000000..22f084d0fff32 --- /dev/null +++ b/recipes/bioconductor-mu11ksubbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu11ksubbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f9691ea74e19dfe57bf6cca6ed396947 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu11KsubB.CDF file.' + diff --git a/recipes/bioconductor-mu11ksubbcdf/post-link.sh b/recipes/bioconductor-mu11ksubbcdf/post-link.sh new file mode 100644 index 0000000000000..ff17bc6af04e3 --- /dev/null +++ b/recipes/bioconductor-mu11ksubbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksubbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksubbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbcdf/bioconductor-mu11ksubbcdf_2.18.0_src_all.tar.gz" +) +MD5="f9691ea74e19dfe57bf6cca6ed396947" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksubbcdf/pre-unlink.sh b/recipes/bioconductor-mu11ksubbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..a08b2f770adb0 --- /dev/null +++ b/recipes/bioconductor-mu11ksubbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksubbcdf diff --git a/recipes/bioconductor-mu11ksubbprobe/meta.yaml b/recipes/bioconductor-mu11ksubbprobe/meta.yaml new file mode 100644 index 0000000000000..46df0e0f551ae --- /dev/null +++ b/recipes/bioconductor-mu11ksubbprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu11ksubbprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 28d162e18e4e16e3c6db47195d2ea0ac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Mu11KsubB\_probe\_tab.' + diff --git a/recipes/bioconductor-mu11ksubbprobe/post-link.sh b/recipes/bioconductor-mu11ksubbprobe/post-link.sh new file mode 100644 index 0000000000000..fecda913ffa46 --- /dev/null +++ b/recipes/bioconductor-mu11ksubbprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu11ksubbprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu11ksubbprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu11ksubbprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu11ksubbprobe/bioconductor-mu11ksubbprobe_2.18.0_src_all.tar.gz" +) +MD5="28d162e18e4e16e3c6db47195d2ea0ac" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu11ksubbprobe/pre-unlink.sh b/recipes/bioconductor-mu11ksubbprobe/pre-unlink.sh new file mode 100644 index 0000000000000..7fddcebd1fd69 --- /dev/null +++ b/recipes/bioconductor-mu11ksubbprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu11ksubbprobe diff --git a/recipes/bioconductor-mu15v1.db/meta.yaml b/recipes/bioconductor-mu15v1.db/meta.yaml new file mode 100644 index 0000000000000..f7cbe3c383b7f --- /dev/null +++ b/recipes/bioconductor-mu15v1.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "Mu15v1.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e9297b5fe223b046bc65dc6ea0b4376d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Genomics Shared Resource Mu15v1 Annotation Data (Mu15v1) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu15v1.db/post-link.sh b/recipes/bioconductor-mu15v1.db/post-link.sh new file mode 100644 index 0000000000000..c95fa4f398763 --- /dev/null +++ b/recipes/bioconductor-mu15v1.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Mu15v1.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mu15v1.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/Mu15v1.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu15v1.db/bioconductor-mu15v1.db_3.2.3_src_all.tar.gz" +) +MD5="e9297b5fe223b046bc65dc6ea0b4376d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu15v1.db/pre-unlink.sh b/recipes/bioconductor-mu15v1.db/pre-unlink.sh new file mode 100644 index 0000000000000..8325026a27644 --- /dev/null +++ b/recipes/bioconductor-mu15v1.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Mu15v1.db diff --git a/recipes/bioconductor-mu19ksuba.db/meta.yaml b/recipes/bioconductor-mu19ksuba.db/meta.yaml new file mode 100644 index 0000000000000..0825a74f872cd --- /dev/null +++ b/recipes/bioconductor-mu19ksuba.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mu19ksuba.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 668c92eb1b9e2367c5a69dc8d0498cca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome 19k Set annotation data (chip mu19ksuba) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu19ksuba.db/post-link.sh b/recipes/bioconductor-mu19ksuba.db/post-link.sh new file mode 100644 index 0000000000000..11d20d3a86d16 --- /dev/null +++ b/recipes/bioconductor-mu19ksuba.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksuba.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksuba.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksuba.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksuba.db/bioconductor-mu19ksuba.db_3.2.3_src_all.tar.gz" +) +MD5="668c92eb1b9e2367c5a69dc8d0498cca" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksuba.db/pre-unlink.sh b/recipes/bioconductor-mu19ksuba.db/pre-unlink.sh new file mode 100644 index 0000000000000..a57ccc46326cb --- /dev/null +++ b/recipes/bioconductor-mu19ksuba.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksuba.db diff --git a/recipes/bioconductor-mu19ksubacdf/meta.yaml b/recipes/bioconductor-mu19ksubacdf/meta.yaml new file mode 100644 index 0000000000000..5785479903c07 --- /dev/null +++ b/recipes/bioconductor-mu19ksubacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu19ksubacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83a9e7a3bac665b655786e66dbd77848 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu19KsubA.CDF file.' + diff --git a/recipes/bioconductor-mu19ksubacdf/post-link.sh b/recipes/bioconductor-mu19ksubacdf/post-link.sh new file mode 100644 index 0000000000000..6ba6dc32afcf3 --- /dev/null +++ b/recipes/bioconductor-mu19ksubacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksubacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksubacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubacdf/bioconductor-mu19ksubacdf_2.18.0_src_all.tar.gz" +) +MD5="83a9e7a3bac665b655786e66dbd77848" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksubacdf/pre-unlink.sh b/recipes/bioconductor-mu19ksubacdf/pre-unlink.sh new file mode 100644 index 0000000000000..a1627c4c7be92 --- /dev/null +++ b/recipes/bioconductor-mu19ksubacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksubacdf diff --git a/recipes/bioconductor-mu19ksubb.db/meta.yaml b/recipes/bioconductor-mu19ksubb.db/meta.yaml new file mode 100644 index 0000000000000..3915f7dce8eb7 --- /dev/null +++ b/recipes/bioconductor-mu19ksubb.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mu19ksubb.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 54ffae3e05d9fd79caadf51954473b93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome 19k Set annotation data (chip mu19ksubb) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu19ksubb.db/post-link.sh b/recipes/bioconductor-mu19ksubb.db/post-link.sh new file mode 100644 index 0000000000000..b838768053646 --- /dev/null +++ b/recipes/bioconductor-mu19ksubb.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksubb.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubb.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksubb.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubb.db/bioconductor-mu19ksubb.db_3.2.3_src_all.tar.gz" +) +MD5="54ffae3e05d9fd79caadf51954473b93" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksubb.db/pre-unlink.sh b/recipes/bioconductor-mu19ksubb.db/pre-unlink.sh new file mode 100644 index 0000000000000..473efb2ed3a9d --- /dev/null +++ b/recipes/bioconductor-mu19ksubb.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksubb.db diff --git a/recipes/bioconductor-mu19ksubbcdf/meta.yaml b/recipes/bioconductor-mu19ksubbcdf/meta.yaml new file mode 100644 index 0000000000000..41602cc41749e --- /dev/null +++ b/recipes/bioconductor-mu19ksubbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu19ksubbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 35e5ebcb4cb51950a85c1e3622bb39f0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu19KsubB.CDF file.' + diff --git a/recipes/bioconductor-mu19ksubbcdf/post-link.sh b/recipes/bioconductor-mu19ksubbcdf/post-link.sh new file mode 100644 index 0000000000000..0196a17c07402 --- /dev/null +++ b/recipes/bioconductor-mu19ksubbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksubbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksubbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubbcdf/bioconductor-mu19ksubbcdf_2.18.0_src_all.tar.gz" +) +MD5="35e5ebcb4cb51950a85c1e3622bb39f0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksubbcdf/pre-unlink.sh b/recipes/bioconductor-mu19ksubbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..f20f2940974b0 --- /dev/null +++ b/recipes/bioconductor-mu19ksubbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksubbcdf diff --git a/recipes/bioconductor-mu19ksubc.db/meta.yaml b/recipes/bioconductor-mu19ksubc.db/meta.yaml new file mode 100644 index 0000000000000..401061ac74a50 --- /dev/null +++ b/recipes/bioconductor-mu19ksubc.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "mu19ksubc.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0cb0abb16337b8acc9dd365f5225856c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Murine Genome 19k Set annotation data (chip mu19ksubc) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu19ksubc.db/post-link.sh b/recipes/bioconductor-mu19ksubc.db/post-link.sh new file mode 100644 index 0000000000000..60b5e13d6973a --- /dev/null +++ b/recipes/bioconductor-mu19ksubc.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksubc.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubc.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksubc.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubc.db/bioconductor-mu19ksubc.db_3.2.3_src_all.tar.gz" +) +MD5="0cb0abb16337b8acc9dd365f5225856c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksubc.db/pre-unlink.sh b/recipes/bioconductor-mu19ksubc.db/pre-unlink.sh new file mode 100644 index 0000000000000..e073925e52b12 --- /dev/null +++ b/recipes/bioconductor-mu19ksubc.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksubc.db diff --git a/recipes/bioconductor-mu19ksubccdf/meta.yaml b/recipes/bioconductor-mu19ksubccdf/meta.yaml new file mode 100644 index 0000000000000..ec2a46f586ddf --- /dev/null +++ b/recipes/bioconductor-mu19ksubccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu19ksubccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e53ef2716f88022e5e41e2cd857fc2a3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu19KsubC.CDF file.' + diff --git a/recipes/bioconductor-mu19ksubccdf/post-link.sh b/recipes/bioconductor-mu19ksubccdf/post-link.sh new file mode 100644 index 0000000000000..fd12c362e9932 --- /dev/null +++ b/recipes/bioconductor-mu19ksubccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu19ksubccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu19ksubccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu19ksubccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu19ksubccdf/bioconductor-mu19ksubccdf_2.18.0_src_all.tar.gz" +) +MD5="e53ef2716f88022e5e41e2cd857fc2a3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu19ksubccdf/pre-unlink.sh b/recipes/bioconductor-mu19ksubccdf/pre-unlink.sh new file mode 100644 index 0000000000000..67444d70a1b0f --- /dev/null +++ b/recipes/bioconductor-mu19ksubccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu19ksubccdf diff --git a/recipes/bioconductor-mu22v3.db/meta.yaml b/recipes/bioconductor-mu22v3.db/meta.yaml new file mode 100644 index 0000000000000..1337ee591df6a --- /dev/null +++ b/recipes/bioconductor-mu22v3.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "Mu22v3.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 44aaebe909be9b0108256194c55cf6fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Genomics Shared Resource Mu22v3 Annotation Data (Mu22v3) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mu22v3.db/post-link.sh b/recipes/bioconductor-mu22v3.db/post-link.sh new file mode 100644 index 0000000000000..f2e531eb850d4 --- /dev/null +++ b/recipes/bioconductor-mu22v3.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Mu22v3.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mu22v3.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/Mu22v3.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu22v3.db/bioconductor-mu22v3.db_3.2.3_src_all.tar.gz" +) +MD5="44aaebe909be9b0108256194c55cf6fb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu22v3.db/pre-unlink.sh b/recipes/bioconductor-mu22v3.db/pre-unlink.sh new file mode 100644 index 0000000000000..f851d8aef03b5 --- /dev/null +++ b/recipes/bioconductor-mu22v3.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Mu22v3.db diff --git a/recipes/bioconductor-mu6500subacdf/meta.yaml b/recipes/bioconductor-mu6500subacdf/meta.yaml new file mode 100644 index 0000000000000..807ab229d3cfe --- /dev/null +++ b/recipes/bioconductor-mu6500subacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu6500subacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e72152fc4bae307e3858160e018b7f92 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu6500subA.CDF file.' + diff --git a/recipes/bioconductor-mu6500subacdf/post-link.sh b/recipes/bioconductor-mu6500subacdf/post-link.sh new file mode 100644 index 0000000000000..c4349060f3bcf --- /dev/null +++ b/recipes/bioconductor-mu6500subacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu6500subacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu6500subacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subacdf/bioconductor-mu6500subacdf_2.18.0_src_all.tar.gz" +) +MD5="e72152fc4bae307e3858160e018b7f92" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu6500subacdf/pre-unlink.sh b/recipes/bioconductor-mu6500subacdf/pre-unlink.sh new file mode 100644 index 0000000000000..51f048c205ee0 --- /dev/null +++ b/recipes/bioconductor-mu6500subacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu6500subacdf diff --git a/recipes/bioconductor-mu6500subbcdf/meta.yaml b/recipes/bioconductor-mu6500subbcdf/meta.yaml new file mode 100644 index 0000000000000..4d7dfdf64999d --- /dev/null +++ b/recipes/bioconductor-mu6500subbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu6500subbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5000bea2a018b4b6ec05cda111438bc1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu6500subB.CDF file.' + diff --git a/recipes/bioconductor-mu6500subbcdf/post-link.sh b/recipes/bioconductor-mu6500subbcdf/post-link.sh new file mode 100644 index 0000000000000..0b44f226e2ba2 --- /dev/null +++ b/recipes/bioconductor-mu6500subbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu6500subbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu6500subbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subbcdf/bioconductor-mu6500subbcdf_2.18.0_src_all.tar.gz" +) +MD5="5000bea2a018b4b6ec05cda111438bc1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu6500subbcdf/pre-unlink.sh b/recipes/bioconductor-mu6500subbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..3b78915a1a670 --- /dev/null +++ b/recipes/bioconductor-mu6500subbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu6500subbcdf diff --git a/recipes/bioconductor-mu6500subccdf/meta.yaml b/recipes/bioconductor-mu6500subccdf/meta.yaml new file mode 100644 index 0000000000000..8eb1988a22edb --- /dev/null +++ b/recipes/bioconductor-mu6500subccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu6500subccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c7cbbe6c70a0a3ae11600ad6c0e540c1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu6500subC.CDF file.' + diff --git a/recipes/bioconductor-mu6500subccdf/post-link.sh b/recipes/bioconductor-mu6500subccdf/post-link.sh new file mode 100644 index 0000000000000..27881cd4c4d77 --- /dev/null +++ b/recipes/bioconductor-mu6500subccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu6500subccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu6500subccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subccdf/bioconductor-mu6500subccdf_2.18.0_src_all.tar.gz" +) +MD5="c7cbbe6c70a0a3ae11600ad6c0e540c1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu6500subccdf/pre-unlink.sh b/recipes/bioconductor-mu6500subccdf/pre-unlink.sh new file mode 100644 index 0000000000000..e8d4279a08997 --- /dev/null +++ b/recipes/bioconductor-mu6500subccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu6500subccdf diff --git a/recipes/bioconductor-mu6500subdcdf/meta.yaml b/recipes/bioconductor-mu6500subdcdf/meta.yaml new file mode 100644 index 0000000000000..d44b8a0512dc9 --- /dev/null +++ b/recipes/bioconductor-mu6500subdcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "mu6500subdcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a614674e8bc60fefd8520dd25d45f8d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Mu6500subD.CDF file.' + diff --git a/recipes/bioconductor-mu6500subdcdf/post-link.sh b/recipes/bioconductor-mu6500subdcdf/post-link.sh new file mode 100644 index 0000000000000..2cfb719da7c45 --- /dev/null +++ b/recipes/bioconductor-mu6500subdcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mu6500subdcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mu6500subdcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mu6500subdcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mu6500subdcdf/bioconductor-mu6500subdcdf_2.18.0_src_all.tar.gz" +) +MD5="a614674e8bc60fefd8520dd25d45f8d0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mu6500subdcdf/pre-unlink.sh b/recipes/bioconductor-mu6500subdcdf/pre-unlink.sh new file mode 100644 index 0000000000000..bf9a04884966b --- /dev/null +++ b/recipes/bioconductor-mu6500subdcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mu6500subdcdf diff --git a/recipes/bioconductor-mugaexampledata/meta.yaml b/recipes/bioconductor-mugaexampledata/meta.yaml new file mode 100644 index 0000000000000..e304cd33ae9c5 --- /dev/null +++ b/recipes/bioconductor-mugaexampledata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "MUGAExampleData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 66132942d0d409057570d914ec435e39 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This package contains example data for the MUGA array that is used by the R package DOQTL.' + diff --git a/recipes/bioconductor-mugaexampledata/post-link.sh b/recipes/bioconductor-mugaexampledata/post-link.sh new file mode 100644 index 0000000000000..b22b8d0c57c5b --- /dev/null +++ b/recipes/bioconductor-mugaexampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="MUGAExampleData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/MUGAExampleData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/MUGAExampleData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mugaexampledata/bioconductor-mugaexampledata_1.2.0_src_all.tar.gz" +) +MD5="66132942d0d409057570d914ec435e39" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mugaexampledata/pre-unlink.sh b/recipes/bioconductor-mugaexampledata/pre-unlink.sh new file mode 100644 index 0000000000000..794a335a0e79e --- /dev/null +++ b/recipes/bioconductor-mugaexampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ MUGAExampleData diff --git a/recipes/bioconductor-mulcom/build.sh b/recipes/bioconductor-mulcom/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mulcom/build.sh +++ b/recipes/bioconductor-mulcom/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mulcom/meta.yaml b/recipes/bioconductor-mulcom/meta.yaml index 5988cda4d03c6..05b8c934904a5 100644 --- a/recipes/bioconductor-mulcom/meta.yaml +++ b/recipes/bioconductor-mulcom/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "Mulcom" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 740638739fdd6ca10836a440bb7049fe119aa97baacbdf58c592bf992f3c0d4a + md5: 10bd7bcd1965c6f95c7d5a5c110d9c49 build: number: 0 rpaths: @@ -18,11 +18,11 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fields run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fields build: @@ -33,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identification of differentially expressed genes and false discovery rate (FDR) calculation by Multiple Comparison test' extra: identifiers: - biotools:mulcom - doi:10.1186/1471-2105-12-382 + parent_recipe: + name: bioconductor-mulcom + path: recipes/bioconductor-mulcom + version: 1.30.0 + diff --git a/recipes/bioconductor-mulder2012/meta.yaml b/recipes/bioconductor-mulder2012/meta.yaml new file mode 100644 index 0000000000000..4886d0c732887 --- /dev/null +++ b/recipes/bioconductor-mulder2012/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "0.22.0" %} +{% set name = "Mulder2012" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4c3890e75f415c4978187fb416586b1b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: snow +requirements: + host: + - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-panr >=1.28.0,<1.29.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - r-base + - r-igraph + - r-mass + - r-pvclust + run: + - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-panr >=1.28.0,<1.29.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - r-base + - r-igraph + - r-mass + - r-pvclust + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides functions to reproduce results and figures in Mulder K. et. al. published in Nature Cell Biology 2012 and Wang X. et. al. published in PLoS Computational Biology 2012.' + diff --git a/recipes/bioconductor-mulder2012/post-link.sh b/recipes/bioconductor-mulder2012/post-link.sh new file mode 100644 index 0000000000000..a99bcc19cfb11 --- /dev/null +++ b/recipes/bioconductor-mulder2012/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Mulder2012_0.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Mulder2012_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/Mulder2012_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mulder2012/bioconductor-mulder2012_0.22.0_src_all.tar.gz" +) +MD5="4c3890e75f415c4978187fb416586b1b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mulder2012/pre-unlink.sh b/recipes/bioconductor-mulder2012/pre-unlink.sh new file mode 100644 index 0000000000000..06b0e9c1edacb --- /dev/null +++ b/recipes/bioconductor-mulder2012/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Mulder2012 diff --git a/recipes/bioconductor-multiassayexperiment/build.sh b/recipes/bioconductor-multiassayexperiment/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multiassayexperiment/build.sh +++ b/recipes/bioconductor-multiassayexperiment/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml b/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-multiassayexperiment/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-multiassayexperiment/meta.yaml b/recipes/bioconductor-multiassayexperiment/meta.yaml index ee43d23a286cf..153aab776fe4b 100644 --- a/recipes/bioconductor-multiassayexperiment/meta.yaml +++ b/recipes/bioconductor-multiassayexperiment/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "MultiAssayExperiment" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ab6ff66caa4cbc429f8d160a932c6428e086b65b9e6c1269940467419acab0f4 + md5: 5ee305237b41fa6b1b7af703bdea464a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown, R.rsp, HDF5Array, RaggedExperiment, UpSetR, survival, survminer requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-tidyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-tidyr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Multi-assay ''omics experiments on a set of samples are increasingly commonplace in biomedical research. MultiAssayExperiment implements data structures and methods for representing, manipulating, and integrating multi-assay experiments via efficient construction, subsetting, and extraction operations. These methods are implemented matching Bioconductor user experience by straightforward extending concept and design of single-assay classes such as SummarizedExperiment.' + summary: 'MultiAssayExperiment harmonizes data management of multiple assays performed on an overlapping set of specimens. It provides a familiar Bioconductor user experience by extending concepts from SummarizedExperiment, supporting an open-ended mix of standard data classes for individual assays, and allowing subsetting by genomic ranges or rownames.' extra: identifiers: - biotools:multiassayexperiment - doi:10.1101/144774 + parent_recipe: + name: bioconductor-multiassayexperiment + path: recipes/bioconductor-multiassayexperiment + version: 1.6.0 + diff --git a/recipes/bioconductor-multiclust/build.sh b/recipes/bioconductor-multiclust/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multiclust/build.sh +++ b/recipes/bioconductor-multiclust/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiclust/meta.yaml b/recipes/bioconductor-multiclust/meta.yaml index 48637214d0deb..6b3d7f321b1e2 100644 --- a/recipes/bioconductor-multiclust/meta.yaml +++ b/recipes/bioconductor-multiclust/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "multiClust" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c4032c4c0de98a50b3027a8edae51d7c26c4833d0ec09d246d93c1ffa1087461 + md5: bd8c78d8df3588f2f1cce8b43d17bdcc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, gplots, RUnit, BiocGenerics, preprocessCore, Biobase, GEOquery requirements: host: - - 'bioconductor-ctc >=1.54.0,<1.56.0' + - 'bioconductor-ctc >=1.56.0,<1.57.0' - r-amap - r-base - r-cluster @@ -26,7 +28,7 @@ requirements: - r-mclust - r-survival run: - - 'bioconductor-ctc >=1.54.0,<1.56.0' + - 'bioconductor-ctc >=1.56.0,<1.57.0' - r-amap - r-base - r-cluster @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Clustering is carried out to identify patterns in transcriptomics profiles to determine clinically relevant subgroups of patients. Feature (gene) selection is a critical and an integral part of the process. Currently, there are many feature selection and clustering methods to identify the relevant genes and perform clustering of samples. However, choosing an appropriate methodology is difficult. In addition, extensive feature selection methods have not been supported by the available packages. Hence, we developed an integrative R-package called multiClust that allows researchers to experiment with the choice of combination of methods for gene selection and clustering with ease. Using multiClust, we identified the best performing clustering methodology in the context of clinical outcome. Our observations demonstrate that simple methods such as variance-based ranking perform well on the majority of data sets, provided that the appropriate number of genes is selected. However, different gene ranking and selection methods remain relevant as no methodology works for all studies.' extra: identifiers: - biotools:multiclust - doi:10.4137/cin.s38000 + parent_recipe: + name: bioconductor-multiclust + path: recipes/bioconductor-multiclust + version: 1.10.0 + diff --git a/recipes/bioconductor-multidataset/build.sh b/recipes/bioconductor-multidataset/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multidataset/build.sh +++ b/recipes/bioconductor-multidataset/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multidataset/meta.yaml b/recipes/bioconductor-multidataset/meta.yaml index 9f0aa79bd91ef..9465635b4ae00 100644 --- a/recipes/bioconductor-multidataset/meta.yaml +++ b/recipes/bioconductor-multidataset/meta.yaml @@ -1,42 +1,44 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "MultiDataSet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8da10a20a8088ed48b71e0e96759340a82cb508557571321be2ed0671f817877 + md5: c16950d938bd000b1ba441a751320ed4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: brgedata, minfi, minfiData, knitr, rmarkdown, testthat, omicade4, iClusterPlus, GEOquery, MultiAssayExperiment, BiocStyle, RaggedExperiment requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-ggrepel - r-qqman run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-ggrepel @@ -45,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Implementation of the BRGE''s (Bioinformatic Research Group in Epidemiology from Center for Research in Environmental Epidemiology) MultiDataSet and ResultSet. MultiDataSet is designed for integrating multi omics data sets and ResultSet is a container for omics results. This package contains base classes for MEAL and rexposome packages.' extra: identifiers: - biotools:multidataset + parent_recipe: + name: bioconductor-multidataset + path: recipes/bioconductor-multidataset + version: 1.8.0 + diff --git a/recipes/bioconductor-multihiccompare/build.sh b/recipes/bioconductor-multihiccompare/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-multihiccompare/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multihiccompare/meta.yaml b/recipes/bioconductor-multihiccompare/meta.yaml new file mode 100644 index 0000000000000..a8522508558f9 --- /dev/null +++ b/recipes/bioconductor-multihiccompare/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.0.0" %} +{% set name = "multiHiCcompare" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c33ece7658baba97e8012e67ab1495ae +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, BiocStyle +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-blma >=1.6.0,<1.7.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hiccompare >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-dplyr + - r-metap + - r-pbapply + - r-pheatmap + - r-qqman + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-blma >=1.6.0,<1.7.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hiccompare >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-dplyr + - r-metap + - r-pbapply + - r-pheatmap + - r-qqman +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'multiHiCcompare provides functions for joint normalization and difference detection in multiple Hi-C datasets. This extension of the original HiCcompare package now allows for Hi-C experiments with more than 2 groups and multiple samples per group. multiHiCcompare operates on processed Hi-C data in the form of sparse upper triangular matrices. It accepts four column (chromosome, region1, region2, IF) tab-separated text files storing chromatin interaction matrices. multiHiCcompare provides cyclic loess and fast loess (fastlo) methods adapted to jointly normalizing Hi-C data. Additionally, it provides a general linear model (GLM) framework adapting the edgeR package to detect differences in Hi-C data in a distance dependent manner.' + diff --git a/recipes/bioconductor-multimed/build.sh b/recipes/bioconductor-multimed/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multimed/build.sh +++ b/recipes/bioconductor-multimed/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multimed/meta.yaml b/recipes/bioconductor-multimed/meta.yaml index ab3047b773825..4549d44bd58ab 100644 --- a/recipes/bioconductor-multimed/meta.yaml +++ b/recipes/bioconductor-multimed/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "MultiMed" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0b394a6bafa856306414b1f2e6caa64cd08cfc9ff14154865a24876273848794 + md5: 53df4140afc3b479077ff254370b89af build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'Implements methods for testing multiple mediators' extra: identifiers: - biotools:multimed - doi:10.1093/bioinformatics/btt633 + parent_recipe: + name: bioconductor-multimed + path: recipes/bioconductor-multimed + version: 2.2.0 + diff --git a/recipes/bioconductor-multimir/build.sh b/recipes/bioconductor-multimir/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-multimir/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multimir/meta.yaml b/recipes/bioconductor-multimir/meta.yaml new file mode 100644 index 0000000000000..87afa8780c5f0 --- /dev/null +++ b/recipes/bioconductor-multimir/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.0" %} +{% set name = "multiMiR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 26ca39b201e466a51cdf18d73d243930 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, edgeR, knitr, rmarkdown, testthat (>= 1.0.2) +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-dplyr + - 'r-purrr >=0.2.2' + - r-rcurl + - 'r-tibble >=1.2' + - r-xml + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-dplyr + - 'r-purrr >=0.2.2' + - r-rcurl + - 'r-tibble >=1.2' + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A collection of microRNAs/targets from external resources, including validated microRNA-target databases (miRecords, miRTarBase and TarBase), predicted microRNA-target databases (DIANA-microT, ElMMo, MicroCosm, miRanda, miRDB, PicTar, PITA and TargetScan) and microRNA-disease/drug databases (miR2Disease, Pharmaco-miR VerSe and PhenomiR).' + diff --git a/recipes/bioconductor-multiomicsviz/build.sh b/recipes/bioconductor-multiomicsviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multiomicsviz/build.sh +++ b/recipes/bioconductor-multiomicsviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiomicsviz/meta.yaml b/recipes/bioconductor-multiomicsviz/meta.yaml index 3118b449593fb..0c8b936937237 100644 --- a/recipes/bioconductor-multiomicsviz/meta.yaml +++ b/recipes/bioconductor-multiomicsviz/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "multiOmicsViz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f130b07ba454588aab44c38dd1f9755c10b3c47db1751e6386f2767eb43e5f87 + md5: 1fb971e30027eab84bb48dd7552a11a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics requirements: host: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-doparallel - r-foreach run: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-doparallel - r-foreach @@ -31,8 +33,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Calculate the spearman correlation between the source omics data and other target omics data, identify the significant correlations and plot the significant correlations on the heat map in which the x-axis and y-axis are ordered by the chromosomal location.' - +extra: + parent_recipe: + name: bioconductor-multiomicsviz + path: recipes/bioconductor-multiomicsviz + version: 1.4.0 diff --git a/recipes/bioconductor-multiscan/build.sh b/recipes/bioconductor-multiscan/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multiscan/build.sh +++ b/recipes/bioconductor-multiscan/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multiscan/meta.yaml b/recipes/bioconductor-multiscan/meta.yaml index 5f973ae8242e5..cb3229ce8e839 100644 --- a/recipes/bioconductor-multiscan/meta.yaml +++ b/recipes/bioconductor-multiscan/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "multiscan" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: cda31408f2caff745b30c5c8f9716d0cbc86f652933336908e142fe44c8c8262 + md5: f30405ccb188b9d543f7e32c4c1c1b61 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Estimates gene expressions from several laser scans of the same microarray' extra: identifiers: - biotools:multiscan - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-multiscan + path: recipes/bioconductor-multiscan + version: 1.40.0 + diff --git a/recipes/bioconductor-multtest/build.sh b/recipes/bioconductor-multtest/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-multtest/build.sh +++ b/recipes/bioconductor-multtest/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-multtest/meta.yaml b/recipes/bioconductor-multtest/meta.yaml index 42669b64c87ab..ad075725eed32 100644 --- a/recipes/bioconductor-multtest/meta.yaml +++ b/recipes/bioconductor-multtest/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "2.36.0" %} +{% set version = "2.38.0" %} {% set name = "multtest" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e0d2f003b0afd674fb4f16255b20afa146491e65442a05511f81d337054c2485 + md5: 8d72610b6a4266100d65cb49fca11158 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: snow requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - r-survival run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - r-survival @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Non-parametric bootstrap and permutation resampling-based multiple testing procedures (including empirical Bayes methods) for controlling the family-wise error rate (FWER), generalized family-wise error rate (gFWER), tail probability of the proportion of false positives (TPPFP), and false discovery rate (FDR). Several choices of bootstrap-based null distribution are implemented (centered, centered and scaled, quantile-transformed). Single-step and step-wise methods are available. Tests based on a variety of t- and F-statistics (including t-statistics based on regression parameters from linear and survival models as well as those based on correlation parameters) are included. When probing hypotheses with t-statistics, users may also select a potentially faster null distribution which is multivariate normal with mean zero and variance covariance matrix derived from the vector influence function. Results are reported in terms of adjusted p-values, confidence regions and test statistic cutoffs. The procedures are directly applicable to identifying differentially expressed genes in DNA microarray experiments.' extra: identifiers: - biotools:multtest - doi:10.1007/0-387-29362-0_15 + parent_recipe: + name: bioconductor-multtest + path: recipes/bioconductor-multtest + version: 2.36.0 + diff --git a/recipes/bioconductor-mus.musculus/meta.yaml b/recipes/bioconductor-mus.musculus/meta.yaml new file mode 100644 index 0000000000000..b439af49a307d --- /dev/null +++ b/recipes/bioconductor-mus.musculus/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.3.1" %} +{% set name = "Mus.musculus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b8defe64c2dd308a88d1ac7a4ce04b9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm10.knowngene >=3.4.0,<3.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the Mus.musculus object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-mus.musculus/post-link.sh b/recipes/bioconductor-mus.musculus/post-link.sh new file mode 100644 index 0000000000000..7e34203e64761 --- /dev/null +++ b/recipes/bioconductor-mus.musculus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Mus.musculus_1.3.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Mus.musculus_1.3.1.tar.gz" + "https://bioarchive.galaxyproject.org/Mus.musculus_1.3.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mus.musculus/bioconductor-mus.musculus_1.3.1_src_all.tar.gz" +) +MD5="1b8defe64c2dd308a88d1ac7a4ce04b9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mus.musculus/pre-unlink.sh b/recipes/bioconductor-mus.musculus/pre-unlink.sh new file mode 100644 index 0000000000000..dc12611431e19 --- /dev/null +++ b/recipes/bioconductor-mus.musculus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Mus.musculus diff --git a/recipes/bioconductor-muscle/build.sh b/recipes/bioconductor-muscle/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-muscle/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-muscle/meta.yaml b/recipes/bioconductor-muscle/meta.yaml new file mode 100644 index 0000000000000..1fe1d6ee0af77 --- /dev/null +++ b/recipes/bioconductor-muscle/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.24.0" %} +{% set name = "muscle" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3fe18a5e6501d11231663070b783e744 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Unlimited + summary: 'MUSCLE performs multiple sequence alignments of nucleotide or amino acid sequences.' + diff --git a/recipes/bioconductor-mutationalpatterns/build.sh b/recipes/bioconductor-mutationalpatterns/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mutationalpatterns/build.sh +++ b/recipes/bioconductor-mutationalpatterns/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mutationalpatterns/meta.yaml b/recipes/bioconductor-mutationalpatterns/meta.yaml index 7a5ead38e7f90..2d78ef1f1fe4c 100644 --- a/recipes/bioconductor-mutationalpatterns/meta.yaml +++ b/recipes/bioconductor-mutationalpatterns/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "MutationalPatterns" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 49726301308e489ec9de4d42bc29d1858af57b5b858de690edb20a22431907fb + md5: 9ce25a78720c4904d5b951f9d37b901a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome (>= 1.40.0), BSgenome.Hsapiens.1000genomes.hs37d5 (>= 0.99.1), BSgenome.Hsapiens.UCSC.hg19 (>= 1.4.0), BiocStyle (>= 2.0.3), TxDb.Hsapiens.UCSC.hg19.knownGene (>= 3.2.2), biomaRt (>= 2.28.0), gridExtra (>= 2.2.1), rtracklayer (>= 1.32.2), testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - 'r-cowplot >=0.9.2' - 'r-ggdendro >=0.1-20' @@ -35,14 +37,14 @@ requirements: - 'r-pracma >=1.8.8' - 'r-reshape2 >=1.4.1' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - 'r-cowplot >=0.9.2' - 'r-ggdendro >=0.1-20' @@ -55,8 +57,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'An extensive toolset for the characterization and visualization of a wide range of mutational patterns in base substitution catalogs.' - +extra: + parent_recipe: + name: bioconductor-mutationalpatterns + path: recipes/bioconductor-mutationalpatterns + version: 1.6.1 diff --git a/recipes/bioconductor-mvcclass/build.sh b/recipes/bioconductor-mvcclass/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mvcclass/build.sh +++ b/recipes/bioconductor-mvcclass/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mvcclass/meta.yaml b/recipes/bioconductor-mvcclass/meta.yaml index e83d9c70a5041..bc0f40dfc8dbe 100644 --- a/recipes/bioconductor-mvcclass/meta.yaml +++ b/recipes/bioconductor-mvcclass/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "MVCClass" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 734c2f1b85cf8975ba7dd4c0083ca72df406e5904fd76921b53576a6f4d6ed98 + md5: 7bcceaf0251bfe3b06c2ff5bd6d95e80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Creates classes used in model-view-controller (MVC) design' extra: identifiers: - biotools:mvcclass - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mvcclass + path: recipes/bioconductor-mvcclass + version: 1.54.0 + diff --git a/recipes/bioconductor-mvoutdata/meta.yaml b/recipes/bioconductor-mvoutdata/meta.yaml new file mode 100644 index 0000000000000..63be83e51c17a --- /dev/null +++ b/recipes/bioconductor-mvoutdata/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.18.0" %} +{% set name = "mvoutData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8927221feca30eeac834f6b88ab2d83b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'affy and illumina raw data for assessing outlier detector performance' + diff --git a/recipes/bioconductor-mvoutdata/post-link.sh b/recipes/bioconductor-mvoutdata/post-link.sh new file mode 100644 index 0000000000000..cddd4b27e724a --- /dev/null +++ b/recipes/bioconductor-mvoutdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mvoutData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/mvoutData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/mvoutData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mvoutdata/bioconductor-mvoutdata_1.18.0_src_all.tar.gz" +) +MD5="8927221feca30eeac834f6b88ab2d83b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mvoutdata/pre-unlink.sh b/recipes/bioconductor-mvoutdata/pre-unlink.sh new file mode 100644 index 0000000000000..d9197a7de8c12 --- /dev/null +++ b/recipes/bioconductor-mvoutdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mvoutData diff --git a/recipes/bioconductor-mwastools/build.sh b/recipes/bioconductor-mwastools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mwastools/build.sh +++ b/recipes/bioconductor-mwastools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mwastools/meta.yaml b/recipes/bioconductor-mwastools/meta.yaml index 549b280a9194c..b17e8c6f818f7 100644 --- a/recipes/bioconductor-mwastools/meta.yaml +++ b/recipes/bioconductor-mwastools/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "MWASTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fab7dc5e332606b16f1332e3a623458e251b712086b012c23e4e10c3a4a73ad1 + md5: 9cc4188f3ca64ea0f6161c11876fe795 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, BiocStyle, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-boot - r-car @@ -33,11 +35,11 @@ requirements: - r-ppcor - r-rcurl run: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-boot - r-car @@ -51,8 +53,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0' summary: 'MWASTools provides a complete pipeline to perform metabolome-wide association studies. Key functionalities of the package include: quality control analysis of metabonomic data; MWAS using different association models (partial correlations; generalized linear models); model validation using non-parametric bootstrapping; visualization of MWAS results; NMR metabolite identification using STOCSY; and biological interpretation of MWAS results.' - +extra: + parent_recipe: + name: bioconductor-mwastools + path: recipes/bioconductor-mwastools + version: 1.4.0 diff --git a/recipes/bioconductor-mwgcod.db/meta.yaml b/recipes/bioconductor-mwgcod.db/meta.yaml new file mode 100644 index 0000000000000..29602703ce11e --- /dev/null +++ b/recipes/bioconductor-mwgcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "mwgcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3d6e2af6b05d6e07a212c043dc9d37c4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Mouse Whole Genome Bioarray (~36 000 mouse gene targets) annotation data (chip mwgcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-mwgcod.db/post-link.sh b/recipes/bioconductor-mwgcod.db/post-link.sh new file mode 100644 index 0000000000000..0fce1669cc165 --- /dev/null +++ b/recipes/bioconductor-mwgcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="mwgcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/mwgcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/mwgcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-mwgcod.db/bioconductor-mwgcod.db_3.4.0_src_all.tar.gz" +) +MD5="3d6e2af6b05d6e07a212c043dc9d37c4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-mwgcod.db/pre-unlink.sh b/recipes/bioconductor-mwgcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..fc8b2cd887fb7 --- /dev/null +++ b/recipes/bioconductor-mwgcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ mwgcod.db diff --git a/recipes/bioconductor-mygene/build.sh b/recipes/bioconductor-mygene/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mygene/build.sh +++ b/recipes/bioconductor-mygene/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mygene/meta.yaml b/recipes/bioconductor-mygene/meta.yaml index 5cd6f483178c5..984f1430b0663 100644 --- a/recipes/bioconductor-mygene/meta.yaml +++ b/recipes/bioconductor-mygene/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.16.2" %} +{% set version = "1.18.0" %} {% set name = "mygene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 7cfa9b71549c5148d7f126525ba9aea82ba1492a8c8350bb0d687724ffe2b23f + md5: 3a0f8aff0ef5eef0df7ed072ef98b771 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -27,8 +29,8 @@ requirements: - r-plyr - r-sqldf run: - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc - 'r-httr >=0.3' @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MyGene.Info_ provides simple-to-use REST web services to query/retrieve gene annotation data. It''s designed with simplicity and performance emphasized. *mygene*, is an easy-to-use R wrapper to access MyGene.Info_ services.' extra: identifiers: - biotools:mygene - doi:10.1101/009333 + parent_recipe: + name: bioconductor-mygene + path: recipes/bioconductor-mygene + version: 1.16.2 + diff --git a/recipes/bioconductor-myvariant/build.sh b/recipes/bioconductor-myvariant/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-myvariant/build.sh +++ b/recipes/bioconductor-myvariant/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-myvariant/meta.yaml b/recipes/bioconductor-myvariant/meta.yaml index 822f74daaccaf..69d3f2951e373 100644 --- a/recipes/bioconductor-myvariant/meta.yaml +++ b/recipes/bioconductor-myvariant/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "myvariant" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b2f7cf18c94d9462a74877a9ec8a65465d54bcc13ce72e9c5e35ee5e91e038a8 + md5: 186efbf26d9009e544d8874bb3f5778e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-hmisc - r-httr @@ -28,9 +30,9 @@ requirements: - r-magrittr - r-plyr run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-hmisc - r-httr @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'MyVariant.info is a comprehensive aggregation of variant annotation resources. myvariant is a wrapper for querying MyVariant.info services' extra: identifiers: - biotools:myvariant - doi:10.1101/035667 + parent_recipe: + name: bioconductor-myvariant + path: recipes/bioconductor-myvariant + version: 1.10.0 + diff --git a/recipes/bioconductor-mzid/build.sh b/recipes/bioconductor-mzid/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mzid/build.sh +++ b/recipes/bioconductor-mzid/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mzid/meta.yaml b/recipes/bioconductor-mzid/meta.yaml index 4c2fa342b3043..c3392d5426eae 100644 --- a/recipes/bioconductor-mzid/meta.yaml +++ b/recipes/bioconductor-mzid/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "mzID" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 80cc2da24167f589b7b60f7ce5974f8d31a02f5a64e96f980008a30769071318 + md5: 96dcf79f76a23d3838f0c3c4d20bb8b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat requirements: host: - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - r-base - r-doparallel - r-foreach @@ -26,7 +28,7 @@ requirements: - r-plyr - r-xml run: - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' - r-base - r-doparallel - r-foreach @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A parser for mzIdentML files implemented using the XML package. The parser tries to be general and able to handle all types of mzIdentML files with the drawback of having less ''pretty'' output than a vendor specific parser. Please contact the maintainer with any problems and supply an mzIdentML file so the problems can be fixed quickly.' extra: identifiers: - biotools:mzid - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-mzid + path: recipes/bioconductor-mzid + version: 1.18.0 + diff --git a/recipes/bioconductor-mzr/build.sh b/recipes/bioconductor-mzr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-mzr/build.sh +++ b/recipes/bioconductor-mzr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-mzr/meta.yaml b/recipes/bioconductor-mzr/meta.yaml index 91163ff7c6457..a6ae1e41b312f 100644 --- a/recipes/bioconductor-mzr/meta.yaml +++ b/recipes/bioconductor-mzr/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "mzR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2fabfa09eb86627bab92e57ed4ba52b4c02279fafb382295a4b0e355f01215a4 - + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c128a4818c53768a01464b1e824290a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: msdata (>= 0.15.1), RUnit, mzID, BiocStyle (>= 2.5.19), knitr, XML +# SystemRequirements: C++11, GNU make requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - - libnetcdf + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-ncdf4 - 'r-rcpp >=0.10.1' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' - - libnetcdf + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-ncdf4 - 'r-rcpp >=0.10.1' build: - {{ compiler('c') }} @@ -44,10 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'mzR provides a unified API to the common file formats and parsers available for mass spectrometry data. It comes with a wrapper for the ISB random access parser for mass spectrometry mzXML, mzData and mzML files. The package contains the original code written by the ISB, and a subset of the proteowizard library for mzML and mzIdentML. The netCDF reading code has previously been used in XCMS.' - extra: identifiers: - biotools:mzr + parent_recipe: + name: bioconductor-mzr + path: recipes/bioconductor-mzr + version: 2.14.0 + diff --git a/recipes/bioconductor-nadfinder/build.sh b/recipes/bioconductor-nadfinder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nadfinder/build.sh +++ b/recipes/bioconductor-nadfinder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nadfinder/conda_build_config.yaml b/recipes/bioconductor-nadfinder/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-nadfinder/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-nadfinder/meta.yaml b/recipes/bioconductor-nadfinder/meta.yaml index a6e9cf809d3c1..fda00cfbbacd5 100644 --- a/recipes/bioconductor-nadfinder/meta.yaml +++ b/recipes/bioconductor-nadfinder/meta.yaml @@ -1,68 +1,76 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "NADfinder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 01928a0c1fb3bf283a7a9fdd1a31ddaa3276cfdd5d155856fa701288425a6c2a + md5: b34fd2ba65777d26f1012cef1411888b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, knitr, BSgenome.Mmusculus.UCSC.mm10, testthat, BiocManager requirements: host: - - 'bioconductor-atacseqqc >=1.4.3,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-csaw >=1.14.1,<1.16.0' - - 'bioconductor-empiricalbrownsmethod >=1.8.0,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-trackviewer >=1.16.1,<1.18.0' + - 'bioconductor-atacseqqc >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-empiricalbrownsmethod >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-trackviewer >=1.18.0,<1.19.0' - r-base - r-baseline - r-corrplot - r-metap + - r-rbamtools - r-signal run: - - 'bioconductor-atacseqqc >=1.4.3,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-csaw >=1.14.1,<1.16.0' - - 'bioconductor-empiricalbrownsmethod >=1.8.0,<1.10.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-trackviewer >=1.16.1,<1.18.0' + - 'bioconductor-atacseqqc >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-empiricalbrownsmethod >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-trackviewer >=1.18.0,<1.19.0' - r-base - r-baseline - r-corrplot - r-metap + - r-rbamtools - r-signal test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Nucleolus is an important structure inside the nucleus in eukaryotic cells. It is the site for transcribing rDNA into rRNA and for assembling ribosomes, aka ribosome biogenesis. In addition, nucleoli are dynamic hubs through which numerous proteins shuttle and contact specific non-rDNA genomic loci. Deep sequencing analyses of DNA associated with isolated nucleoli (NAD- seq) have shown that specific loci, termed nucleolus- associated domains (NADs) form frequent three- dimensional associations with nucleoli. NAD-seq has been used to study the biological functions of NAD and the dynamics of NAD distribution during embryonic stem cell (ESC) differentiation. Here, we developed a Bioconductor package NADfinder for bioinformatic analysis of the NAD-seq data, including normalization, smoothing, peak calling, peak trimming and annotation.' - +extra: + parent_recipe: + name: bioconductor-nadfinder + path: recipes/bioconductor-nadfinder + version: 1.4.0 diff --git a/recipes/bioconductor-nanostringdiff/build.sh b/recipes/bioconductor-nanostringdiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nanostringdiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nanostringdiff/meta.yaml b/recipes/bioconductor-nanostringdiff/meta.yaml new file mode 100644 index 0000000000000..233b314550dbc --- /dev/null +++ b/recipes/bioconductor-nanostringdiff/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.12.0" %} +{% set name = "NanoStringDiff" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a651308ff607d0b38673ad2849dcd81b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-matrixstats + - r-rcpp + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-matrixstats + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'This Package utilizes a generalized linear model(GLM) of the negative binomial family to characterize count data and allows for multi-factor design. NanoStrongDiff incorporate size factors, calculated from positive controls and housekeeping controls, and background level, obtained from negative controls, in the model framework so that all the normalization information provided by NanoString nCounter Analyzer is fully utilized.' + diff --git a/recipes/bioconductor-nanostringqcpro/build.sh b/recipes/bioconductor-nanostringqcpro/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nanostringqcpro/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nanostringqcpro/meta.yaml b/recipes/bioconductor-nanostringqcpro/meta.yaml new file mode 100644 index 0000000000000..1bbf30e7c0e84 --- /dev/null +++ b/recipes/bioconductor-nanostringqcpro/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.14.0" %} +{% set name = "NanoStringQCPro" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40009524e65ceb0fca927bfbda64acd0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: roxygen2 (>= 4.0.1), testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - 'r-knitr >=1.12' + - 'r-nmf >=0.20.5' + - 'r-png >=0.1-7' + - 'r-rcolorbrewer >=1.0-5' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - 'r-knitr >=1.12' + - 'r-nmf >=0.20.5' + - 'r-png >=0.1-7' + - 'r-rcolorbrewer >=1.0-5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'NanoStringQCPro provides a set of quality metrics that can be used to assess the quality of NanoString mRNA gene expression data -- i.e. to identify outlier probes and outlier samples. It also provides different background subtraction and normalization approaches for this data. It outputs suggestions for flagging samples/probes and an easily sharable html quality control output.' + diff --git a/recipes/bioconductor-narrowpeaks/build.sh b/recipes/bioconductor-narrowpeaks/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-narrowpeaks/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-narrowpeaks/meta.yaml b/recipes/bioconductor-narrowpeaks/meta.yaml new file mode 100644 index 0000000000000..04e6e6fccc8b5 --- /dev/null +++ b/recipes/bioconductor-narrowpeaks/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.26.0" %} +{% set name = "NarrowPeaks" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 31857409c4a4c04e695e58839670127e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: rtracklayer, BiocStyle, GenomicRanges, CSAR +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-csar >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-fda + - r-icsnp + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-csar >=1.34.0,<1.35.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-fda + - r-icsnp + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package applies a functional version of principal component analysis (FPCA) to: (1) Postprocess data in wiggle track format, commonly produced by generic ChIP-seq peak callers, by applying FPCA over a set of read-enriched regions (ChIP-seq peaks). This is done to study variability of the the peaks, or to shorten their genomic locations accounting for a given proportion of variation among the enrichment-score profiles. (2) Analyse differential variation between multiple ChIP-seq samples with replicates. The function ''narrowpeaksDiff'' quantifies differences between the shapes, and uses Hotelling''s T2 tests on the functional principal component scores to identify significant differences across conditions. An application of the package for Arabidopsis datasets is described in Mateos, Madrigal, et al. (2015) Genome Biology: 16:31.' + diff --git a/recipes/bioconductor-nbsplice/build.sh b/recipes/bioconductor-nbsplice/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nbsplice/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nbsplice/meta.yaml b/recipes/bioconductor-nbsplice/meta.yaml new file mode 100644 index 0000000000000..35fb19f25a9fe --- /dev/null +++ b/recipes/bioconductor-nbsplice/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.0.0" %} +{% set name = "NBSplice" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f5d28756bfed8278763929fc262baa7e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - r-base + - r-car + - r-ggplot2 + - r-mass + - r-mppa + - r-reshape2 + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - r-base + - r-car + - r-ggplot2 + - r-mass + - r-mppa + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'The package proposes a differential splicing evaluation method based on isoform quantification. It applies generalized linear models with negative binomial distribution to infer changes in isoform relative expression.' + diff --git a/recipes/bioconductor-ncdfflow/build.sh b/recipes/bioconductor-ncdfflow/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ncdfflow/build.sh +++ b/recipes/bioconductor-ncdfflow/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ncdfflow/meta.yaml b/recipes/bioconductor-ncdfflow/meta.yaml index 070a05a9b0166..9cce2aef28ed6 100644 --- a/recipes/bioconductor-ncdfflow/meta.yaml +++ b/recipes/bioconductor-ncdfflow/meta.yaml @@ -1,40 +1,41 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "ncdfFlow" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4207f655bebb5b0186616730967db07b9e413f5448b2e3a943e79c2a0ce63f7d + md5: d1d388e38cccf77dafef7d4f5ef8be9f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat,parallel requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-bh - r-rcpp - r-rcpparmadillo run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-bh - r-rcpp @@ -47,10 +48,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides HDF5 storage based methods and functions for manipulation of flow cytometry data.' extra: identifiers: - biotools:ncdfflow - doi:10.1016/j.copbio.2012.09.003 + parent_recipe: + name: bioconductor-ncdfflow + path: recipes/bioconductor-ncdfflow + version: 2.26.0 + diff --git a/recipes/bioconductor-ncigraph/build.sh b/recipes/bioconductor-ncigraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ncigraph/build.sh +++ b/recipes/bioconductor-ncigraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ncigraph/meta.yaml b/recipes/bioconductor-ncigraph/meta.yaml index 5df9fb7c25a06..af537a213086d 100644 --- a/recipes/bioconductor-ncigraph/meta.yaml +++ b/recipes/bioconductor-ncigraph/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "NCIgraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ac8d694bb1f475c72417160e51f3f059aca04f5c99dd97b84564580d0339bcf + md5: d43797d5c080c69cfd2ac24545dec3a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rcy3 >=2.0.88,<2.2.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rcy3 >=2.2.0,<2.3.0' - r-base - r-r.methodss3 run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rcy3 >=2.0.88,<2.2.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rcy3 >=2.2.0,<2.3.0' - r-base - r-r.methodss3 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Provides various methods to load the pathways from the NCI Pathways Database in R graph objects and to re-format them.' extra: identifiers: - biotools:ncigraph - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ncigraph + path: recipes/bioconductor-ncigraph + version: 1.28.0 + diff --git a/recipes/bioconductor-ncigraphdata/meta.yaml b/recipes/bioconductor-ncigraphdata/meta.yaml new file mode 100644 index 0000000000000..7638fe543b200 --- /dev/null +++ b/recipes/bioconductor-ncigraphdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "NCIgraphData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fc2723da5d02c9f6baa7d05054f912a1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Rgraphviz +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides pathways from the NCI Pathways Database as R graph objects' + diff --git a/recipes/bioconductor-ncigraphdata/post-link.sh b/recipes/bioconductor-ncigraphdata/post-link.sh new file mode 100644 index 0000000000000..dd96ed39f5837 --- /dev/null +++ b/recipes/bioconductor-ncigraphdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="NCIgraphData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/NCIgraphData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/NCIgraphData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ncigraphdata/bioconductor-ncigraphdata_1.18.0_src_all.tar.gz" +) +MD5="fc2723da5d02c9f6baa7d05054f912a1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ncigraphdata/pre-unlink.sh b/recipes/bioconductor-ncigraphdata/pre-unlink.sh new file mode 100644 index 0000000000000..001ed56b9ce21 --- /dev/null +++ b/recipes/bioconductor-ncigraphdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ NCIgraphData diff --git a/recipes/bioconductor-ndexr/build.sh b/recipes/bioconductor-ndexr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ndexr/build.sh +++ b/recipes/bioconductor-ndexr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ndexr/meta.yaml b/recipes/bioconductor-ndexr/meta.yaml index 9e194468c3ea8..70d6788d72352 100644 --- a/recipes/bioconductor-ndexr/meta.yaml +++ b/recipes/bioconductor-ndexr/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "ndexr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 738a9d8ef249857b38ba863cf2958b069c3ebc0b5a7c42681f0ff8aa41580b62 + md5: 3028152656c2a2b5361713bfc713a6ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, testthat, knitr, rmarkdown requirements: host: - r-base @@ -35,8 +37,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: BSD summary: 'This package offers an interface to NDEx servers, e.g. the public server at http://ndexbio.org/. It can retrieve and save networks via the API. Networks are offered as RCX object and as igraph representation.' - +extra: + parent_recipe: + name: bioconductor-ndexr + path: recipes/bioconductor-ndexr + version: 1.2.0 diff --git a/recipes/bioconductor-neighbornet/build.sh b/recipes/bioconductor-neighbornet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-neighbornet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-neighbornet/meta.yaml b/recipes/bioconductor-neighbornet/meta.yaml new file mode 100644 index 0000000000000..9250d2dac3636 --- /dev/null +++ b/recipes/bioconductor-neighbornet/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "NeighborNet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a3341ae47afcce8284786132a3bdf393 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY-NC-ND 4.0' + summary: 'Identify the putative mechanism explaining the active interactions between genes in the investigated phenotype.' + diff --git a/recipes/bioconductor-nem/build.sh b/recipes/bioconductor-nem/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nem/build.sh +++ b/recipes/bioconductor-nem/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nem/meta.yaml b/recipes/bioconductor-nem/meta.yaml index 04b66ab22969d..de476bb3cb19a 100644 --- a/recipes/bioconductor-nem/meta.yaml +++ b/recipes/bioconductor-nem/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "2.54.0" %} +{% set version = "2.56.0" %} {% set name = "nem" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5a4fbc3eec8738bbfad002bb17a8a1e9d0263fe73441cc88fbbd7a70923c3910 + md5: 0f3029446be3426d2e2ea986073e0122 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Biobase (>= 1.10) requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-boot - r-e1071 @@ -29,10 +30,10 @@ requirements: - r-rcolorbrewer - r-statmod run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-boot - r-e1071 @@ -46,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package ''nem'' allows to reconstruct features of pathways from the nested structure of perturbation effects. It takes as input (1.) a set of pathway components, which were perturbed, and (2.) phenotypic readout of these perturbations (e.g. gene expression, protein expression). The output is a directed graph representing the phenotypic hierarchy.' extra: identifiers: - biotools:nem - doi:10.1093/bioinformatics/btq385 + parent_recipe: + name: bioconductor-nem + path: recipes/bioconductor-nem + version: 2.54.0 + diff --git a/recipes/bioconductor-netbenchmark/build.sh b/recipes/bioconductor-netbenchmark/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netbenchmark/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netbenchmark/meta.yaml b/recipes/bioconductor-netbenchmark/meta.yaml new file mode 100644 index 0000000000000..6d45634d20837 --- /dev/null +++ b/recipes/bioconductor-netbenchmark/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.14.0" %} +{% set name = "netbenchmark" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3d0c34121a30be63e0fc2837c021f253 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics, knitr, graph +requirements: + host: + - 'bioconductor-genie3 >=1.4.0,<1.5.0' + - 'bioconductor-grndata >=1.14.0,<1.15.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - r-base + - r-c3net + - r-corpcor + - r-fdrtool + - r-genenet + - r-matrix + - r-pcit + - r-pracma + - 'r-rcpp >=0.11.0' + run: + - 'bioconductor-genie3 >=1.4.0,<1.5.0' + - 'bioconductor-grndata >=1.14.0,<1.15.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - r-base + - r-c3net + - r-corpcor + - r-fdrtool + - r-genenet + - r-matrix + - r-pcit + - r-pracma + - 'r-rcpp >=0.11.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY-NC-SA 4.0' + summary: 'This package implements a benchmarking of several gene network inference algorithms from gene expression data.' + diff --git a/recipes/bioconductor-netbiov/build.sh b/recipes/bioconductor-netbiov/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-netbiov/build.sh +++ b/recipes/bioconductor-netbiov/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netbiov/meta.yaml b/recipes/bioconductor-netbiov/meta.yaml index 08992288d2ec7..60d7c4ccd14a4 100644 --- a/recipes/bioconductor-netbiov/meta.yaml +++ b/recipes/bioconductor-netbiov/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "netbiov" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 198051eefeef33e89b625387d421150a4fb5fb2e6f4004fb99934f30bf89ab80 + md5: 41e9eece65723f5328ca9f15ffce01b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle,RUnit,BiocGenerics,Matrix requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A package that provides an effective visualization of large biological networks' extra: identifiers: - biotools:netbiov - doi:10.1093/bioinformatics/btu384 + parent_recipe: + name: bioconductor-netbiov + path: recipes/bioconductor-netbiov + version: 1.14.0 + diff --git a/recipes/bioconductor-nethet/build.sh b/recipes/bioconductor-nethet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nethet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nethet/meta.yaml b/recipes/bioconductor-nethet/meta.yaml new file mode 100644 index 0000000000000..46453697aa2da --- /dev/null +++ b/recipes/bioconductor-nethet/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.14.0" %} +{% set name = "nethet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: de7f46b2f5c400fde16c3954ebc9ff1b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, xtable, BiocStyle +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-compquadform + - r-genenet + - r-ggm + - r-ggplot2 + - r-glasso + - r-glmnet + - r-gsa + - r-huge + - r-icsnp + - r-mclust + - r-mvtnorm + - r-network + - r-parcor + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + - r-compquadform + - r-genenet + - r-ggm + - r-ggplot2 + - r-glasso + - r-glmnet + - r-gsa + - r-huge + - r-icsnp + - r-mclust + - r-mvtnorm + - r-network + - r-parcor + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Package nethet is an implementation of statistical solid methodology enabling the analysis of network heterogeneity from high-dimensional data. It combines several implementations of recent statistical innovations useful for estimation and comparison of networks in a heterogeneous, high-dimensional setting. In particular, we provide code for formal two-sample testing in Gaussian graphical models (differential network and GGM-GSA; Stadler and Mukherjee, 2013, 2014) and make a novel network-based clustering algorithm available (mixed graphical lasso, Stadler and Mukherjee, 2013).' + diff --git a/recipes/bioconductor-netpathminer/build.sh b/recipes/bioconductor-netpathminer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-netpathminer/build.sh +++ b/recipes/bioconductor-netpathminer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netpathminer/meta.yaml b/recipes/bioconductor-netpathminer/meta.yaml index 810846c1aa6ef..335f8db3313e5 100644 --- a/recipes/bioconductor-netpathminer/meta.yaml +++ b/recipes/bioconductor-netpathminer/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "NetPathMiner" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f6882eedbd2240810596239a08d9e8847e8bbdc042c9791cfb0a35b2a9f73923 + md5: a7126fcb4431a1f78cb8e4742ae70635 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: rBiopaxParser (>= 2.1), RCurl, graph +# SystemRequirements: libxml2, libSBML (>= 5.5) requirements: host: - r-base @@ -32,9 +34,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'NetPathMiner is a general framework for network path mining using genome-scale networks. It constructs networks from KGML, SBML and BioPAX files, providing three network representations, metabolic, reaction and gene representations. NetPathMiner finds active paths and applies machine learning methods to summarize found paths for easy interpretation. It also provides static and interactive visualizations of networks and paths to aid manual investigation.' extra: identifiers: - biotools:netpathminer + parent_recipe: + name: bioconductor-netpathminer + path: recipes/bioconductor-netpathminer + version: 1.16.0 + diff --git a/recipes/bioconductor-netprior/build.sh b/recipes/bioconductor-netprior/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netprior/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netprior/meta.yaml b/recipes/bioconductor-netprior/meta.yaml new file mode 100644 index 0000000000000..b8723633fcf39 --- /dev/null +++ b/recipes/bioconductor-netprior/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.8.0" %} +{% set name = "netprioR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0ba93c44b932baa86bae46d44db8e21a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, pander +requirements: + host: + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gridextra + - r-matrix + - r-proc + - r-sparsemvn + run: + - r-base + - r-doparallel + - r-dplyr + - r-foreach + - r-ggplot2 + - r-gridextra + - r-matrix + - r-proc + - r-sparsemvn +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A model for semi-supervised prioritisation of genes integrating network data, phenotypes and additional prior knowledge about TP and TN gene labels from the literature or experts.' + diff --git a/recipes/bioconductor-netreg/build.sh b/recipes/bioconductor-netreg/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-netreg/build.sh +++ b/recipes/bioconductor-netreg/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netreg/meta.yaml b/recipes/bioconductor-netreg/meta.yaml index 98700d1989d27..f186ebd818c73 100644 --- a/recipes/bioconductor-netreg/meta.yaml +++ b/recipes/bioconductor-netreg/meta.yaml @@ -1,43 +1,47 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "netReg" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 696418c4f8f2b938316eb12e9349d4d588c44428310ec97fd8e7327c174bfc4a + md5: 8f3db56ff84e07615627658da1c40bff build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle, lintr, lassoshooting +# SystemRequirements: C++11 requirements: - build: - - {{ compiler('c') }} - - {{ compiler('cxx') }} - - automake - - make host: - r-base - r-rcpp - r-rcpparmadillo - - openblas run: - r-base - r-rcpp - r-rcpparmadillo - - openblas + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | BSL-1.0 + file LICENSE' summary: 'netReg fits linear regression models using network-penalization. Graph prior knowledge, in the form of biological networks, is being incorporated into the loss function of the linear model. The networks describe biological relationships such as co-regulation or dependency of the same transcription factors/metabolites/etc. yielding a part sparse and part smooth solution for coefficient profiles.' - +extra: + parent_recipe: + name: bioconductor-netreg + path: recipes/bioconductor-netreg + version: 1.4.0 diff --git a/recipes/bioconductor-netresponse/build.sh b/recipes/bioconductor-netresponse/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netresponse/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netresponse/meta.yaml b/recipes/bioconductor-netresponse/meta.yaml new file mode 100644 index 0000000000000..9e59b062950a2 --- /dev/null +++ b/recipes/bioconductor-netresponse/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.42.0" %} +{% set name = "netresponse" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f7b9e38c87012015f0bb9ba8f53b718 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-dmt + - r-ggplot2 + - r-igraph + - r-mclust + - r-plyr + - r-rcolorbrewer + - r-reshape2 + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-dmt + - r-ggplot2 + - r-igraph + - r-mclust + - r-plyr + - r-rcolorbrewer + - r-reshape2 + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Algorithms for functional network analysis. Includes an implementation of a variational Dirichlet process Gaussian mixture model for nonparametric mixture modeling.' + diff --git a/recipes/bioconductor-netsam/build.sh b/recipes/bioconductor-netsam/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netsam/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netsam/meta.yaml b/recipes/bioconductor-netsam/meta.yaml new file mode 100644 index 0000000000000..37ca3df031f8c --- /dev/null +++ b/recipes/bioconductor-netsam/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.22.0" %} +{% set name = "NetSAM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 38f4ae15c77a17e4b2774fc0b6ce9e8d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - 'r-igraph >=0.6-1' + - 'r-seriation >=1.0-6' + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - 'r-igraph >=0.6-1' + - 'r-seriation >=1.0-6' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'The NetSAM (Network Seriation and Modularization) package takes an edge-list representation of a network as an input, performs network seriation and modularization analysis, and generates as files that can be used as an input for the one-dimensional network visualization tool NetGestalt (http://www.netgestalt.org) or other network analysis.' + diff --git a/recipes/bioconductor-netsmooth/build.sh b/recipes/bioconductor-netsmooth/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-netsmooth/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-netsmooth/meta.yaml b/recipes/bioconductor-netsmooth/meta.yaml new file mode 100644 index 0000000000000..66606dccaa53b --- /dev/null +++ b/recipes/bioconductor-netsmooth/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "netSmooth" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 30774513e8fa21902cc5d68b92e4ca54 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, Rtsne, biomaRt, igraph, STRINGdb, NMI, pheatmap, ggplot2, BiocStyle, rmarkdown, BiocParallel +requirements: + host: + - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-data.table + - r-entropy + - r-matrix + run: + - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-data.table + - r-entropy + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.' + diff --git a/recipes/bioconductor-networkbma/build.sh b/recipes/bioconductor-networkbma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-networkbma/build.sh +++ b/recipes/bioconductor-networkbma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-networkbma/meta.yaml b/recipes/bioconductor-networkbma/meta.yaml index fb67520985b21..aa640aa89e0b9 100644 --- a/recipes/bioconductor-networkbma/meta.yaml +++ b/recipes/bioconductor-networkbma/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "networkBMA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 996b0c7e10f738ff01f8aeecd1f42ebfe9da2e1206c7c49918dcfa8ab403dbc0 + md5: 44c5d02a7bd54f626209644786f8a5d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# SystemRequirements: liblapack-dev requirements: host: - r-base @@ -41,10 +42,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'An extension of Bayesian Model Averaging (BMA) for network construction using time series gene expression data. Includes assessment functions and sample test data.' extra: identifiers: - biotools:networkbma - doi:10.1186/1752-0509-8-47 + parent_recipe: + name: bioconductor-networkbma + path: recipes/bioconductor-networkbma + version: 2.20.0 + diff --git a/recipes/bioconductor-neve2006/meta.yaml b/recipes/bioconductor-neve2006/meta.yaml new file mode 100644 index 0000000000000..1ae36fe02bc52 --- /dev/null +++ b/recipes/bioconductor-neve2006/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "0.20.0" %} +{% set name = "Neve2006" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b20d24255cdccb1d06f070bc60879d28 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - r-base + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Experimental organization of combined expression and CGH data' + diff --git a/recipes/bioconductor-neve2006/post-link.sh b/recipes/bioconductor-neve2006/post-link.sh new file mode 100644 index 0000000000000..7f42d040d3f5d --- /dev/null +++ b/recipes/bioconductor-neve2006/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Neve2006_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Neve2006_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/Neve2006_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-neve2006/bioconductor-neve2006_0.20.0_src_all.tar.gz" +) +MD5="b20d24255cdccb1d06f070bc60879d28" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-neve2006/pre-unlink.sh b/recipes/bioconductor-neve2006/pre-unlink.sh new file mode 100644 index 0000000000000..e9049a9f3220b --- /dev/null +++ b/recipes/bioconductor-neve2006/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Neve2006 diff --git a/recipes/bioconductor-ngscopy/build.sh b/recipes/bioconductor-ngscopy/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ngscopy/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ngscopy/meta.yaml b/recipes/bioconductor-ngscopy/meta.yaml new file mode 100644 index 0000000000000..25f5702d6f33a --- /dev/null +++ b/recipes/bioconductor-ngscopy/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.16.0" %} +{% set name = "NGScopy" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cccbbac752a9036d95223e1e9cf5c28e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, NGScopyData, GenomicRanges +requirements: + host: + - r-base + - 'r-changepoint >=2.1.1' + - 'r-rbamtools >=2.6.0' + - 'r-xmisc >=0.2.1' + run: + - r-base + - 'r-changepoint >=2.1.1' + - 'r-rbamtools >=2.6.0' + - 'r-xmisc >=0.2.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'NGScopy provides a quantitative caller for detecting copy number variations in next generation sequencing (NGS), including whole genome sequencing (WGS), whole exome sequencing (WES) and targeted panel sequencing (TPS). The caller can be parallelized by chromosomes to use multiple processors/cores on one computer.' + diff --git a/recipes/bioconductor-ngscopydata/meta.yaml b/recipes/bioconductor-ngscopydata/meta.yaml new file mode 100644 index 0000000000000..3db076f159366 --- /dev/null +++ b/recipes/bioconductor-ngscopydata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "NGScopyData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5a873e124972f000b294486fd2512c12 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Subset of BAM files of human lung tumor and pooled normal samples by targeted panel sequencing. [Zhao et al 2014. Targeted Sequencing in Non-Small Cell Lung Cancer (NSCLC) Using the University of North Carolina (UNC) Sequencing Assay Captures Most Previously Described Genetic Aberrations in NSCLC. In preparation.] Each sample is a 10 percent random subsample drawn from the original sequencing data. The pooled normal sample has been rescaled accroding to the total number of normal samples in the "pool". Here provided is the subsampled data on chr6 (hg19).' + diff --git a/recipes/bioconductor-ngscopydata/post-link.sh b/recipes/bioconductor-ngscopydata/post-link.sh new file mode 100644 index 0000000000000..ff06cc0f9990b --- /dev/null +++ b/recipes/bioconductor-ngscopydata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="NGScopyData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/NGScopyData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/NGScopyData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ngscopydata/bioconductor-ngscopydata_1.2.0_src_all.tar.gz" +) +MD5="5a873e124972f000b294486fd2512c12" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ngscopydata/pre-unlink.sh b/recipes/bioconductor-ngscopydata/pre-unlink.sh new file mode 100644 index 0000000000000..899467b670ff7 --- /dev/null +++ b/recipes/bioconductor-ngscopydata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ NGScopyData diff --git a/recipes/bioconductor-nnnorm/build.sh b/recipes/bioconductor-nnnorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nnnorm/build.sh +++ b/recipes/bioconductor-nnnorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nnnorm/meta.yaml b/recipes/bioconductor-nnnorm/meta.yaml index b2453f9152d1a..807b8d6761478 100644 --- a/recipes/bioconductor-nnnorm/meta.yaml +++ b/recipes/bioconductor-nnnorm/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "2.44.0" %} +{% set version = "2.46.0" %} {% set name = "nnNorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e213fc1f4d6089520b2a547d20fcd96af40c9ff68388b24c39d7f904c193207a + md5: f9f516d28deb61db8d90266ed1adce97 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-nnet run: - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-nnet test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package allows to detect and correct for spatial and intensity biases with two-channel microarray data. The normalization method implemented in this package is based on robust neural networks fitting.' extra: identifiers: - biotools:nnnorm - doi:10.1093/bioinformatics/bti397 + parent_recipe: + name: bioconductor-nnnorm + path: recipes/bioconductor-nnnorm + version: 2.44.0 + diff --git a/recipes/bioconductor-noiseq/build.sh b/recipes/bioconductor-noiseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-noiseq/build.sh +++ b/recipes/bioconductor-noiseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-noiseq/meta.yaml b/recipes/bioconductor-noiseq/meta.yaml index c1af239df1613..e503b80362d85 100644 --- a/recipes/bioconductor-noiseq/meta.yaml +++ b/recipes/bioconductor-noiseq/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "NOISeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cb151bea959fbafa2a96a24ba507f158f740d66c2da5e306efd78fbf268a522a + md5: f728302120066899e26e919b509a04e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - 'r-matrix >=1.2' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - 'r-matrix >=1.2' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analysis of RNA-seq expression data or other similar kind of data. Exploratory plots to evualuate saturation, count distribution, expression per chromosome, type of detected features, features length, etc. Differential expression between two experimental conditions with no parametric assumptions.' extra: identifiers: - biotools:noiseq + parent_recipe: + name: bioconductor-noiseq + path: recipes/bioconductor-noiseq + version: 2.24.0 + diff --git a/recipes/bioconductor-nondetects/build.sh b/recipes/bioconductor-nondetects/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nondetects/build.sh +++ b/recipes/bioconductor-nondetects/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nondetects/conda_build_config.yaml b/recipes/bioconductor-nondetects/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-nondetects/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-nondetects/meta.yaml b/recipes/bioconductor-nondetects/meta.yaml index 517202de67f1f..b3584d8886461 100644 --- a/recipes/bioconductor-nondetects/meta.yaml +++ b/recipes/bioconductor-nondetects/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "nondetects" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 46044bcb1f09f71b7f0d17a1ca215ba1ee97fe4c0b14869ef0b688f0f78a9567 + md5: 38eb1814c20ef744c713f59b42707d47 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle (>= 1.0.0), RUnit, BiocGenerics (>= 0.8.0) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-htqpcr >=1.34.0,<1.36.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-htqpcr >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-arm - r-base - r-mvtnorm run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-htqpcr >=1.34.0,<1.36.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-htqpcr >=1.36.0,<1.37.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-arm - r-base - r-mvtnorm @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Methods to model and impute non-detects in the results of qPCR experiments.' extra: identifiers: - biotools:nondetects + parent_recipe: + name: bioconductor-nondetects + path: recipes/bioconductor-nondetects + version: 2.10.0 + diff --git a/recipes/bioconductor-normalize450k/build.sh b/recipes/bioconductor-normalize450k/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-normalize450k/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-normalize450k/meta.yaml b/recipes/bioconductor-normalize450k/meta.yaml new file mode 100644 index 0000000000000..ee1e8fbd3f36d --- /dev/null +++ b/recipes/bioconductor-normalize450k/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.10.0" %} +{% set name = "normalize450K" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0a46946dedab5b5e7ae7f269aedd7664 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - r-base + - r-quadprog + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - r-base + - r-quadprog +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_2_clause + file LICENSE' + summary: 'Precise measurements are important for epigenome-wide studies investigating DNA methylation in whole blood samples, where effect sizes are expected to be small in magnitude. The 450K platform is often affected by batch effects and proper preprocessing is recommended. This package provides functions to read and normalize 450K ''.idat'' files. The normalization corrects for dye bias and biases related to signal intensity and methylation of probes using local regression. No adjustment for probe type bias is performed to avoid the trade-off of precision for accuracy of beta-values.' + diff --git a/recipes/bioconductor-normalyzerde/build.sh b/recipes/bioconductor-normalyzerde/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-normalyzerde/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-normalyzerde/meta.yaml b/recipes/bioconductor-normalyzerde/meta.yaml new file mode 100644 index 0000000000000..5e7a1d5274b87 --- /dev/null +++ b/recipes/bioconductor-normalyzerde/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "NormalyzerDE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e1ce8d162271f6aa58b181ea8135dfd8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, rmarkdown, roxygen2, hexbin +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-ape + - r-base + - r-car + - r-ggplot2 + - r-mass + - r-matrixstats + - r-raster + - r-rcmdrmisc + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-ape + - r-base + - r-car + - r-ggplot2 + - r-mass + - r-matrixstats + - r-raster + - r-rcmdrmisc +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'NormalyzerDE provides screening of normalization methods for LC-MS based expression data. It calculates a range of normalized matrices using both existing approaches and a novel time-segmented approach, calculates performance measures and generates an evaluation report. Furthermore, it provides an easy utility for Limma- or ANOVA- based differential expression analysis.' + diff --git a/recipes/bioconductor-normqpcr/build.sh b/recipes/bioconductor-normqpcr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-normqpcr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-normqpcr/meta.yaml b/recipes/bioconductor-normqpcr/meta.yaml new file mode 100644 index 0000000000000..5585b453eaa74 --- /dev/null +++ b/recipes/bioconductor-normqpcr/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.28.0" %} +{% set name = "NormqPCR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b1753d4e090d39b0d490eb14ff5d47c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-readqpcr >=1.28.0,<1.29.0' + - r-base + - r-qpcr + - r-rcolorbrewer + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-readqpcr >=1.28.0,<1.29.0' + - r-base + - r-qpcr + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'Functions for the selection of optimal reference genes and the normalisation of real-time quantitative PCR data.' + diff --git a/recipes/bioconductor-normr/build.sh b/recipes/bioconductor-normr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-normr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-normr/meta.yaml b/recipes/bioconductor-normr/meta.yaml new file mode 100644 index 0000000000000..4224cfad88863 --- /dev/null +++ b/recipes/bioconductor-normr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.8.0" %} +{% set name = "normr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b809094a96f2751f7562dfa70759b690 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, testthat (>= 1.0), knitr, rmarkdown +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - 'r-rcpp >=0.11' + run: + - 'bioconductor-bamsignals >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - 'r-rcpp >=0.11' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Robust normalization and difference calling procedures for ChIP-seq and alike data. Read counts are modeled jointly as a binomial mixture model with a user-specified number of components. A fitted background estimate accounts for the effect of enrichment in certain regions and, therefore, represents an appropriate null hypothesis. This robust background is used to identify significantly enriched or depleted regions.' + diff --git a/recipes/bioconductor-norway981.db/meta.yaml b/recipes/bioconductor-norway981.db/meta.yaml new file mode 100644 index 0000000000000..2329354595ba6 --- /dev/null +++ b/recipes/bioconductor-norway981.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "Norway981.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 85367390919bba9018438585e59fbb87 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Norway981 http://genome-www5.stanford.edu/ Annotation Data (Norway981) assembled using data from public repositories' + diff --git a/recipes/bioconductor-norway981.db/post-link.sh b/recipes/bioconductor-norway981.db/post-link.sh new file mode 100644 index 0000000000000..33f8c337b5aaf --- /dev/null +++ b/recipes/bioconductor-norway981.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Norway981.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Norway981.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/Norway981.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-norway981.db/bioconductor-norway981.db_3.2.3_src_all.tar.gz" +) +MD5="85367390919bba9018438585e59fbb87" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-norway981.db/pre-unlink.sh b/recipes/bioconductor-norway981.db/pre-unlink.sh new file mode 100644 index 0000000000000..4e1795ce4c52c --- /dev/null +++ b/recipes/bioconductor-norway981.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Norway981.db diff --git a/recipes/bioconductor-npgsea/build.sh b/recipes/bioconductor-npgsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-npgsea/build.sh +++ b/recipes/bioconductor-npgsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-npgsea/meta.yaml b/recipes/bioconductor-npgsea/meta.yaml index 8be80611ba54c..8a3ab763e235d 100644 --- a/recipes/bioconductor-npgsea/meta.yaml +++ b/recipes/bioconductor-npgsea/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "npGSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 40ca8fdafbda0b288f8c3465a91d23f7db6feaf3dc9ea63a63ef691f67f13cf6 + md5: 6cb8b32d6c6c22ce37e259a411912495 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, genefilter, limma, hgu95av2.db, ReportingTools, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Current gene set enrichment methods rely upon permutations for inference. These approaches are computationally expensive and have minimum achievable p-values based on the number of permutations, not on the actual observed statistics. We have derived three parametric approximations to the permutation distributions of two gene set enrichment test statistics. We are able to reduce the computational burden and granularity issues of permutation testing with our method, which is implemented in this package. npGSEA calculates gene set enrichment statistics and p-values without the computational cost of permutations. It is applicable in settings where one or many gene sets are of interest. There are also built-in plotting functions to help users visualize results.' extra: identifiers: - biotools:npgsea + parent_recipe: + name: bioconductor-npgsea + path: recipes/bioconductor-npgsea + version: 1.16.0 + diff --git a/recipes/bioconductor-ntw/build.sh b/recipes/bioconductor-ntw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ntw/build.sh +++ b/recipes/bioconductor-ntw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ntw/meta.yaml b/recipes/bioconductor-ntw/meta.yaml index f26e7582047ce..4416605459695 100644 --- a/recipes/bioconductor-ntw/meta.yaml +++ b/recipes/bioconductor-ntw/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "NTW" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 311829ee41e2ac40ca82331958451a16a148235611b5a6ae34030315c61a089a + md5: 68f21a43a4f188db6c040831e7385b10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package predicts the gene-gene interaction network and identifies the direct transcriptional targets of the perturbation using an ODE (Ordinary Differential Equation) based method.' extra: identifiers: - biotools:ntw - doi:10.1093/bioinformatics/btq629 + parent_recipe: + name: bioconductor-ntw + path: recipes/bioconductor-ntw + version: 1.30.0 + diff --git a/recipes/bioconductor-nucleosim/build.sh b/recipes/bioconductor-nucleosim/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nucleosim/build.sh +++ b/recipes/bioconductor-nucleosim/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nucleosim/meta.yaml b/recipes/bioconductor-nucleosim/meta.yaml index f5071218fc135..7879f514e54de 100644 --- a/recipes/bioconductor-nucleosim/meta.yaml +++ b/recipes/bioconductor-nucleosim/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "nucleoSim" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2f8448759d313c54f61cfe069dba508ae62529c09f9a69e6c85bb26c8e3e65a2 + md5: 29ba1741cbd3ec9feee1a274523abc2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics, knitr, rmarkdown, RUnit requirements: host: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package can generate a synthetic map with reads covering the nucleosome regions as well as a synthetic map with forward and reverse reads emulating next-generation sequencing. The user has choice between three different distributions for the read positioning: Normal, Student and Uniform.' extra: identifiers: - biotools:nucleosim - doi:10.1515/sagmb-2014-0098 + parent_recipe: + name: bioconductor-nucleosim + path: recipes/bioconductor-nucleosim + version: 1.8.0 + diff --git a/recipes/bioconductor-nucler/build.sh b/recipes/bioconductor-nucler/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-nucler/build.sh +++ b/recipes/bioconductor-nucler/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nucler/meta.yaml b/recipes/bioconductor-nucler/meta.yaml index d2b7c046bdbe8..147355f992817 100644 --- a/recipes/bioconductor-nucler/meta.yaml +++ b/recipes/bioconductor-nucler/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "2.12.1" %} +{% set version = "2.14.0" %} {% set name = "nucleR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b20deb9686ab3a6d55ed0818d7d71fdf3763a3b0495c08912691d5eaf9291d99 + md5: 076a8f41e0d540563418f0874b2f3590 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Starr, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 - r-magrittr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-dplyr - r-ggplot2 @@ -49,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'Nucleosome positioning for Tiling Arrays and NGS experiments.' extra: identifiers: - biotools:nucler + parent_recipe: + name: bioconductor-nucler + path: recipes/bioconductor-nucler + version: 2.12.1 + diff --git a/recipes/bioconductor-nucpos/build.sh b/recipes/bioconductor-nucpos/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nucpos/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nucpos/meta.yaml b/recipes/bioconductor-nucpos/meta.yaml new file mode 100644 index 0000000000000..9cd9e4a862c91 --- /dev/null +++ b/recipes/bioconductor-nucpos/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "nuCpos" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 684898e835d61d85bb42a625265b6911 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: NuPoP, Biostrings, testthat +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'nuCpos, a derivative of NuPoP, is an R package for prediction of nucleosome positions. In nuCpos, a duration hidden Markov model is trained with a chemical map of nucleosomes either from budding yeast, fission yeast, or mouse embryonic stem cells. nuCpos outputs the Viterbi (most probable) path of nucleosome-linker states, predicted nucleosome occupancy scores and histone binding affinity (HBA) scores as NuPoP does. nuCpos can also calculate local and whole nucleosomal HBA scores for a given 147-bp sequence. Furthermore, effect of genetic alterations on nucleosome occupancy can be predicted with this package. The parental package NuPoP, which is based on an MNase-seq-based map of budding yeast nucleosomes, was developed by Ji-Ping Wang and Liqun Xi, licensed under GPL-2.' + diff --git a/recipes/bioconductor-nugohs1a520180.db/meta.yaml b/recipes/bioconductor-nugohs1a520180.db/meta.yaml new file mode 100644 index 0000000000000..daab94f21138b --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "nugohs1a520180.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f83701b35b07e69e1ad503b546bb5eaf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix nugohs1a520180 annotation data (chip nugohs1a520180) assembled using data from public repositories' + diff --git a/recipes/bioconductor-nugohs1a520180.db/post-link.sh b/recipes/bioconductor-nugohs1a520180.db/post-link.sh new file mode 100644 index 0000000000000..85ed043f449db --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugohs1a520180.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugohs1a520180.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180.db/bioconductor-nugohs1a520180.db_3.4.0_src_all.tar.gz" +) +MD5="f83701b35b07e69e1ad503b546bb5eaf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugohs1a520180.db/pre-unlink.sh b/recipes/bioconductor-nugohs1a520180.db/pre-unlink.sh new file mode 100644 index 0000000000000..017ee362c7f18 --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugohs1a520180.db diff --git a/recipes/bioconductor-nugohs1a520180cdf/meta.yaml b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml new file mode 100644 index 0000000000000..0f34f7b793e3f --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.4.0" %} +{% set name = "nugohs1a520180cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: aa152658a4a801cc0edb552a98aee841 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the NuGO_Hs1a520180.cdf file.' + diff --git a/recipes/bioconductor-nugohs1a520180cdf/post-link.sh b/recipes/bioconductor-nugohs1a520180cdf/post-link.sh new file mode 100644 index 0000000000000..3bac5f680930e --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugohs1a520180cdf_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180cdf_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugohs1a520180cdf_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180cdf/bioconductor-nugohs1a520180cdf_3.4.0_src_all.tar.gz" +) +MD5="aa152658a4a801cc0edb552a98aee841" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugohs1a520180cdf/pre-unlink.sh b/recipes/bioconductor-nugohs1a520180cdf/pre-unlink.sh new file mode 100644 index 0000000000000..1cdca7f72ade3 --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugohs1a520180cdf diff --git a/recipes/bioconductor-nugohs1a520180probe/meta.yaml b/recipes/bioconductor-nugohs1a520180probe/meta.yaml new file mode 100644 index 0000000000000..270127b234506 --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.4.0" %} +{% set name = "nugohs1a520180probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6acf20ac4a799eaae97d0a64426d6ac3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com.' + diff --git a/recipes/bioconductor-nugohs1a520180probe/post-link.sh b/recipes/bioconductor-nugohs1a520180probe/post-link.sh new file mode 100644 index 0000000000000..14feef1997906 --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugohs1a520180probe_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugohs1a520180probe_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugohs1a520180probe_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugohs1a520180probe/bioconductor-nugohs1a520180probe_3.4.0_src_all.tar.gz" +) +MD5="6acf20ac4a799eaae97d0a64426d6ac3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugohs1a520180probe/pre-unlink.sh b/recipes/bioconductor-nugohs1a520180probe/pre-unlink.sh new file mode 100644 index 0000000000000..ff15506e41dc2 --- /dev/null +++ b/recipes/bioconductor-nugohs1a520180probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugohs1a520180probe diff --git a/recipes/bioconductor-nugomm1a520177.db/meta.yaml b/recipes/bioconductor-nugomm1a520177.db/meta.yaml new file mode 100644 index 0000000000000..8330d945e9f44 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "nugomm1a520177.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 99f69ea2cbb80a79bedee99e3d726e50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix nugomm1a520177 annotation data (chip nugomm1a520177) assembled using data from public repositories' + diff --git a/recipes/bioconductor-nugomm1a520177.db/post-link.sh b/recipes/bioconductor-nugomm1a520177.db/post-link.sh new file mode 100644 index 0000000000000..cf84b41742f3f --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugomm1a520177.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugomm1a520177.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177.db/bioconductor-nugomm1a520177.db_3.4.0_src_all.tar.gz" +) +MD5="99f69ea2cbb80a79bedee99e3d726e50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugomm1a520177.db/pre-unlink.sh b/recipes/bioconductor-nugomm1a520177.db/pre-unlink.sh new file mode 100644 index 0000000000000..4910d94bfd7fe --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugomm1a520177.db diff --git a/recipes/bioconductor-nugomm1a520177cdf/meta.yaml b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml new file mode 100644 index 0000000000000..709265f1f3771 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.4.0" %} +{% set name = "nugomm1a520177cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fc60c2018580decaea30f09de55142fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the NuGO_Mm1a520177.cdf file.' + diff --git a/recipes/bioconductor-nugomm1a520177cdf/post-link.sh b/recipes/bioconductor-nugomm1a520177cdf/post-link.sh new file mode 100644 index 0000000000000..61e45ccfdd064 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugomm1a520177cdf_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177cdf_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugomm1a520177cdf_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177cdf/bioconductor-nugomm1a520177cdf_3.4.0_src_all.tar.gz" +) +MD5="fc60c2018580decaea30f09de55142fb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugomm1a520177cdf/pre-unlink.sh b/recipes/bioconductor-nugomm1a520177cdf/pre-unlink.sh new file mode 100644 index 0000000000000..c206584a100b9 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugomm1a520177cdf diff --git a/recipes/bioconductor-nugomm1a520177probe/meta.yaml b/recipes/bioconductor-nugomm1a520177probe/meta.yaml new file mode 100644 index 0000000000000..0a3c9479520d0 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.4.0" %} +{% set name = "nugomm1a520177probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7fa974389ad2be6ebda8810496221a9b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.20. The probe sequence data was obtained from http://www.affymetrix.com.' + diff --git a/recipes/bioconductor-nugomm1a520177probe/post-link.sh b/recipes/bioconductor-nugomm1a520177probe/post-link.sh new file mode 100644 index 0000000000000..798dff26d5c81 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="nugomm1a520177probe_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/nugomm1a520177probe_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/nugomm1a520177probe_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-nugomm1a520177probe/bioconductor-nugomm1a520177probe_3.4.0_src_all.tar.gz" +) +MD5="7fa974389ad2be6ebda8810496221a9b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-nugomm1a520177probe/pre-unlink.sh b/recipes/bioconductor-nugomm1a520177probe/pre-unlink.sh new file mode 100644 index 0000000000000..6e4d6e87e3cf9 --- /dev/null +++ b/recipes/bioconductor-nugomm1a520177probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ nugomm1a520177probe diff --git a/recipes/bioconductor-nupop/build.sh b/recipes/bioconductor-nupop/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-nupop/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-nupop/meta.yaml b/recipes/bioconductor-nupop/meta.yaml new file mode 100644 index 0000000000000..02e9195d889f4 --- /dev/null +++ b/recipes/bioconductor-nupop/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.32.0" %} +{% set name = "NuPoP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4770138a010896a75cfedbde935bc816 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('fortran') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'NuPoP is an R package for Nucleosome Positioning Prediction.This package is built upon a duration hidden Markov model proposed in Xi et al, 2010; Wang et al, 2008. The core of the package was written in Fotran. In addition to the R package, a stand-alone Fortran software tool is also available at http://nucleosome.stats.northwestern.edu.' + diff --git a/recipes/bioconductor-occugene/build.sh b/recipes/bioconductor-occugene/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-occugene/build.sh +++ b/recipes/bioconductor-occugene/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-occugene/meta.yaml b/recipes/bioconductor-occugene/meta.yaml index c9a8beeb907c6..35c68a95c9589 100644 --- a/recipes/bioconductor-occugene/meta.yaml +++ b/recipes/bioconductor-occugene/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "occugene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 73eb1db8d96deaa1e2ba5137f1e02fafd15c6d8366ff59256337520c1ab2df2f + md5: c294febad5ded94b6e0f1223beac3b78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Statistical tools for building random mutagenesis libraries for prokaryotes. The package has functions for handling the occupancy distribution for a multinomial and for estimating the number of essential genes in random transposon mutagenesis libraries.' extra: identifiers: - biotools:occugene - doi:10.1007/978-1-59745-321-9_22 + parent_recipe: + name: bioconductor-occugene + path: recipes/bioconductor-occugene + version: 1.40.0 + diff --git a/recipes/bioconductor-ocplus/build.sh b/recipes/bioconductor-ocplus/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ocplus/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ocplus/meta.yaml b/recipes/bioconductor-ocplus/meta.yaml new file mode 100644 index 0000000000000..4e70e2c90bbb6 --- /dev/null +++ b/recipes/bioconductor-ocplus/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.56.0" %} +{% set name = "OCplus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 318784b120a74c9a49abecfdeb6d0891 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-akima + - r-base + run: + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-akima + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This package allows to characterize the operating characteristics of a microarray experiment, i.e. the trade-off between false discovery rate and the power to detect truly regulated genes. The package includes tools both for planned experiments (for sample size assessment) and for already collected data (identification of differentially expressed genes).' + diff --git a/recipes/bioconductor-odseq/build.sh b/recipes/bioconductor-odseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-odseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-odseq/meta.yaml b/recipes/bioconductor-odseq/meta.yaml new file mode 100644 index 0000000000000..62b19ede042bb --- /dev/null +++ b/recipes/bioconductor-odseq/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.10.0" %} +{% set name = "odseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 18974dd1cc6085e325565b9a4f01e635 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr(>= 1.11) +requirements: + host: + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-msa >=1.14.0,<1.15.0' + - r-base + - 'r-mclust >=5.1' + run: + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-msa >=1.14.0,<1.15.0' + - r-base + - 'r-mclust >=5.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Performs outlier detection of sequences in a multiple sequence alignment using bootstrap of predefined distance metrics. Outlier sequences can make downstream analyses unreliable or make the alignments less accurate while they are being constructed. This package implements the OD-seq algorithm proposed by Jehl et al (doi 10.1186/s12859-015-0702-1) for aligned sequences and a variant using string kernels for unaligned sequences.' + diff --git a/recipes/bioconductor-ogsa/build.sh b/recipes/bioconductor-ogsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ogsa/build.sh +++ b/recipes/bioconductor-ogsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ogsa/meta.yaml b/recipes/bioconductor-ogsa/meta.yaml index 6d1e5f2caaf3f..7a378cf39df2c 100644 --- a/recipes/bioconductor-ogsa/meta.yaml +++ b/recipes/bioconductor-ogsa/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "OGSA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4e6fbb9d12b9283d26d4543c5d513c829c0c8a1061ab0d3591f7877095849434 + md5: 3e46b50f76f97e0da3c912e661bd5e12 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - 'r-gplots >=2.8.0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - 'r-gplots >=2.8.0' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (== 2)' summary: 'OGSA provides a global estimate of pathway deregulation in cancer subtypes by integrating the estimates of significance for individual pathway members that have been identified by outlier analysis.' extra: identifiers: - biotools:ogsa - doi:10.1109/TCBB.2013.153 + parent_recipe: + name: bioconductor-ogsa + path: recipes/bioconductor-ogsa + version: 1.10.0 + diff --git a/recipes/bioconductor-oligo/build.sh b/recipes/bioconductor-oligo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oligo/build.sh +++ b/recipes/bioconductor-oligo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oligo/conda_build_config.yaml b/recipes/bioconductor-oligo/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-oligo/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-oligo/meta.yaml b/recipes/bioconductor-oligo/meta.yaml index b48d25885cfd0..df50408444dfb 100644 --- a/recipes/bioconductor-oligo/meta.yaml +++ b/recipes/bioconductor-oligo/meta.yaml @@ -1,44 +1,45 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "oligo" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4c7d85628fec0db359e58bd42b16f084cdcbe7ab07044310b9162e95ede4b073 + md5: a3ecdc244b8f0b20408c7251c13cc0ca build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, GenomeGraphs, RCurl, ACME, biomaRt, AnnotationDbi, GenomeGraphs, RCurl requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-dbi >=0.3.1' - r-ff - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-dbi >=0.3.1' - r-ff @@ -50,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).' extra: identifiers: - biotools:oligo + parent_recipe: + name: bioconductor-oligo + path: recipes/bioconductor-oligo + version: 1.44.0 + diff --git a/recipes/bioconductor-oligoclasses/build.sh b/recipes/bioconductor-oligoclasses/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oligoclasses/build.sh +++ b/recipes/bioconductor-oligoclasses/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oligoclasses/conda_build_config.yaml b/recipes/bioconductor-oligoclasses/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-oligoclasses/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-oligoclasses/meta.yaml b/recipes/bioconductor-oligoclasses/meta.yaml index 4cf4709a72528..acef8e6c452ac 100644 --- a/recipes/bioconductor-oligoclasses/meta.yaml +++ b/recipes/bioconductor-oligoclasses/meta.yaml @@ -1,48 +1,50 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "oligoClasses" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 62c218d5484e9e55d352b351c8cee23a89f5301f3ff66a9a65a330f79a7ee11b + md5: c58277928932218857e89afeeffc7aa9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hapmapsnp5, hapmapsnp6, pd.genomewidesnp.6, pd.genomewidesnp.5, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.mapping250k.sty, pd.mapping250k.nsp, genomewidesnp6Crlmm (>= 1.0.7), genomewidesnp5Crlmm (>= 1.0.6), RUnit, human370v1cCrlmm, SNPchip, VanillaICE, crlmm requirements: host: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dbi - r-ff - r-foreach - r-rsqlite run: - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base + - r-biocmanager - r-dbi - r-ff - r-foreach @@ -51,10 +53,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains class definitions, validity checks, and initialization methods for classes used by the oligo and crlmm packages.' extra: identifiers: - biotools:oligoclasses - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-oligoclasses + path: recipes/bioconductor-oligoclasses + version: 1.42.0 + diff --git a/recipes/bioconductor-oligodata/meta.yaml b/recipes/bioconductor-oligodata/meta.yaml new file mode 100644 index 0000000000000..9a4853479a6e2 --- /dev/null +++ b/recipes/bioconductor-oligodata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.8.0" %} +{% set name = "oligoData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9625cfd4b31bb575c4029a0632a7ee12 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pd.hg.u95av2, pd.huex.1.0.st.v2, pd.mapping50k.xba240, pd.hg18.60mer.expr, pd.2006.07.18.hg18.refseq.promoter, pd.hugene.1.0.st.v1 +requirements: + host: + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - r-base + run: + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'Dataset samples (Affymetrix: Expression, Gene, Exon, SNP; NimbleGen: Expression, Tiling) to be used with the oligo package.' + diff --git a/recipes/bioconductor-oligodata/post-link.sh b/recipes/bioconductor-oligodata/post-link.sh new file mode 100644 index 0000000000000..d911d5e768893 --- /dev/null +++ b/recipes/bioconductor-oligodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="oligoData_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/oligoData_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/oligoData_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-oligodata/bioconductor-oligodata_1.8.0_src_all.tar.gz" +) +MD5="9625cfd4b31bb575c4029a0632a7ee12" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-oligodata/pre-unlink.sh b/recipes/bioconductor-oligodata/pre-unlink.sh new file mode 100644 index 0000000000000..207fbf1bedf98 --- /dev/null +++ b/recipes/bioconductor-oligodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ oligoData diff --git a/recipes/bioconductor-olin/build.sh b/recipes/bioconductor-olin/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-olin/build.sh +++ b/recipes/bioconductor-olin/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-olin/meta.yaml b/recipes/bioconductor-olin/meta.yaml index b84694aa7bf00..69a0a23a61cd4 100644 --- a/recipes/bioconductor-olin/meta.yaml +++ b/recipes/bioconductor-olin/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.58.0" %} +{% set version = "1.60.0" %} {% set name = "OLIN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a84c520b2ef0976afb0cb4aa5bb8b8c3e1bda0f2ddf241d42554626af692dcf9 + md5: 8c56f4b27a4c0fd7d3554d7153ba260b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: convert requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-locfit run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-locfit test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions for normalisation of two-color microarrays by optimised local regression and for detection of artefacts in microarray data' extra: identifiers: - biotools:olin + parent_recipe: + name: bioconductor-olin + path: recipes/bioconductor-olin + version: 1.58.0 + diff --git a/recipes/bioconductor-olingui/build.sh b/recipes/bioconductor-olingui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-olingui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-olingui/meta.yaml b/recipes/bioconductor-olingui/meta.yaml new file mode 100644 index 0000000000000..dc379c3b825ba --- /dev/null +++ b/recipes/bioconductor-olingui/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.56.0" %} +{% set name = "OLINgui" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d80fde109f35a28abd65089848537969 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-olin >=1.60.0,<1.61.0' + - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-marray >=1.60.0,<1.61.0' + - 'bioconductor-olin >=1.60.0,<1.61.0' + - 'bioconductor-tkwidgets >=1.60.0,<1.61.0' + - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Graphical user interface for the OLIN package' + diff --git a/recipes/bioconductor-omadb/build.sh b/recipes/bioconductor-omadb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omadb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omadb/meta.yaml b/recipes/bioconductor-omadb/meta.yaml new file mode 100644 index 0000000000000..aaffe7996b59d --- /dev/null +++ b/recipes/bioconductor-omadb/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "OmaDB" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 60387eba231f92262948624be804cc12 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-ape + - r-base + - 'r-httr >=1.2.1' + - r-jsonlite + - 'r-plyr >=1.8.4' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-ape + - r-base + - 'r-httr >=1.2.1' + - r-jsonlite + - 'r-plyr >=1.8.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A package for the orthology prediction data download from OMA database.' + diff --git a/recipes/bioconductor-omicade4/build.sh b/recipes/bioconductor-omicade4/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-omicade4/build.sh +++ b/recipes/bioconductor-omicade4/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicade4/meta.yaml b/recipes/bioconductor-omicade4/meta.yaml index bf8257fb7233b..e1320ccfaa3a3 100644 --- a/recipes/bioconductor-omicade4/meta.yaml +++ b/recipes/bioconductor-omicade4/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "omicade4" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 522895abae63a4b3c1bdb2b237875543793139fe2a5363d90d1d7d38583549ee + md5: 5a5e6def3842ea64955d6f4004c01ca0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-made4 >=1.54.0,<1.56.0' + - 'bioconductor-made4 >=1.56.0,<1.57.0' - r-ade4 - r-base run: - - 'bioconductor-made4 >=1.54.0,<1.56.0' + - 'bioconductor-made4 >=1.56.0,<1.57.0' - r-ade4 - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Multiple co-inertia analysis of omics datasets' extra: identifiers: - biotools:omicade4 + parent_recipe: + name: bioconductor-omicade4 + path: recipes/bioconductor-omicade4 + version: 1.20.0 + diff --git a/recipes/bioconductor-omiccircos/build.sh b/recipes/bioconductor-omiccircos/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-omiccircos/build.sh +++ b/recipes/bioconductor-omiccircos/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omiccircos/meta.yaml b/recipes/bioconductor-omiccircos/meta.yaml index ecec856992876..f8e8393bcb042 100644 --- a/recipes/bioconductor-omiccircos/meta.yaml +++ b/recipes/bioconductor-omiccircos/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "OmicCircos" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 250785e0b674c03fbad7c822ea281edc1c3d8f540dc27e6b432d3e7ed9b0b775 + md5: 6f138f977152b3f86101ae451fc9368d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'OmicCircos is an R application and package for generating high-quality circular plots for omics data.' extra: identifiers: - biotools:omiccircos - doi:10.4137/cin.s13495 + parent_recipe: + name: bioconductor-omiccircos + path: recipes/bioconductor-omiccircos + version: 1.18.0 + diff --git a/recipes/bioconductor-omicplotr/build.sh b/recipes/bioconductor-omicplotr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicplotr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicplotr/meta.yaml b/recipes/bioconductor-omicplotr/meta.yaml new file mode 100644 index 0000000000000..08bf7516af493 --- /dev/null +++ b/recipes/bioconductor-omicplotr/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.2.0" %} +{% set name = "omicplotR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 90b98aa96f0ed392ab2fc92c038ee9f8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-aldex2 >=1.14.0,<1.15.0' + - r-base + - r-compositions + - r-knitr + - r-matrixstats + - r-rmarkdown + - r-shiny + - r-vegan + - r-zcompositions + run: + - 'bioconductor-aldex2 >=1.14.0,<1.15.0' + - r-base + - r-compositions + - r-knitr + - r-matrixstats + - r-rmarkdown + - r-shiny + - r-vegan + - r-zcompositions +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A Shiny app for visual exploration of omic datasets as compositions, and differential abundance analysis using ALDEx2. Useful for exploring RNA-seq, meta-RNA-seq, 16s rRNA gene sequencing with visualizations such as principal component analysis biplots (coloured using metadata for visualizing each variable), dendrograms and stacked bar plots, and effect plots (ALDEx2). Input is a table of counts and metadata file (if metadata exists), with options to filter data by count or by metadata to remove low counts, or to visualize select samples according to selected metadata.' + diff --git a/recipes/bioconductor-omicrexposome/build.sh b/recipes/bioconductor-omicrexposome/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicrexposome/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicrexposome/meta.yaml b/recipes/bioconductor-omicrexposome/meta.yaml new file mode 100644 index 0000000000000..c97ddcbb4e6ec --- /dev/null +++ b/recipes/bioconductor-omicrexposome/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.0" %} +{% set name = "omicRexposome" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 84a97bc40482e4ac0b1bf9524b0d30a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, snpStats, brgedata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multidataset >=1.10.0,<1.11.0' + - 'bioconductor-omicade4 >=1.22.0,<1.23.0' + - 'bioconductor-rexposome >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-isva + - r-pma + - r-smartsva + - r-stringr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multidataset >=1.10.0,<1.11.0' + - 'bioconductor-omicade4 >=1.22.0,<1.23.0' + - 'bioconductor-rexposome >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-gridextra + - r-isva + - r-pma + - r-smartsva + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'omicRexposome systematizes the association evaluation between exposures and omic data, taking advantage of MultiDataSet for coordinated data management, rexposome for exposome data definition and limma for association testing. Also to perform data integration mixing exposome and omic data using multi co-inherent analysis (omicade4) and multi-canonical correlation analysis (PMA).' + diff --git a/recipes/bioconductor-omicsmarker/build.sh b/recipes/bioconductor-omicsmarker/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicsmarker/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicsmarker/meta.yaml b/recipes/bioconductor-omicsmarker/meta.yaml new file mode 100644 index 0000000000000..ee498290a5a21 --- /dev/null +++ b/recipes/bioconductor-omicsmarker/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.14.0" %} +{% set name = "OmicsMarkeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 10593af3dcc1bdf37ac363bf3956af43 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr +requirements: + host: + - 'r-assertive >=0.3-0' + - 'r-assertive.base >=0.0-1' + - r-base + - 'r-caret >=6.0-37' + - 'r-catools >=1.14' + - 'r-data.table >=1.9.4' + - 'r-discriminer >=0.1-29' + - 'r-e1071 >=1.6-1' + - 'r-foreach >=1.4.1' + - 'r-gbm >=2.1' + - 'r-glmnet >=1.9-5' + - 'r-pamr >=1.54.1' + - 'r-permute >=0.7-0' + - 'r-plyr >=1.8' + - 'r-randomforest >=4.6-10' + run: + - 'r-assertive >=0.3-0' + - 'r-assertive.base >=0.0-1' + - r-base + - 'r-caret >=6.0-37' + - 'r-catools >=1.14' + - 'r-data.table >=1.9.4' + - 'r-discriminer >=0.1-29' + - 'r-e1071 >=1.6-1' + - 'r-foreach >=1.4.1' + - 'r-gbm >=2.1' + - 'r-glmnet >=1.9-5' + - 'r-pamr >=1.54.1' + - 'r-permute >=0.7-0' + - 'r-plyr >=1.8' + - 'r-randomforest >=4.6-10' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Tools for classification and feature selection for ''omics'' level datasets. It is a tool to provide multiple multivariate classification and feature selection techniques complete with multiple stability metrics and aggregation techniques. It is primarily designed for analysis of metabolomics datasets but potentially extendable to proteomics and transcriptomics applications.' + diff --git a/recipes/bioconductor-omicspca/build.sh b/recipes/bioconductor-omicspca/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicspca/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicspca/meta.yaml b/recipes/bioconductor-omicspca/meta.yaml new file mode 100644 index 0000000000000..05796d3d9bafe --- /dev/null +++ b/recipes/bioconductor-omicspca/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.0.0" %} +{% set name = "OMICsPCA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d9087be2af8fe8cc1c0d738d660a153 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-helloranges >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-omicspcadata >=1.0.0,<1.1.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-cluster + - r-clvalid + - r-corrplot + - r-cowplot + - r-data.table + - r-factoextra + - r-factominer + - r-fpc + - r-ggplot2 + - r-kableextra + - r-magick + - r-mass + - r-nbclust + - r-pdftools + - r-performanceanalytics + - r-reshape2 + - r-rgl + - r-rmarkdown + - r-tidyr + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-helloranges >=1.8.0,<1.9.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-omicspcadata >=1.0.0,<1.1.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - r-base + - r-cluster + - r-clvalid + - r-corrplot + - r-cowplot + - r-data.table + - r-factoextra + - r-factominer + - r-fpc + - r-ggplot2 + - r-kableextra + - r-magick + - r-mass + - r-nbclust + - r-pdftools + - r-performanceanalytics + - r-reshape2 + - r-rgl + - r-rmarkdown + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'OMICsPCA is an analysis pipeline designed to integrate multi OMICs experiments done on various subjects (e.g. Cell lines, individuals), treatments (e.g. disease/control) or time points and to analyse such integrated data from various various angles and perspectives. In it''s core OMICsPCA uses Principal Component Analysis (PCA) to integrate multiomics experiments from various sources and thus has ability to over data insufficiency issues by using the ingegrated data as representatives. OMICsPCA can be used in various application including analysis of overall distribution of OMICs assays across various samples /individuals /time points; grouping assays by user-defined conditions; identification of source of variation, similarity/dissimilarity between assays, variables or individuals.' + diff --git a/recipes/bioconductor-omicspcadata/meta.yaml b/recipes/bioconductor-omicspcadata/meta.yaml new file mode 100644 index 0000000000000..142c6f8133679 --- /dev/null +++ b/recipes/bioconductor-omicspcadata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "OMICsPCAdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aec265a048e822143e27ad37dbde1c38 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, kableExtra, rmarkdown +requirements: + host: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Supporting data for package OMICsPCA' + diff --git a/recipes/bioconductor-omicspcadata/post-link.sh b/recipes/bioconductor-omicspcadata/post-link.sh new file mode 100644 index 0000000000000..305cbbe3b5ed5 --- /dev/null +++ b/recipes/bioconductor-omicspcadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="OMICsPCAdata_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/OMICsPCAdata_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/OMICsPCAdata_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-omicspcadata/bioconductor-omicspcadata_1.0.0_src_all.tar.gz" +) +MD5="aec265a048e822143e27ad37dbde1c38" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-omicspcadata/pre-unlink.sh b/recipes/bioconductor-omicspcadata/pre-unlink.sh new file mode 100644 index 0000000000000..9ab8763c9ceab --- /dev/null +++ b/recipes/bioconductor-omicspcadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ OMICsPCAdata diff --git a/recipes/bioconductor-omicsprint/build.sh b/recipes/bioconductor-omicsprint/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-omicsprint/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-omicsprint/meta.yaml b/recipes/bioconductor-omicsprint/meta.yaml new file mode 100644 index 0000000000000..768b6d55f0eac --- /dev/null +++ b/recipes/bioconductor-omicsprint/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "omicsPrint" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1ce70666bb820661dc9b55c525acdbf6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, GEOquery, VariantAnnotation, Rsamtools, BiocParallel, GenomicRanges, FDb.InfiniumMethylation.hg19, snpStats +requirements: + host: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mass + - r-matrixstats + run: + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mass + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'omicsPrint provides functionality for cross omic genetic fingerprinting, for example, to verify sample relationships between multiple omics data types, i.e. genomic, transcriptomic and epigenetic (DNA methylation).' + diff --git a/recipes/bioconductor-onassis/build.sh b/recipes/bioconductor-onassis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-onassis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-onassis/meta.yaml b/recipes/bioconductor-onassis/meta.yaml new file mode 100644 index 0000000000000..94e3a2a2f53c7 --- /dev/null +++ b/recipes/bioconductor-onassis/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.4.5" %} +{% set name = "Onassis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 89a0e8751411bc21806a3159112bc2b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, rmarkdown, htmltools, org.Hs.eg.db, gplots, GenomicRanges, kableExtra +# SystemRequirements: Java (>= 1.8) +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-geometadb >=1.44.0,<1.45.0' + - 'bioconductor-onassisjavalibs >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-dt + - r-knitr + - r-rcurl + - r-rjava + - r-rsqlite + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-geometadb >=1.44.0,<1.45.0' + - 'bioconductor-onassisjavalibs >=1.4.0,<1.5.0' + - r-base + - r-data.table + - r-dt + - r-knitr + - r-rcurl + - r-rjava + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A package that allows the annotation of text with ontology terms (mainly from OBO ontologies) and the computation of semantic similarity measures based on the structure of the ontology between different annotated samples.' + diff --git a/recipes/bioconductor-onassisjavalibs/meta.yaml b/recipes/bioconductor-onassisjavalibs/meta.yaml new file mode 100644 index 0000000000000..bd450781fb8e1 --- /dev/null +++ b/recipes/bioconductor-onassisjavalibs/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.4.2" %} +{% set name = "OnassisJavaLibs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06e52b38a80a47e6b340cc0365e47554 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, rmarkdown, knitr +# SystemRequirements: Java (>= 1.8) +requirements: + host: + - r-base + - r-rjava + run: + - r-base + - r-rjava + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'A package that contains java libraries to call conceptmapper and compute semnatic similarity from R' + diff --git a/recipes/bioconductor-onassisjavalibs/post-link.sh b/recipes/bioconductor-onassisjavalibs/post-link.sh new file mode 100644 index 0000000000000..d42ae05d9a199 --- /dev/null +++ b/recipes/bioconductor-onassisjavalibs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="OnassisJavaLibs_1.4.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/OnassisJavaLibs_1.4.2.tar.gz" + "https://bioarchive.galaxyproject.org/OnassisJavaLibs_1.4.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-onassisjavalibs/bioconductor-onassisjavalibs_1.4.2_src_all.tar.gz" +) +MD5="06e52b38a80a47e6b340cc0365e47554" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-onassisjavalibs/pre-unlink.sh b/recipes/bioconductor-onassisjavalibs/pre-unlink.sh new file mode 100644 index 0000000000000..ca1289f40eba5 --- /dev/null +++ b/recipes/bioconductor-onassisjavalibs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ OnassisJavaLibs diff --git a/recipes/bioconductor-oncomix/build.sh b/recipes/bioconductor-oncomix/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-oncomix/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncomix/meta.yaml b/recipes/bioconductor-oncomix/meta.yaml new file mode 100644 index 0000000000000..fab012e181e6f --- /dev/null +++ b/recipes/bioconductor-oncomix/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "oncomix" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 24f731f87764297454ff5a4a9357f994 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, RMySQL +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-mclust + - r-rcolorbrewer + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-mclust + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package helps identify mRNAs that are overexpressed in subsets of tumors relative to normal tissue. Ideal inputs would be paired tumor-normal data from the same tissue from many patients (>15 pairs). This unsupervised approach relies on the observation that oncogenes are characteristically overexpressed in only a subset of tumors in the population, and may help identify oncogene candidates purely based on differences in mRNA expression between previously unknown subtypes.' + diff --git a/recipes/bioconductor-oncoscore/build.sh b/recipes/bioconductor-oncoscore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-oncoscore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncoscore/meta.yaml b/recipes/bioconductor-oncoscore/meta.yaml new file mode 100644 index 0000000000000..5a8d3261d8164 --- /dev/null +++ b/recipes/bioconductor-oncoscore/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.10.0" %} +{% set name = "OncoScore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2037b880068e7ce59e92d799f28a9c4d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, knitr, testthat, +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'OncoScore is a tool to measure the association of genes to cancer based on citation frequencies in biomedical literature. The score is evaluated from PubMed literature by dynamically updatable web queries.' + diff --git a/recipes/bioconductor-oncosimulr/build.sh b/recipes/bioconductor-oncosimulr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oncosimulr/build.sh +++ b/recipes/bioconductor-oncosimulr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oncosimulr/meta.yaml b/recipes/bioconductor-oncosimulr/meta.yaml index 5b622b64daa84..c94d14aaae409 100644 --- a/recipes/bioconductor-oncosimulr/meta.yaml +++ b/recipes/bioconductor-oncosimulr/meta.yaml @@ -1,26 +1,27 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "OncoSimulR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7d3e904dbfc41ff07295646fae09ebab391c8ee279c1a1552bbf8fe0e773190 + md5: 44f9be22a9965fe0389aad902c2d08d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, Oncotree, testthat (>= 1.0.0), rmarkdown, bookdown, pander requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-nem >=2.54.0,<2.56.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-car - r-data.table @@ -33,9 +34,9 @@ requirements: - 'r-rcpp >=0.12.4' - r-smatr run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-nem >=2.54.0,<2.56.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-nem >=2.56.0,<2.57.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-car - r-data.table @@ -55,9 +56,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Functions for forward population genetic simulation in asexual populations, with special focus on cancer progression. Fitness can be an arbitrary function of genetic interactions between multiple genes or modules of genes, including epistasis, order restrictions in mutation accumulation, and order effects. Mutation rates can differ between genes, and we can include mutator/antimutator genes (to model mutator phenotypes). Simulations use continuous-time models and can include driver and passenger genes and modules. Also included are functions for: simulating random DAGs of the type found in Oncogenetic Tress, Conjunctive Bayesian Networks, and other tumor progression models; plotting and sampling from single or multiple realizations of the simulations, including single-cell sampling; plotting the parent-child relationships of the clones; generating random fitness landscapes (Rough Mount Fuji, House of Cards, and additive models) and plotting them.' extra: identifiers: - biotools:oncosimulr + parent_recipe: + name: bioconductor-oncosimulr + path: recipes/bioconductor-oncosimulr + version: 2.10.0 + diff --git a/recipes/bioconductor-onesense/build.sh b/recipes/bioconductor-onesense/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-onesense/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-onesense/meta.yaml b/recipes/bioconductor-onesense/meta.yaml new file mode 100644 index 0000000000000..288eb659f698a --- /dev/null +++ b/recipes/bioconductor-onesense/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.4.0" %} +{% set name = "oneSENSE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2bf3f4b39f72aab46b8a59d1475a0057 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-gplots + - r-plotly + - r-rtsne + - r-scatterplot3d + - r-shiny + - r-shinyfiles + - r-webshot + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-gplots + - r-plotly + - r-rtsne + - r-scatterplot3d + - r-shiny + - r-shinyfiles + - r-webshot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'A graphical user interface that facilitates the dimensional reduction method based on the t-distributed stochastic neighbor embedding (t-SNE) algorithm, for categorical analysis of mass cytometry data. With One-SENSE, measured parameters are grouped into predefined categories, and cells are projected onto a space composed of one dimension for each category. Each dimension is informative and can be annotated through the use of heatplots aligned in parallel to each axis, allowing for simultaneous visualization of two catergories across a two-dimensional plot. The cellular occupancy of the resulting plots alllows for direct assessment of the relationships between the categories.' + diff --git a/recipes/bioconductor-onlinefdr/build.sh b/recipes/bioconductor-onlinefdr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-onlinefdr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-onlinefdr/meta.yaml b/recipes/bioconductor-onlinefdr/meta.yaml new file mode 100644 index 0000000000000..4dd94fe4fc2cb --- /dev/null +++ b/recipes/bioconductor-onlinefdr/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.0" %} +{% set name = "onlineFDR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f6c5c4dc344739ada4dc4be60aea0a5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package allows users to control the false discovery rate for online hypothesis testing, where hypotheses arrive sequentially in a stream, as presented by Javanmard and Montanari (2015, 2018). In this framework, a null hypothesis is rejected based only on the previous decisions, as the future p-values and the number of hypotheses to be tested are unknown.' + diff --git a/recipes/bioconductor-ontoproc/build.sh b/recipes/bioconductor-ontoproc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ontoproc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ontoproc/meta.yaml b/recipes/bioconductor-ontoproc/meta.yaml new file mode 100644 index 0000000000000..5cf1ab6e4b240 --- /dev/null +++ b/recipes/bioconductor-ontoproc/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.4.0" %} +{% set name = "ontoProc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6c923d964ffaa80eff31fb0049e554ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, org.Hs.eg.db, org.Mm.eg.db, testthat, BiocStyle +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ontologyindex + - r-shiny + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ontologyindex + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Support harvesting of diverse bioinformatic ontologies, making particular use of the ontologyIndex package on CRAN. We provide snapshots of key ontologies for terms about cells, cell lines, chemical compounds, and anatomy, to help analyze genome-scale experiments, particularly cell x compound screens. Another purpose is to strengthen development of compelling use cases for richer interfaces to emerging ontologies.' + diff --git a/recipes/bioconductor-opencyto/build.sh b/recipes/bioconductor-opencyto/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-opencyto/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-opencyto/meta.yaml b/recipes/bioconductor-opencyto/meta.yaml new file mode 100644 index 0000000000000..4fa77095f4541 --- /dev/null +++ b/recipes/bioconductor-opencyto/meta.yaml @@ -0,0 +1,78 @@ +{% set version = "1.20.0" %} +{% set name = "openCyto" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 36812f18ed317a05afae096aa98cea5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: flowWorkspaceData, knitr, testthat, utils, tools, parallel, ggcyto +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-clue + - r-data.table + - r-gtools + - r-ks + - r-lattice + - r-mass + - r-plyr + - r-r.utils + - r-rcolorbrewer + - r-rcpp + - r-rrcov + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-flowclust >=3.20.0,<3.21.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-clue + - r-data.table + - r-gtools + - r-ks + - r-lattice + - r-mass + - r-plyr + - r-r.utils + - r-rcolorbrewer + - r-rcpp + - r-rrcov + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.' + diff --git a/recipes/bioconductor-openprimer/build.sh b/recipes/bioconductor-openprimer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-openprimer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-openprimer/meta.yaml b/recipes/bioconductor-openprimer/meta.yaml new file mode 100644 index 0000000000000..15d6b04217c8e --- /dev/null +++ b/recipes/bioconductor-openprimer/meta.yaml @@ -0,0 +1,90 @@ +{% set version = "1.4.1" %} +{% set name = "openPrimeR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a1bc7c07f1486703b09f7f291737fe84 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat (>= 1.0.2), knitr (>= 1.13), rmarkdown (>= 1.0), devtools (>= 1.12.0), doParallel (>= 1.0.10), pander (>= 0.6.0), learnr (>= 0.9) +# SystemRequirements: MAFFT (>= 7.305), OligoArrayAux (>= 3.8), ViennaRNA (>= 2.4.1), MELTING (>= 5.1.1), Pandoc (>= 1.12.3) +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-ape >=3.5' + - r-base + - 'r-digest >=0.6.9' + - 'r-distr >=2.6' + - 'r-distrex >=2.6' + - 'r-dplyr >=0.5.0' + - 'r-fitdistrplus >=1.0-7' + - 'r-foreach >=1.4.3' + - 'r-ggplot2 >=2.1.0' + - 'r-hmisc >=3.17-4' + - 'r-lpsolveapi >=5.5.2.0-17' + - 'r-magrittr >=1.5' + - 'r-openxlsx >=4.0.17' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1-2' + - 'r-reshape2 >=1.4.1' + - 'r-scales >=0.4.0' + - 'r-seqinr >=3.3-3' + - 'r-stringdist >=0.9.4.1' + - 'r-stringr >=1.0.0' + - 'r-tinytex >=0.5' + - 'r-uniqtag >=1.0' + - 'r-xml >=3.98-1.4' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-decipher >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'r-ape >=3.5' + - r-base + - 'r-digest >=0.6.9' + - 'r-distr >=2.6' + - 'r-distrex >=2.6' + - 'r-dplyr >=0.5.0' + - 'r-fitdistrplus >=1.0-7' + - 'r-foreach >=1.4.3' + - 'r-ggplot2 >=2.1.0' + - 'r-hmisc >=3.17-4' + - 'r-lpsolveapi >=5.5.2.0-17' + - 'r-magrittr >=1.5' + - 'r-openxlsx >=4.0.17' + - 'r-plyr >=1.8.4' + - 'r-rcolorbrewer >=1.1-2' + - 'r-reshape2 >=1.4.1' + - 'r-scales >=0.4.0' + - 'r-seqinr >=3.3-3' + - 'r-stringdist >=0.9.4.1' + - 'r-stringr >=1.0.0' + - 'r-tinytex >=0.5' + - 'r-uniqtag >=1.0' + - 'r-xml >=3.98-1.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'An implementation of methods for designing, evaluating, and comparing primer sets for multiplex PCR. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected. A Shiny app providing a user interface for the functionalities of this package is provided by the ''openPrimeRui'' package.' + diff --git a/recipes/bioconductor-openprimerui/build.sh b/recipes/bioconductor-openprimerui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-openprimerui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-openprimerui/meta.yaml b/recipes/bioconductor-openprimerui/meta.yaml new file mode 100644 index 0000000000000..da3fd3492c617 --- /dev/null +++ b/recipes/bioconductor-openprimerui/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.1" %} +{% set name = "openPrimeRui" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c68b6e58d4425b89b2e45289a83878d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr (>= 1.13) +requirements: + host: + - 'bioconductor-openprimer >=1.4.0,<1.5.0' + - r-base + - 'r-dt >=0.2' + - 'r-rmarkdown >=1.0' + - 'r-shiny >=1.0.2' + - 'r-shinybs >=0.61' + - 'r-shinyjs >=0.9' + run: + - 'bioconductor-openprimer >=1.4.0,<1.5.0' + - r-base + - 'r-dt >=0.2' + - 'r-rmarkdown >=1.0' + - 'r-shiny >=1.0.2' + - 'r-shinybs >=0.61' + - 'r-shinyjs >=0.9' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A Shiny application providing methods for designing, evaluating, and comparing primer sets for multiplex polymerase chain reaction. Primers are designed by solving a set cover problem such that the number of covered template sequences is maximized with the smallest possible set of primers. To guarantee that high-quality primers are generated, only primers fulfilling constraints on their physicochemical properties are selected.' + diff --git a/recipes/bioconductor-operonhumanv3.db/meta.yaml b/recipes/bioconductor-operonhumanv3.db/meta.yaml new file mode 100644 index 0000000000000..a5f2f55a6b589 --- /dev/null +++ b/recipes/bioconductor-operonhumanv3.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "OperonHumanV3.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 648da5d4d63c6c8327f6035ee09f2b65 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Nelson Lab OperonHumanV3 Annotation Data (OperonHumanV3) assembled using data from public repositories' + diff --git a/recipes/bioconductor-operonhumanv3.db/post-link.sh b/recipes/bioconductor-operonhumanv3.db/post-link.sh new file mode 100644 index 0000000000000..d963aaf9105e7 --- /dev/null +++ b/recipes/bioconductor-operonhumanv3.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="OperonHumanV3.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/OperonHumanV3.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/OperonHumanV3.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-operonhumanv3.db/bioconductor-operonhumanv3.db_3.2.3_src_all.tar.gz" +) +MD5="648da5d4d63c6c8327f6035ee09f2b65" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-operonhumanv3.db/pre-unlink.sh b/recipes/bioconductor-operonhumanv3.db/pre-unlink.sh new file mode 100644 index 0000000000000..cdfbc3749f8bd --- /dev/null +++ b/recipes/bioconductor-operonhumanv3.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ OperonHumanV3.db diff --git a/recipes/bioconductor-opossom/build.sh b/recipes/bioconductor-opossom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-opossom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-opossom/meta.yaml b/recipes/bioconductor-opossom/meta.yaml new file mode 100644 index 0000000000000..b7c3e7d70e813 --- /dev/null +++ b/recipes/bioconductor-opossom/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "2.0.0" %} +{% set name = "oposSOM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b313fe4f7305c8e1c1bcc5738e6924ff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-ape + - r-base + - r-fastica + - r-fdrtool + - 'r-igraph >=1.0.0' + - r-pixmap + - r-rcpp + - r-rcppparallel + - r-scatterplot3d + - r-tsne + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-ape + - r-base + - r-fastica + - r-fdrtool + - 'r-igraph >=1.0.0' + - r-pixmap + - r-rcpp + - r-rcppparallel + - r-scatterplot3d + - r-tsne + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package translates microarray expression data into metadata of reduced dimension. It provides various sample-centered and group-centered visualizations, sample similarity analyses and functional enrichment analyses. The underlying SOM algorithm combines feature clustering, multidimensional scaling and dimension reduction, along with strong visualization capabilities. It enables extraction and description of functional expression modules inherent in the data.' + diff --git a/recipes/bioconductor-oppar/build.sh b/recipes/bioconductor-oppar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oppar/build.sh +++ b/recipes/bioconductor-oppar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oppar/meta.yaml b/recipes/bioconductor-oppar/meta.yaml index afbfbc8bd9b24..794ef8208da8e 100644 --- a/recipes/bioconductor-oppar/meta.yaml +++ b/recipes/bioconductor-oppar/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "oppar" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c88064bde4d6d43720023b0a69c91802fdf6b80adae10b65c6ae7f1fe170b7b0 + md5: 03de1726e43965f7622a81ccfc411f4d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown, limma, org.Hs.eg.db, GO.db, snow, parallel requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' - r-base build: - {{ compiler('c') }} @@ -34,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The R implementation of mCOPA package published by Wang et al. (2012). Oppar provides methods for Cancer Outlier profile Analysis. Although initially developed to detect outlier genes in cancer studies, methods presented in oppar can be used for outlier profile analysis in general. In addition, tools are provided for gene set enrichment and pathway analysis.' extra: identifiers: - biotools:oppar + parent_recipe: + name: bioconductor-oppar + path: recipes/bioconductor-oppar + version: 1.8.0 + diff --git a/recipes/bioconductor-opweight/build.sh b/recipes/bioconductor-opweight/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-opweight/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-opweight/meta.yaml b/recipes/bioconductor-opweight/meta.yaml new file mode 100644 index 0000000000000..fa193e899620e --- /dev/null +++ b/recipes/bioconductor-opweight/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.4.0" %} +{% set name = "OPWeight" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 78f54491a8bf7d38ccf65e1241f2100e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: airway, BiocStyle, cowplot, DESeq2, devtools, ggplot2, gridExtra, knitr, Matrix, rmarkdown, scales, testthat +requirements: + host: + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - r-mass + - r-tibble + run: + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - r-base + - r-mass + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package perform weighted-pvalue based multiple hypothesis test and provides corresponding information such as ranking probability, weight, significant tests, etc . To conduct this testing procedure, the testing method apply a probabilistic relationship between the test rank and the corresponding test effect size.' + diff --git a/recipes/bioconductor-orderedlist/build.sh b/recipes/bioconductor-orderedlist/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-orderedlist/build.sh +++ b/recipes/bioconductor-orderedlist/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-orderedlist/meta.yaml b/recipes/bioconductor-orderedlist/meta.yaml index 8dadd5feb335b..f7b2091f55d7d 100644 --- a/recipes/bioconductor-orderedlist/meta.yaml +++ b/recipes/bioconductor-orderedlist/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "OrderedList" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 267ddf93548d5aa25f7b639e5787ceb9c02fbdf534156a0abc9be0cb5fa7c3f5 + md5: 6bd1c5786a4c4d6aec16c91f6c481984 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-twilight >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-twilight >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-twilight >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-twilight >=1.58.0,<1.59.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Detection of similarities between ordered lists of genes. Thereby, either simple lists can be compared or gene expression data can be used to deduce the lists. Significance of similarities is evaluated by shuffling lists or by resampling in microarray data, respectively.' extra: identifiers: - biotools:orderedlist - doi:10.1093/bioinformatics/btl385 + parent_recipe: + name: bioconductor-orderedlist + path: recipes/bioconductor-orderedlist + version: 1.52.0 + diff --git a/recipes/bioconductor-orfik/build.sh b/recipes/bioconductor-orfik/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-orfik/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-orfik/meta.yaml b/recipes/bioconductor-orfik/meta.yaml new file mode 100644 index 0000000000000..36fbc32d5db5f --- /dev/null +++ b/recipes/bioconductor-orfik/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "1.2.0" %} +{% set name = "ORFik" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9892e6673964b186680c6a39e5f97873 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, rmarkdown, knitr, BiocStyle, BSgenome, BSgenome.Hsapiens.UCSC.hg19, ggplot2 (>= 2.2.1) +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-data.table >=1.10.4-3' + - 'r-rcpp >=0.12.16' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-data.table >=1.10.4-3' + - 'r-rcpp >=0.12.16' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Tools for manipulation of RiboSeq, RNASeq and CageSeq data. ORFik is extremely fast through use of C, data.table and GenomicRanges. Package allows to reassign starts of the transcripts with the use of CageSeq data, automatic shifting of RiboSeq reads, finding of Open Reading Frames for the whole genomes and many more.' + diff --git a/recipes/bioconductor-org.ag.eg.db/meta.yaml b/recipes/bioconductor-org.ag.eg.db/meta.yaml new file mode 100644 index 0000000000000..033c23d3766bf --- /dev/null +++ b/recipes/bioconductor-org.ag.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.Ag.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 29ff8024311fc6e9dab0ac508aa25093 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Anopheles, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.ag.eg.db/post-link.sh b/recipes/bioconductor-org.ag.eg.db/post-link.sh new file mode 100644 index 0000000000000..f6e3ba8c3343b --- /dev/null +++ b/recipes/bioconductor-org.ag.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Ag.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ag.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ag.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ag.eg.db/bioconductor-org.ag.eg.db_3.7.0_src_all.tar.gz" +) +MD5="29ff8024311fc6e9dab0ac508aa25093" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.ag.eg.db/pre-unlink.sh b/recipes/bioconductor-org.ag.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..1e9e5ad72f0d9 --- /dev/null +++ b/recipes/bioconductor-org.ag.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Ag.eg.db diff --git a/recipes/bioconductor-org.at.tair.db/meta.yaml b/recipes/bioconductor-org.at.tair.db/meta.yaml new file mode 100644 index 0000000000000..e6e52a348ceea --- /dev/null +++ b/recipes/bioconductor-org.at.tair.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.At.tair.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 31ee4b1608601ad431d3baf1693c485d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Arabidopsis, primarily based on mapping using TAIR identifiers.' + diff --git a/recipes/bioconductor-org.at.tair.db/post-link.sh b/recipes/bioconductor-org.at.tair.db/post-link.sh new file mode 100644 index 0000000000000..091e1c6486ff5 --- /dev/null +++ b/recipes/bioconductor-org.at.tair.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.At.tair.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.At.tair.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.At.tair.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.at.tair.db/bioconductor-org.at.tair.db_3.7.0_src_all.tar.gz" +) +MD5="31ee4b1608601ad431d3baf1693c485d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.at.tair.db/pre-unlink.sh b/recipes/bioconductor-org.at.tair.db/pre-unlink.sh new file mode 100644 index 0000000000000..09bcd8e0a434e --- /dev/null +++ b/recipes/bioconductor-org.at.tair.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.At.tair.db diff --git a/recipes/bioconductor-org.bt.eg.db/meta.yaml b/recipes/bioconductor-org.bt.eg.db/meta.yaml index e537cb4fed12e..d33d0c131cca5 100644 --- a/recipes/bioconductor-org.bt.eg.db/meta.yaml +++ b/recipes/bioconductor-org.bt.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Bt.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 246a3b073ea158b65924959efda8ee93dc46d37f7c67ef12ebcaaec283763dd2 + md5: 04acb6baf4ea87f5643604afc38994d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Bovine, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.bt.eg.db + path: recipes/bioconductor-org.bt.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.bt.eg.db/post-link.sh b/recipes/bioconductor-org.bt.eg.db/post-link.sh index 5c14f8bad2fe7..3fac1bcd5b882 100644 --- a/recipes/bioconductor-org.bt.eg.db/post-link.sh +++ b/recipes/bioconductor-org.bt.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Bt.eg.db_3.6.0.tar.gz" +FN="org.Bt.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Bt.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Bt.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Bt.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.bt.eg.db/bioconductor-org.bt.eg.db_3.7.0_src_all.tar.gz" ) -MD5="1d8a03220647ee7256efa1008ea0a5af" +MD5="04acb6baf4ea87f5643604afc38994d9" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.ce.eg.db/meta.yaml b/recipes/bioconductor-org.ce.eg.db/meta.yaml index d232d799961d6..91a2b14fdda4a 100644 --- a/recipes/bioconductor-org.ce.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ce.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Ce.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2f51c3d9f4bbea08ce6bda32dc2facfc947683358e2df24339992e945bd754b + md5: fd97efab38b5106699a913440f5ebd10 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Worm, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.ce.eg.db + path: recipes/bioconductor-org.ce.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.ce.eg.db/post-link.sh b/recipes/bioconductor-org.ce.eg.db/post-link.sh index 6c428a911297b..b249790a061ce 100644 --- a/recipes/bioconductor-org.ce.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ce.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ce.eg.db_3.6.0.tar.gz" +FN="org.Ce.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Ce.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ce.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ce.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ce.eg.db/bioconductor-org.ce.eg.db_3.7.0_src_all.tar.gz" ) -MD5="0e9ad2243b191e62f1c3979313aa71f5" +MD5="fd97efab38b5106699a913440f5ebd10" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.cf.eg.db/meta.yaml b/recipes/bioconductor-org.cf.eg.db/meta.yaml index 555741a7c663a..7e47623969f87 100644 --- a/recipes/bioconductor-org.cf.eg.db/meta.yaml +++ b/recipes/bioconductor-org.cf.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Cf.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a3dc6907618777570e16974ca3c2a3ed5be32a1eb4bb9f03384545414988fcf7 + md5: 7be91e9255dc1db7ab8231040c1bf973 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Canine, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.cf.eg.db + path: recipes/bioconductor-org.cf.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.cf.eg.db/post-link.sh b/recipes/bioconductor-org.cf.eg.db/post-link.sh index b7b665d0903f4..df80df8384913 100644 --- a/recipes/bioconductor-org.cf.eg.db/post-link.sh +++ b/recipes/bioconductor-org.cf.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Cf.eg.db_3.6.0.tar.gz" +FN="org.Cf.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Cf.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Cf.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Cf.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.cf.eg.db/bioconductor-org.cf.eg.db_3.7.0_src_all.tar.gz" ) -MD5="7cc3516927a6458cbfb8b9e7176823ea" +MD5="7be91e9255dc1db7ab8231040c1bf973" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.dm.eg.db/meta.yaml b/recipes/bioconductor-org.dm.eg.db/meta.yaml index 3a1fe2a664a7a..7233bef36acda 100644 --- a/recipes/bioconductor-org.dm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dm.eg.db/meta.yaml @@ -1,6 +1,6 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Dm.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' @@ -10,26 +10,32 @@ source: - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fd83e931a4921b5171b9ad4445eac1c3c8166eaa63dd0c16ed8185751ce2927e + md5: 8b1f0d67805df142418829c440796566 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Fly, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.dm.eg.db + path: recipes/bioconductor-org.dm.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.dm.eg.db/post-link.sh b/recipes/bioconductor-org.dm.eg.db/post-link.sh index c8aee75217a76..f8344fd154fff 100644 --- a/recipes/bioconductor-org.dm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dm.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Dm.eg.db_3.6.0.tar.gz" +FN="org.Dm.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Dm.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Dm.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dm.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dm.eg.db/bioconductor-org.dm.eg.db_3.7.0_src_all.tar.gz" ) -MD5="a7cada385422fb2098293db5756cb7d4" +MD5="8b1f0d67805df142418829c440796566" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.dr.eg.db/meta.yaml b/recipes/bioconductor-org.dr.eg.db/meta.yaml index e61b8b071eaf5..af9f51f4873c2 100644 --- a/recipes/bioconductor-org.dr.eg.db/meta.yaml +++ b/recipes/bioconductor-org.dr.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Dr.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8e3a7e70140bf960125a1578b42596af2c1fad7096d6ab0295f4d8de5fff4142 + md5: 0e0c2337494c3175f0bb09341e45a2a0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Zebrafish, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.dr.eg.db + path: recipes/bioconductor-org.dr.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.dr.eg.db/post-link.sh b/recipes/bioconductor-org.dr.eg.db/post-link.sh index 49fb4f1e681f1..a989b171d9e05 100644 --- a/recipes/bioconductor-org.dr.eg.db/post-link.sh +++ b/recipes/bioconductor-org.dr.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Dr.eg.db_3.6.0.tar.gz" +FN="org.Dr.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Dr.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Dr.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Dr.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.dr.eg.db/bioconductor-org.dr.eg.db_3.7.0_src_all.tar.gz" ) -MD5="c4b2a8e03bec92727ac090bf8e7400cf" +MD5="0e0c2337494c3175f0bb09341e45a2a0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.eck12.eg.db/meta.yaml b/recipes/bioconductor-org.eck12.eg.db/meta.yaml new file mode 100644 index 0000000000000..f9663ba1d723c --- /dev/null +++ b/recipes/bioconductor-org.eck12.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.EcK12.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ed681d12efeabaa6104895ddf8697b65 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for E coli strain K12, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.eck12.eg.db/post-link.sh b/recipes/bioconductor-org.eck12.eg.db/post-link.sh new file mode 100644 index 0000000000000..40c7e8393f758 --- /dev/null +++ b/recipes/bioconductor-org.eck12.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.EcK12.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.EcK12.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.EcK12.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.eck12.eg.db/bioconductor-org.eck12.eg.db_3.7.0_src_all.tar.gz" +) +MD5="ed681d12efeabaa6104895ddf8697b65" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.eck12.eg.db/pre-unlink.sh b/recipes/bioconductor-org.eck12.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..84cc43c463161 --- /dev/null +++ b/recipes/bioconductor-org.eck12.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.EcK12.eg.db diff --git a/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml new file mode 100644 index 0000000000000..99530d9970532 --- /dev/null +++ b/recipes/bioconductor-org.ecsakai.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.EcSakai.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c03bf25879cee8d40a3362d8bb4a7ced +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for E coli strain Sakai, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh new file mode 100644 index 0000000000000..20edb54a39dd9 --- /dev/null +++ b/recipes/bioconductor-org.ecsakai.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.EcSakai.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.EcSakai.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.EcSakai.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ecsakai.eg.db/bioconductor-org.ecsakai.eg.db_3.7.0_src_all.tar.gz" +) +MD5="c03bf25879cee8d40a3362d8bb4a7ced" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.ecsakai.eg.db/pre-unlink.sh b/recipes/bioconductor-org.ecsakai.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..cc357c090f1a4 --- /dev/null +++ b/recipes/bioconductor-org.ecsakai.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.EcSakai.eg.db diff --git a/recipes/bioconductor-org.gg.eg.db/meta.yaml b/recipes/bioconductor-org.gg.eg.db/meta.yaml index 1702d8cce1f9c..1b570aaf8a40c 100644 --- a/recipes/bioconductor-org.gg.eg.db/meta.yaml +++ b/recipes/bioconductor-org.gg.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Gg.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a6f0f0b30b09b035d8cb543dc1ccfcba0a6112056cad60219c2bf7852899a74a + md5: 341bd6dcd6fc11ca7519a06b478dc9c1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Chicken, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.gg.eg.db + path: recipes/bioconductor-org.gg.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.gg.eg.db/post-link.sh b/recipes/bioconductor-org.gg.eg.db/post-link.sh index f5a674b53ceb1..b82e464d0189e 100644 --- a/recipes/bioconductor-org.gg.eg.db/post-link.sh +++ b/recipes/bioconductor-org.gg.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Gg.eg.db_3.6.0.tar.gz" +FN="org.Gg.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Gg.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Gg.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Gg.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.gg.eg.db/bioconductor-org.gg.eg.db_3.7.0_src_all.tar.gz" ) -MD5="72d349d2b23ce102db13cd8266458994" +MD5="341bd6dcd6fc11ca7519a06b478dc9c1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.hs.eg.db/meta.yaml b/recipes/bioconductor-org.hs.eg.db/meta.yaml index 137b7d8ec8e5c..d5df7b38ac4d4 100644 --- a/recipes/bioconductor-org.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-org.hs.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Hs.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 27c838a6d343e9cb869d20dacf489fc0e3eac7a881a8bc2840a3a0ad10235b49 + md5: cfa2c28b70a64cbec969b42e993ff5de build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Human, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.hs.eg.db + path: recipes/bioconductor-org.hs.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.hs.eg.db/post-link.sh b/recipes/bioconductor-org.hs.eg.db/post-link.sh index ebc72584bd388..0c4e620d21279 100644 --- a/recipes/bioconductor-org.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-org.hs.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Hs.eg.db_3.6.0.tar.gz" +FN="org.Hs.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Hs.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Hs.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Hs.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.hs.eg.db/bioconductor-org.hs.eg.db_3.7.0_src_all.tar.gz" ) -MD5="3fa8de2859f317b59636f0e41b132e85" +MD5="cfa2c28b70a64cbec969b42e993ff5de" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.mm.eg.db/meta.yaml b/recipes/bioconductor-org.mm.eg.db/meta.yaml index 1a9571b92ad87..db9b73ca6c713 100644 --- a/recipes/bioconductor-org.mm.eg.db/meta.yaml +++ b/recipes/bioconductor-org.mm.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Mm.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f93956413ce7a76e24bb6b9243de357f49d6a03cfe6584a694451a8f4c84a450 + md5: fcb8cc04ab5918c38c91ab77aeab0ad8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Mouse, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.mm.eg.db + path: recipes/bioconductor-org.mm.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.mm.eg.db/post-link.sh b/recipes/bioconductor-org.mm.eg.db/post-link.sh index 39a487db71fa5..3328cfa1923c3 100644 --- a/recipes/bioconductor-org.mm.eg.db/post-link.sh +++ b/recipes/bioconductor-org.mm.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Mm.eg.db_3.6.0.tar.gz" +FN="org.Mm.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Mm.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mm.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Mm.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mm.eg.db/bioconductor-org.mm.eg.db_3.7.0_src_all.tar.gz" ) -MD5="1cb7de12010250de0b6fbbe799d653ea" +MD5="fcb8cc04ab5918c38c91ab77aeab0ad8" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.mmu.eg.db/meta.yaml b/recipes/bioconductor-org.mmu.eg.db/meta.yaml new file mode 100644 index 0000000000000..0f08b9b4548ff --- /dev/null +++ b/recipes/bioconductor-org.mmu.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.Mmu.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 02540628677b237dd3800faf6325aaf6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Rhesus, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.mmu.eg.db/post-link.sh b/recipes/bioconductor-org.mmu.eg.db/post-link.sh new file mode 100644 index 0000000000000..6bf545b5b5d9f --- /dev/null +++ b/recipes/bioconductor-org.mmu.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Mmu.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Mmu.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Mmu.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.mmu.eg.db/bioconductor-org.mmu.eg.db_3.7.0_src_all.tar.gz" +) +MD5="02540628677b237dd3800faf6325aaf6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.mmu.eg.db/pre-unlink.sh b/recipes/bioconductor-org.mmu.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..38c59afe4fed5 --- /dev/null +++ b/recipes/bioconductor-org.mmu.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Mmu.eg.db diff --git a/recipes/bioconductor-org.pf.plasmo.db/meta.yaml b/recipes/bioconductor-org.pf.plasmo.db/meta.yaml new file mode 100644 index 0000000000000..24b7af438375e --- /dev/null +++ b/recipes/bioconductor-org.pf.plasmo.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.Pf.plasmo.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ec01cc690e01acb3af144a44b5ee2f5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Malaria, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.pf.plasmo.db/post-link.sh b/recipes/bioconductor-org.pf.plasmo.db/post-link.sh new file mode 100644 index 0000000000000..b40d07d654d52 --- /dev/null +++ b/recipes/bioconductor-org.pf.plasmo.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Pf.plasmo.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Pf.plasmo.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Pf.plasmo.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.pf.plasmo.db/bioconductor-org.pf.plasmo.db_3.7.0_src_all.tar.gz" +) +MD5="ec01cc690e01acb3af144a44b5ee2f5b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.pf.plasmo.db/pre-unlink.sh b/recipes/bioconductor-org.pf.plasmo.db/pre-unlink.sh new file mode 100644 index 0000000000000..4b9e70acda086 --- /dev/null +++ b/recipes/bioconductor-org.pf.plasmo.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Pf.plasmo.db diff --git a/recipes/bioconductor-org.pt.eg.db/meta.yaml b/recipes/bioconductor-org.pt.eg.db/meta.yaml new file mode 100644 index 0000000000000..fc7c4ab993330 --- /dev/null +++ b/recipes/bioconductor-org.pt.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.Pt.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 302ef39a2501087cc252a0b3afb48135 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Chimp, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.pt.eg.db/post-link.sh b/recipes/bioconductor-org.pt.eg.db/post-link.sh new file mode 100644 index 0000000000000..f4cc1a4255907 --- /dev/null +++ b/recipes/bioconductor-org.pt.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Pt.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Pt.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Pt.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.pt.eg.db/bioconductor-org.pt.eg.db_3.7.0_src_all.tar.gz" +) +MD5="302ef39a2501087cc252a0b3afb48135" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.pt.eg.db/pre-unlink.sh b/recipes/bioconductor-org.pt.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..30335e14f32c8 --- /dev/null +++ b/recipes/bioconductor-org.pt.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Pt.eg.db diff --git a/recipes/bioconductor-org.rn.eg.db/meta.yaml b/recipes/bioconductor-org.rn.eg.db/meta.yaml index 15ff0a33244c7..8aa185303a5aa 100644 --- a/recipes/bioconductor-org.rn.eg.db/meta.yaml +++ b/recipes/bioconductor-org.rn.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Rn.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0e0927f75b4005c782fa06c39c09a52730ab87e3a6ab4f897b9a53f860e8586c + md5: 62ddd7b20549e4c3aa455377f0efa17a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.rn.eg.db + path: recipes/bioconductor-org.rn.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.rn.eg.db/post-link.sh b/recipes/bioconductor-org.rn.eg.db/post-link.sh index 62b0e6712ca4f..21e0d4bef49e9 100644 --- a/recipes/bioconductor-org.rn.eg.db/post-link.sh +++ b/recipes/bioconductor-org.rn.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Rn.eg.db_3.6.0.tar.gz" +FN="org.Rn.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Rn.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Rn.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Rn.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.rn.eg.db/bioconductor-org.rn.eg.db_3.7.0_src_all.tar.gz" ) -MD5="e6b4e03ec625bdfc7515ffacc4681659" +MD5="62ddd7b20549e4c3aa455377f0efa17a" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.sc.sgd.db/meta.yaml b/recipes/bioconductor-org.sc.sgd.db/meta.yaml index c114242d699ed..57db8617ab408 100644 --- a/recipes/bioconductor-org.sc.sgd.db/meta.yaml +++ b/recipes/bioconductor-org.sc.sgd.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Sc.sgd.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2e0efb7d0d273a79fb082fea8561c7651a7800dca340b4f66be2419d2bcf95e + md5: ab71de66c00d1abc7941768408eb8e80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Yeast, primarily based on mapping using ORF identifiers from SGD.' - +extra: + parent_recipe: + name: bioconductor-org.sc.sgd.db + path: recipes/bioconductor-org.sc.sgd.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.sc.sgd.db/post-link.sh b/recipes/bioconductor-org.sc.sgd.db/post-link.sh index 6c7bd2a3a6a48..abec8fb534d9e 100644 --- a/recipes/bioconductor-org.sc.sgd.db/post-link.sh +++ b/recipes/bioconductor-org.sc.sgd.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Sc.sgd.db_3.6.0.tar.gz" +FN="org.Sc.sgd.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Sc.sgd.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Sc.sgd.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Sc.sgd.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.sc.sgd.db/bioconductor-org.sc.sgd.db_3.7.0_src_all.tar.gz" ) -MD5="ba42c9278bf146817519a97723c018d6" +MD5="ab71de66c00d1abc7941768408eb8e80" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.ss.eg.db/meta.yaml b/recipes/bioconductor-org.ss.eg.db/meta.yaml index f0cda8db6e227..ad3a2bffec69d 100644 --- a/recipes/bioconductor-org.ss.eg.db/meta.yaml +++ b/recipes/bioconductor-org.ss.eg.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "org.Ss.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 32096d204442da58ecbc2ef3f758caef1b74364ed1302a1d7194bb8a7b6eb40a + md5: 9186f97704df0af8b485be518be405cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Genome wide annotation for Pig, primarily based on mapping using Entrez Gene identifiers.' - +extra: + parent_recipe: + name: bioconductor-org.ss.eg.db + path: recipes/bioconductor-org.ss.eg.db + version: 3.6.0 diff --git a/recipes/bioconductor-org.ss.eg.db/post-link.sh b/recipes/bioconductor-org.ss.eg.db/post-link.sh index ed0c4765083ba..6eb61c0dfab6b 100644 --- a/recipes/bioconductor-org.ss.eg.db/post-link.sh +++ b/recipes/bioconductor-org.ss.eg.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="org.Ss.eg.db_3.6.0.tar.gz" +FN="org.Ss.eg.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/org.Ss.eg.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Ss.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Ss.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.ss.eg.db/bioconductor-org.ss.eg.db_3.7.0_src_all.tar.gz" ) -MD5="77a060d5d281ec94dbcd2a7a623c3c24" +MD5="9186f97704df0af8b485be518be405cc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-org.xl.eg.db/meta.yaml b/recipes/bioconductor-org.xl.eg.db/meta.yaml new file mode 100644 index 0000000000000..dd0a1e04d6fbe --- /dev/null +++ b/recipes/bioconductor-org.xl.eg.db/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "3.7.0" %} +{% set name = "org.Xl.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2459dc4156660821213b1086bd9bcbcf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Genome wide annotation for Xenopus, primarily based on mapping using Entrez Gene identifiers.' + diff --git a/recipes/bioconductor-org.xl.eg.db/post-link.sh b/recipes/bioconductor-org.xl.eg.db/post-link.sh new file mode 100644 index 0000000000000..d74c6132abff7 --- /dev/null +++ b/recipes/bioconductor-org.xl.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="org.Xl.eg.db_3.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/org.Xl.eg.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/org.Xl.eg.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-org.xl.eg.db/bioconductor-org.xl.eg.db_3.7.0_src_all.tar.gz" +) +MD5="2459dc4156660821213b1086bd9bcbcf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-org.xl.eg.db/pre-unlink.sh b/recipes/bioconductor-org.xl.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..83de81639bbe3 --- /dev/null +++ b/recipes/bioconductor-org.xl.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ org.Xl.eg.db diff --git a/recipes/bioconductor-organism.dplyr/build.sh b/recipes/bioconductor-organism.dplyr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-organism.dplyr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-organism.dplyr/meta.yaml b/recipes/bioconductor-organism.dplyr/meta.yaml new file mode 100644 index 0000000000000..19b7f5b4f0987 --- /dev/null +++ b/recipes/bioconductor-organism.dplyr/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.10.0" %} +{% set name = "Organism.dplyr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2852cd417e6f66dea89e0c4dbb7cd9d4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Mm.eg.db, TxDb.Mmusculus.UCSC.mm10.ensGene, testthat, knitr, rmarkdown, BiocStyle, ggplot2 +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - r-dbplyr + - 'r-dplyr >=0.7.0' + - r-rsqlite + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - r-dbplyr + - 'r-dplyr >=0.7.0' + - r-rsqlite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides an alternative interface to Bioconductor ''annotation'' resources, in particular the gene identifier mapping functionality of the ''org'' packages (e.g., org.Hs.eg.db) and the genome coordinate functionality of the ''TxDb'' packages (e.g., TxDb.Hsapiens.UCSC.hg38.knownGene).' + diff --git a/recipes/bioconductor-organismdbi/build.sh b/recipes/bioconductor-organismdbi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-organismdbi/build.sh +++ b/recipes/bioconductor-organismdbi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-organismdbi/conda_build_config.yaml b/recipes/bioconductor-organismdbi/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-organismdbi/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-organismdbi/meta.yaml b/recipes/bioconductor-organismdbi/meta.yaml index 13b11f80a2efc..f1052ae9d7834 100644 --- a/recipes/bioconductor-organismdbi/meta.yaml +++ b/recipes/bioconductor-organismdbi/meta.yaml @@ -1,56 +1,63 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "OrganismDbi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b99d5edbdc7ee1b1ea2e0057e883c71742d34ae58709f8b2edec91548b46941 + md5: 5b61c03153b43c626fbdbbd1780e7652 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Homo.sapiens, Rattus.norvegicus, BSgenome.Hsapiens.UCSC.hg19, AnnotationHub, FDb.UCSC.tRNAs, rtracklayer, biomaRt, RUnit, RMariaDB requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-dbi run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base + - r-biocmanager - r-dbi test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package enables a simple unified interface to several annotation packages each of which has its own schema by taking advantage of the fact that each of these packages implements a select methods.' extra: identifiers: - biotools:organismdbi - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-organismdbi + path: recipes/bioconductor-organismdbi + version: 1.22.0 + diff --git a/recipes/bioconductor-osat/build.sh b/recipes/bioconductor-osat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-osat/build.sh +++ b/recipes/bioconductor-osat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-osat/meta.yaml b/recipes/bioconductor-osat/meta.yaml index 6f445e97cfcb2..a28d244e56eba 100644 --- a/recipes/bioconductor-osat/meta.yaml +++ b/recipes/bioconductor-osat/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "OSAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ea3bdf56713e324382d3890cac56be4c9a71c3098161e5ce235684b8af51b4c + md5: 25da0a3ebe891d2149a22612d0e2884e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: xtable, Biobase requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A sizable genomics study such as microarray often involves the use of multiple batches (groups) of experiment due to practical complication. To minimize batch effects, a careful experiment design should ensure the even distribution of biological groups and confounding factors across batches. OSAT (Optimal Sample Assignment Tool) is developed to facilitate the allocation of collected samples to different batches. With minimum steps, it produces setup that optimizes the even distribution of samples in groups of biological interest into different batches, reducing the confounding or correlation between batches and the biological variables of interest. It can also optimize the even distribution of confounding factors across batches. Our tool can handle challenging instances where incomplete and unbalanced sample collections are involved as well as ideal balanced RCBD. OSAT provides a number of predefined layout for some of the most commonly used genomics platform. Related paper can be find at http://www.biomedcentral.com/1471-2164/13/689 .' extra: identifiers: - biotools:osat - doi:10.1186/1471-2164-13-689 + parent_recipe: + name: bioconductor-osat + path: recipes/bioconductor-osat + version: 1.28.0 + diff --git a/recipes/bioconductor-oscope/build.sh b/recipes/bioconductor-oscope/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-oscope/build.sh +++ b/recipes/bioconductor-oscope/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-oscope/meta.yaml b/recipes/bioconductor-oscope/meta.yaml index 7f043cf795a74..4a509bccf9dd6 100644 --- a/recipes/bioconductor-oscope/meta.yaml +++ b/recipes/bioconductor-oscope/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Oscope" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e742d116992e508e20cc54bcb7214eaf8d913c7f50a60dc27ac8fd1f62236e78 + md5: 2f6cd292ac7ee57052f9e35cc0f9336c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-ebseq >=1.20.0,<1.22.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' - r-base - r-cluster - r-testthat run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-ebseq >=1.20.0,<1.22.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' - r-base - r-cluster - r-testthat @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Oscope is a statistical pipeline developed to identifying and recovering the base cycle profiles of oscillating genes in an unsynchronized single cell RNA-seq experiment. The Oscope pipeline includes three modules: a sine model module to search for candidate oscillator pairs; a K-medoids clustering module to cluster candidate oscillators into groups; and an extended nearest insertion module to recover the base cycle order for each oscillator group.' extra: identifiers: - biotools:oscope - doi:10.1038/nmeth.3549 + parent_recipe: + name: bioconductor-oscope + path: recipes/bioconductor-oscope + version: 1.10.0 + diff --git a/recipes/bioconductor-otubase/build.sh b/recipes/bioconductor-otubase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-otubase/build.sh +++ b/recipes/bioconductor-otubase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-otubase/meta.yaml b/recipes/bioconductor-otubase/meta.yaml index f82c3cdd6d394..9105d2a7b4e1a 100644 --- a/recipes/bioconductor-otubase/meta.yaml +++ b/recipes/bioconductor-otubase/meta.yaml @@ -1,46 +1,52 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "OTUbase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bc52aa0248f25745a4c04ff5f2fee01e838f196b1c4ff2c8c567fd94a559c024 + md5: 1d7602393bcbe0d127f647249cf9a0e9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-vegan run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base - r-vegan test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides a platform for Operational Taxonomic Unit based analysis' extra: identifiers: - biotools:otubase - doi:10.1093/bioinformatics/btr196 + parent_recipe: + name: bioconductor-otubase + path: recipes/bioconductor-otubase + version: 1.30.0 + diff --git a/recipes/bioconductor-outlierd/build.sh b/recipes/bioconductor-outlierd/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-outlierd/build.sh +++ b/recipes/bioconductor-outlierd/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-outlierd/meta.yaml b/recipes/bioconductor-outlierd/meta.yaml index d1aa4e8539c22..10d0eaa51dd41 100644 --- a/recipes/bioconductor-outlierd/meta.yaml +++ b/recipes/bioconductor-outlierd/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "OutlierD" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3246b79211deb22ff471af1959ddccb1f619e8680968d2ca52f28bab26dd8ccb + md5: faccbb13610392cf250252e1d03498f5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-quantreg run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-quantreg test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package detects outliers using quantile regression on the M-A scatterplots of high-throughput data.' extra: identifiers: - biotools:outlierd - doi:10.1093/bioinformatics/btn012 + parent_recipe: + name: bioconductor-outlierd + path: recipes/bioconductor-outlierd + version: 1.44.0 + diff --git a/recipes/bioconductor-outrider/build.sh b/recipes/bioconductor-outrider/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-outrider/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-outrider/meta.yaml b/recipes/bioconductor-outrider/meta.yaml new file mode 100644 index 0000000000000..6202c450c8b5a --- /dev/null +++ b/recipes/bioconductor-outrider/meta.yaml @@ -0,0 +1,84 @@ +{% set version = "1.0.0" %} +{% set name = "OUTRIDER" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 589f062de187f5b31a2ab045181d9f34 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, rmarkdown, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, RMySQL, AnnotationDbi, beeswarm, covr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bbmisc + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-matrixstats + - r-plotly + - r-plyr + - r-prroc + - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-reticulate + - r-scales + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bbmisc + - r-data.table + - r-ggplot2 + - r-ggpubr + - r-gplots + - r-matrixstats + - r-plotly + - r-plyr + - r-prroc + - r-rcolorbrewer + - r-rcpp + - r-rcpparmadillo + - r-reticulate + - r-scales + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Identification of aberrent gene expression in RNA-seq data. Read count expectations are modeled by an autoencoder to control for confounders in the data. Given these expectations, the RNA-seq read counts are assumed to follow a negative binomial distribution with a gene-specific dispersion. Outliers are then identified as read counts that significantly deviate from this distribution. Further OUTRIDER provides useful plotting function to analyze and visualize the results.' + diff --git a/recipes/bioconductor-paa/build.sh b/recipes/bioconductor-paa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-paa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-paa/meta.yaml b/recipes/bioconductor-paa/meta.yaml new file mode 100644 index 0000000000000..76b9a9ebf862b --- /dev/null +++ b/recipes/bioconductor-paa/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.16.0" %} +{% set name = "PAA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0452cfe09ff503b2cde95e81feafe9d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, RUnit, BiocGenerics, vsn +# SystemRequirements: C++ software package Random Jungle +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-e1071 + - r-gplots + - r-gtools + - r-mass + - r-mrmre + - r-randomforest + - 'r-rcpp >=0.11.6' + - r-rocr + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-e1071 + - r-gplots + - r-gtools + - r-mass + - r-mrmre + - r-randomforest + - 'r-rcpp >=0.11.6' + - r-rocr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'PAA imports single color (protein) microarray data that has been saved in gpr file format - esp. ProtoArray data. After preprocessing (background correction, batch filtering, normalization) univariate feature preselection is performed (e.g., using the "minimum M statistic" approach - hereinafter referred to as "mMs"). Subsequently, a multivariate feature selection is conducted to discover biomarker candidates. Therefore, either a frequency-based backwards elimination aproach or ensemble feature selection can be used. PAA provides a complete toolbox of analysis tools including several different plots for results examination and evaluation.' + diff --git a/recipes/bioconductor-padog/build.sh b/recipes/bioconductor-padog/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-padog/build.sh +++ b/recipes/bioconductor-padog/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-padog/meta.yaml b/recipes/bioconductor-padog/meta.yaml index a690844d7206d..3a4ad3a96350a 100644 --- a/recipes/bioconductor-padog/meta.yaml +++ b/recipes/bioconductor-padog/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "PADOG" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: abbd2c0350d9c80a35ee33c88296bc9cd1bc2a8f67301714cd88a6b91bb9560f + md5: 56431caee5cc198ddfdd7f93646d72d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: doParallel, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-keggdzpathwaysgeo >=1.18.0,<1.20.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dorng - r-foreach - r-gsa - r-nlme run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-hgu133a.db >=3.2.3,<3.4.0' - - 'bioconductor-hgu133plus2.db >=3.2.3,<3.4.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-keggdzpathwaysgeo >=1.18.0,<1.20.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hgu133plus2.db >=3.2.0,<3.3.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-keggdzpathwaysgeo >=1.20.0,<1.21.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-dorng - r-foreach @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements a general purpose gene set analysis method called PADOG that downplays the importance of genes that apear often accross the sets of genes to be analyzed. The package provides also a benchmark for gene set analysis methods in terms of sensitivity and ranking using 24 public datasets from KEGGdzPathwaysGEO package.' extra: identifiers: - biotools:padog - doi:10.1186/1471-2105-13-136 + parent_recipe: + name: bioconductor-padog + path: recipes/bioconductor-padog + version: 1.22.0 + diff --git a/recipes/bioconductor-paeg1acdf/meta.yaml b/recipes/bioconductor-paeg1acdf/meta.yaml new file mode 100644 index 0000000000000..b2db35e597fbb --- /dev/null +++ b/recipes/bioconductor-paeg1acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "paeg1acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 73af974112051db0f715518393e84726 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Pae_G1a.CDF file.' + diff --git a/recipes/bioconductor-paeg1acdf/post-link.sh b/recipes/bioconductor-paeg1acdf/post-link.sh new file mode 100644 index 0000000000000..72f469324e8d0 --- /dev/null +++ b/recipes/bioconductor-paeg1acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="paeg1acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/paeg1acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/paeg1acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-paeg1acdf/bioconductor-paeg1acdf_2.18.0_src_all.tar.gz" +) +MD5="73af974112051db0f715518393e84726" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-paeg1acdf/pre-unlink.sh b/recipes/bioconductor-paeg1acdf/pre-unlink.sh new file mode 100644 index 0000000000000..945ce6345755e --- /dev/null +++ b/recipes/bioconductor-paeg1acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ paeg1acdf diff --git a/recipes/bioconductor-paeg1aprobe/meta.yaml b/recipes/bioconductor-paeg1aprobe/meta.yaml new file mode 100644 index 0000000000000..46403568f91d7 --- /dev/null +++ b/recipes/bioconductor-paeg1aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "paeg1aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 493fa1fc7b92a78c8114b65038113c42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was P\_aeg1a\_probe\_tab.' + diff --git a/recipes/bioconductor-paeg1aprobe/post-link.sh b/recipes/bioconductor-paeg1aprobe/post-link.sh new file mode 100644 index 0000000000000..2a76e15fc73f1 --- /dev/null +++ b/recipes/bioconductor-paeg1aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="paeg1aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/paeg1aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/paeg1aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-paeg1aprobe/bioconductor-paeg1aprobe_2.18.0_src_all.tar.gz" +) +MD5="493fa1fc7b92a78c8114b65038113c42" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-paeg1aprobe/pre-unlink.sh b/recipes/bioconductor-paeg1aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..c224ea9cc150d --- /dev/null +++ b/recipes/bioconductor-paeg1aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ paeg1aprobe diff --git a/recipes/bioconductor-paircompviz/build.sh b/recipes/bioconductor-paircompviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-paircompviz/build.sh +++ b/recipes/bioconductor-paircompviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-paircompviz/meta.yaml b/recipes/bioconductor-paircompviz/meta.yaml index 21d8a5ba10bc0..ced485bde86cc 100644 --- a/recipes/bioconductor-paircompviz/meta.yaml +++ b/recipes/bioconductor-paircompviz/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "paircompviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d84090d6cb65229004d7ce5b23bdf13beefcde83f3079d7564cf0dae56426bce + md5: c2b68b9feed3ae0a7b15ad87e72465d6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: multcomp, reshape, rpart, plyr, xtable requirements: host: - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base run: - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3.0)' summary: 'This package provides visualization of the results from the multiple (i.e. pairwise) comparison tests such as pairwise.t.test, pairwise.prop.test or pairwise.wilcox.test. The groups being compared are visualized as nodes in Hasse diagram. Such approach enables very clear and vivid depiction of which group is significantly greater than which others, especially if comparing a large number of groups.' extra: identifiers: - biotools:paircompviz - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-paircompviz + path: recipes/bioconductor-paircompviz + version: 1.18.0 + diff --git a/recipes/bioconductor-pandar/build.sh b/recipes/bioconductor-pandar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pandar/build.sh +++ b/recipes/bioconductor-pandar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pandar/meta.yaml b/recipes/bioconductor-pandar/meta.yaml index cb6f68985d3d5..d785f58427337 100644 --- a/recipes/bioconductor-pandar/meta.yaml +++ b/recipes/bioconductor-pandar/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pandaR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5ddcf4916cedc12997fd0b6df5eafb377bbb972cb08829e47d30bee996e23022 + md5: adba12e16232b6d5443a2877e53ad90b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-ggplot2 - r-hexbin @@ -29,8 +31,8 @@ requirements: - r-reshape - r-runit run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-ggplot2 - r-hexbin @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Runs PANDA, an algorithm for discovering novel network structure by combining information from multiple complementary data sources.' extra: identifiers: - biotools:pandar + parent_recipe: + name: bioconductor-pandar + path: recipes/bioconductor-pandar + version: 1.12.0 + diff --git a/recipes/bioconductor-panelcn.mops/build.sh b/recipes/bioconductor-panelcn.mops/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-panelcn.mops/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-panelcn.mops/meta.yaml b/recipes/bioconductor-panelcn.mops/meta.yaml new file mode 100644 index 0000000000000..e5f3d92fe7703 --- /dev/null +++ b/recipes/bioconductor-panelcn.mops/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "panelcn.mops" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 974ec0d14c6d3a3d8bca8c3f5140e718 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-cn.mops >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-cn.mops >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 2.0)' + summary: 'CNV detection tool for targeted NGS panel data. Extension of the cn.mops package.' + diff --git a/recipes/bioconductor-panp/build.sh b/recipes/bioconductor-panp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-panp/build.sh +++ b/recipes/bioconductor-panp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-panp/conda_build_config.yaml b/recipes/bioconductor-panp/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-panp/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-panp/meta.yaml b/recipes/bioconductor-panp/meta.yaml index 8189868b695b6..d9905ecba3994 100644 --- a/recipes/bioconductor-panp/meta.yaml +++ b/recipes/bioconductor-panp/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "panp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1ec9fa839fa3f1141dbc9069c46f8da44e3e0c35601c8508e88c6a56e6cdada9 + md5: ce35790cd1d330942a3266e4c391d380 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: gcrma requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A function to make gene presence/absence calls based on distance from negative strand matching probesets (NSMP) which are derived from Affymetrix annotation. PANP is applied after gene expression values are created, and therefore can be used after any preprocessing method such as MAS5 or GCRMA, or PM-only methods like RMA. NSMP sets have been established for the HGU133A and HGU133-Plus-2.0 chipsets to date.' extra: identifiers: - biotools:panp - doi:10.1109/BIBE.2007.4375552 + parent_recipe: + name: bioconductor-panp + path: recipes/bioconductor-panp + version: 1.50.0 + diff --git a/recipes/bioconductor-panr/build.sh b/recipes/bioconductor-panr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-panr/build.sh +++ b/recipes/bioconductor-panr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-panr/meta.yaml b/recipes/bioconductor-panr/meta.yaml index fd645844c6417..4c7f1ab013b08 100644 --- a/recipes/bioconductor-panr/meta.yaml +++ b/recipes/bioconductor-panr/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "PANR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0ee265d6e8fbc3363898396db4bcd8282b56092754c094f0fb71a2af1be99fdd + md5: 46cc5853685709865fa2e0c72dab6f36 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: snow requirements: host: - - 'bioconductor-reder >=1.28.0,<1.30.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' - r-base - r-igraph - r-mass - r-pvclust run: - - 'bioconductor-reder >=1.28.0,<1.30.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' - r-base - r-igraph - r-mass @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides S4 classes and methods for inferring functional gene networks with edges encoding posterior beliefs of gene association types and nodes encoding perturbation effects.' extra: identifiers: - biotools:panr - doi:10.1371/journal.pcbi.1002566 + parent_recipe: + name: bioconductor-panr + path: recipes/bioconductor-panr + version: 1.26.0 + diff --git a/recipes/bioconductor-panther.db/meta.yaml b/recipes/bioconductor-panther.db/meta.yaml index 6680b7a40d557..74b2c273c15ce 100644 --- a/recipes/bioconductor-panther.db/meta.yaml +++ b/recipes/bioconductor-panther.db/meta.yaml @@ -1,28 +1,30 @@ {% set version = "1.0.4" %} {% set name = "PANTHER.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3e583f25e168a2896d20ced50761f80b11ae7c3a647e4dbb4a8bc1d9a35588ee + md5: bfd7362a4823bd3fda1bfab8e5b7908e build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit,knitr,BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-rsqlite - wget @@ -30,8 +32,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of annotation maps describing the entire Gene Ontology assembled using data from PANTHER.' - +extra: + parent_recipe: + name: bioconductor-panther.db + path: recipes/bioconductor-panther.db + version: 1.0.4 diff --git a/recipes/bioconductor-panther.db/post-link.sh b/recipes/bioconductor-panther.db/post-link.sh index c22f8ba242176..1d24ae9984ebe 100644 --- a/recipes/bioconductor-panther.db/post-link.sh +++ b/recipes/bioconductor-panther.db/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="PANTHER.db_1.0.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PANTHER.db_1.0.4.tar.gz" "https://bioarchive.galaxyproject.org/PANTHER.db_1.0.4.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-panther.db/bioconductor-panther.db_1.0.4_src_all.tar.gz" diff --git a/recipes/bioconductor-panvizgenerator/build.sh b/recipes/bioconductor-panvizgenerator/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-panvizgenerator/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-panvizgenerator/meta.yaml b/recipes/bioconductor-panvizgenerator/meta.yaml new file mode 100644 index 0000000000000..b4ad27990dbda --- /dev/null +++ b/recipes/bioconductor-panvizgenerator/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.10.0" %} +{% set name = "PanVizGenerator" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d4415d9cb3e2e6c4e46abfe7e5cf601e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, digest +requirements: + host: + - 'bioconductor-findmyfriends >=1.12.0,<1.13.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - r-base + - r-igraph + - r-jsonlite + - r-shiny + run: + - 'bioconductor-findmyfriends >=1.12.0,<1.13.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - r-base + - r-igraph + - r-jsonlite + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'PanViz is a JavaScript based visualisation tool for functionaly annotated pangenomes. PanVizGenerator is a companion for PanViz that facilitates the necessary data preprocessing step necessary to create a working PanViz visualization. The output is fully self-contained so the recipient of the visualization does not need R or PanVizGenerator installed.' + diff --git a/recipes/bioconductor-papi/build.sh b/recipes/bioconductor-papi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-papi/build.sh +++ b/recipes/bioconductor-papi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-papi/meta.yaml b/recipes/bioconductor-papi/meta.yaml index 45754f95e15b2..503c87dcede6c 100644 --- a/recipes/bioconductor-papi/meta.yaml +++ b/recipes/bioconductor-papi/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "PAPi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c36b1bd9006a2c3439e1cf1a5b6c63c68edcae50026b3867d1576f10ca5f16c + md5: 118ecbaf4baea52351cba63b518b9176 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' - r-base - r-svdialogs run: - - 'bioconductor-keggrest >=1.20.2,<1.22.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' - r-base - r-svdialogs test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL(>= 2)' summary: 'The Pathway Activity Profiling - PAPi - is an R package for predicting the activity of metabolic pathways based solely on a metabolomics data set containing a list of metabolites identified and their respective abundances in different biological samples. PAPi generates hypothesis that improves the final biological interpretation. See Aggio, R.B.M; Ruggiero, K. and Villas-Boas, S.G. (2010) - Pathway Activity Profiling (PAPi): from metabolite profile to metabolic pathway activity. Bioinformatics.' extra: identifiers: - biotools:papi - doi:10.1093/bioinformatics/btq567 + parent_recipe: + name: bioconductor-papi + path: recipes/bioconductor-papi + version: 1.20.0 + diff --git a/recipes/bioconductor-parathyroidse/meta.yaml b/recipes/bioconductor-parathyroidse/meta.yaml new file mode 100644 index 0000000000000..fe5fad1600ee2 --- /dev/null +++ b/recipes/bioconductor-parathyroidse/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.20.0" %} +{% set name = "parathyroidSE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3a64ecf796315fd4b7b86173612b586e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Rsamtools, GenomicAlignments, GEOquery, SRAdb, GenomicFeatures, BiocStyle +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package provides RangedSummarizedExperiment objects of read counts in genes and exonic parts for paired-end RNA-Seq data from experiments on primary cultures of parathyroid tumors. The data were presented in the article "Evidence of a Functional Estrogen Receptor in Parathyroid Adenomas" by Haglund F, Ma R, Huss M, Sulaiman L, Lu M, Nilsson IL, Hoog A, Juhlin CC, Hartman J, Larsson C, J Clin Endocrinol Metab. jc.2012-2484, Epub 2012 Sep 28, PMID: 23024189. The sequencing was performed on tumor cultures from 4 patients at 2 time points over 3 conditions (DPN, OHT and control). One control sample was omitted by the paper authors due to low quality. The package vignette describes the creation of the object from raw sequencing data provided by NCBI Gene Expression Omnibus under accession number GSE37211. The gene and exon features are the GRCh37 Ensembl annotations.' + diff --git a/recipes/bioconductor-parathyroidse/post-link.sh b/recipes/bioconductor-parathyroidse/post-link.sh new file mode 100644 index 0000000000000..d078938102406 --- /dev/null +++ b/recipes/bioconductor-parathyroidse/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="parathyroidSE_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/parathyroidSE_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/parathyroidSE_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-parathyroidse/bioconductor-parathyroidse_1.20.0_src_all.tar.gz" +) +MD5="3a64ecf796315fd4b7b86173612b586e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-parathyroidse/pre-unlink.sh b/recipes/bioconductor-parathyroidse/pre-unlink.sh new file mode 100644 index 0000000000000..25ae8cbfb7657 --- /dev/null +++ b/recipes/bioconductor-parathyroidse/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ parathyroidSE diff --git a/recipes/bioconductor-parglms/build.sh b/recipes/bioconductor-parglms/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-parglms/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-parglms/meta.yaml b/recipes/bioconductor-parglms/meta.yaml new file mode 100644 index 0000000000000..b03b6a19c9332 --- /dev/null +++ b/recipes/bioconductor-parglms/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.14.0" %} +{% set name = "parglms" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 61af77bc2927d500ecba6c0427cd8d68 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, sandwich, MASS, knitr +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-batchjobs + - r-doparallel + - r-foreach + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-batchjobs + - r-doparallel + - r-foreach +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'support for parallelized estimation of GLMs/GEEs, catering for dispersed data' + diff --git a/recipes/bioconductor-parody/build.sh b/recipes/bioconductor-parody/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-parody/build.sh +++ b/recipes/bioconductor-parody/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-parody/meta.yaml b/recipes/bioconductor-parody/meta.yaml index 3f7d3f107e6c1..b52f3a574c909 100644 --- a/recipes/bioconductor-parody/meta.yaml +++ b/recipes/bioconductor-parody/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "parody" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 998ee212bd2ac9fee1fe3f15937826020769afdcc6d6d1192ee92a3c7a86e5e3 + md5: 7fed47b92aa3019bc677948bcd13cde6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'routines for univariate and multivariate outlier detection with a focus on parametric methods, but support for some methods based on resistant statistics' extra: identifiers: - biotools:parody - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-parody + path: recipes/bioconductor-parody + version: 1.38.0 + diff --git a/recipes/bioconductor-partheenmetadata.db/meta.yaml b/recipes/bioconductor-partheenmetadata.db/meta.yaml new file mode 100644 index 0000000000000..3c056e53e1885 --- /dev/null +++ b/recipes/bioconductor-partheenmetadata.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "PartheenMetaData.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c9fd27e13a341b9aba9a235a67ce978 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'PartheenMetaData http://swegene.onk.lu.se Annotation Data (PartheenMetaData) assembled using data from public repositories' + diff --git a/recipes/bioconductor-partheenmetadata.db/post-link.sh b/recipes/bioconductor-partheenmetadata.db/post-link.sh new file mode 100644 index 0000000000000..ed961d9d8a46a --- /dev/null +++ b/recipes/bioconductor-partheenmetadata.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PartheenMetaData.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PartheenMetaData.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/PartheenMetaData.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-partheenmetadata.db/bioconductor-partheenmetadata.db_3.2.3_src_all.tar.gz" +) +MD5="1c9fd27e13a341b9aba9a235a67ce978" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-partheenmetadata.db/pre-unlink.sh b/recipes/bioconductor-partheenmetadata.db/pre-unlink.sh new file mode 100644 index 0000000000000..452b76b734d33 --- /dev/null +++ b/recipes/bioconductor-partheenmetadata.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PartheenMetaData.db diff --git a/recipes/bioconductor-pasilla/meta.yaml b/recipes/bioconductor-pasilla/meta.yaml new file mode 100644 index 0000000000000..8b3169ea7d131 --- /dev/null +++ b/recipes/bioconductor-pasilla/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "pasilla" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 88ad1534662b8442e6d7a61cd0bb40dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DEXSeq, rmarkdown, BiocStyle, knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package provides per-exon and per-gene read counts computed for selected genes from RNA-seq data that were presented in the article "Conservation of an RNA regulatory map between Drosophila and mammals" by Brooks AN, Yang L, Duff MO, Hansen KD, Park JW, Dudoit S, Brenner SE, Graveley BR, Genome Res. 2011 Feb;21(2):193-202, Epub 2010 Oct 4, PMID: 20921232. The experiment studied the effect of RNAi knockdown of Pasilla, the Drosophila melanogaster ortholog of mammalian NOVA1 and NOVA2, on the transcriptome. The package vignette describes how the data provided here were derived from the RNA-Seq read sequence data that are provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181.' + diff --git a/recipes/bioconductor-pasilla/post-link.sh b/recipes/bioconductor-pasilla/post-link.sh new file mode 100644 index 0000000000000..3206ebf59151a --- /dev/null +++ b/recipes/bioconductor-pasilla/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pasilla_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pasilla_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/pasilla_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasilla/bioconductor-pasilla_1.10.0_src_all.tar.gz" +) +MD5="88ad1534662b8442e6d7a61cd0bb40dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pasilla/pre-unlink.sh b/recipes/bioconductor-pasilla/pre-unlink.sh new file mode 100644 index 0000000000000..2a4e5c2e5e818 --- /dev/null +++ b/recipes/bioconductor-pasilla/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pasilla diff --git a/recipes/bioconductor-pasillabamsubset/meta.yaml b/recipes/bioconductor-pasillabamsubset/meta.yaml new file mode 100644 index 0000000000000..4ddce1c20e4c2 --- /dev/null +++ b/recipes/bioconductor-pasillabamsubset/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.20.0" %} +{% set name = "pasillaBamSubset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a418f3d054320e023b3c533c5df9a20a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pasilla +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Subset of BAM files untreated1.bam (single-end reads) and untreated3.bam (paired-end reads) from "Pasilla" experiment (Pasilla knock-down by Brooks et al., Genome Research 2011). See the vignette in the pasilla data package for how BAM files untreated1.bam and untreated3.bam were obtained from the RNA-Seq read sequence data that is provided by NCBI Gene Expression Omnibus under accession numbers GSM461176 to GSM461181. Also contains the DNA sequence for fly chromosome 4 to which the reads can be mapped.' + diff --git a/recipes/bioconductor-pasillabamsubset/post-link.sh b/recipes/bioconductor-pasillabamsubset/post-link.sh new file mode 100644 index 0000000000000..b42804ef48bd1 --- /dev/null +++ b/recipes/bioconductor-pasillabamsubset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pasillaBamSubset_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pasillaBamSubset_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pasillaBamSubset_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasillabamsubset/bioconductor-pasillabamsubset_0.20.0_src_all.tar.gz" +) +MD5="a418f3d054320e023b3c533c5df9a20a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pasillabamsubset/pre-unlink.sh b/recipes/bioconductor-pasillabamsubset/pre-unlink.sh new file mode 100644 index 0000000000000..5ae87736312e6 --- /dev/null +++ b/recipes/bioconductor-pasillabamsubset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pasillaBamSubset diff --git a/recipes/bioconductor-pasillatranscriptexpr/meta.yaml b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml new file mode 100644 index 0000000000000..1c11897d8650e --- /dev/null +++ b/recipes/bioconductor-pasillatranscriptexpr/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "PasillaTranscriptExpr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dd8a68bb858f26a8a675895b7aaf4467 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rtracklayer, BiocStyle, knitr, testthat +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Provides kallisto workflow and transcript expression of RNA-Seq data from Brooks et al.' + diff --git a/recipes/bioconductor-pasillatranscriptexpr/post-link.sh b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh new file mode 100644 index 0000000000000..9a0d50eee8401 --- /dev/null +++ b/recipes/bioconductor-pasillatranscriptexpr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PasillaTranscriptExpr_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PasillaTranscriptExpr_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/PasillaTranscriptExpr_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pasillatranscriptexpr/bioconductor-pasillatranscriptexpr_1.10.0_src_all.tar.gz" +) +MD5="dd8a68bb858f26a8a675895b7aaf4467" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pasillatranscriptexpr/pre-unlink.sh b/recipes/bioconductor-pasillatranscriptexpr/pre-unlink.sh new file mode 100644 index 0000000000000..a7b82e9e95479 --- /dev/null +++ b/recipes/bioconductor-pasillatranscriptexpr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PasillaTranscriptExpr diff --git a/recipes/bioconductor-path2ppi/build.sh b/recipes/bioconductor-path2ppi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-path2ppi/build.sh +++ b/recipes/bioconductor-path2ppi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-path2ppi/meta.yaml b/recipes/bioconductor-path2ppi/meta.yaml index 52926bf486b91..1d985f164aede 100644 --- a/recipes/bioconductor-path2ppi/meta.yaml +++ b/recipes/bioconductor-path2ppi/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Path2PPI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f73f951b581849f76a43a98da5a6fe474533e17a630e78621e0e7f936e0970ba + md5: fa0f1aa93584b7a1d724309e6f8b60c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, RUnit, BiocGenerics, BiocStyle requirements: host: - r-base @@ -27,9 +29,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Package to predict protein-protein interaction (PPI) networks in target organisms for which only a view information about PPIs is available. Path2PPI predicts PPI networks based on sets of proteins which can belong to a certain pathway from well-established model organisms. It helps to combine and transfer information of a certain pathway or biological process from several reference organisms to one target organism. Path2PPI only depends on the sequence similarity of the involved proteins.' extra: identifiers: - biotools:path2ppi + parent_recipe: + name: bioconductor-path2ppi + path: recipes/bioconductor-path2ppi + version: 1.10.0 + diff --git a/recipes/bioconductor-pathifier/build.sh b/recipes/bioconductor-pathifier/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathifier/build.sh +++ b/recipes/bioconductor-pathifier/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathifier/meta.yaml b/recipes/bioconductor-pathifier/meta.yaml index 095790291d319..aaa2feac6aa10 100644 --- a/recipes/bioconductor-pathifier/meta.yaml +++ b/recipes/bioconductor-pathifier/meta.yaml @@ -1,21 +1,22 @@ {% set version = "1.20.0" %} {% set name = "pathifier" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 279b782138587b372ed3a7c6d9a2194202f1e1f652d8e4523e3b415541239742 + md5: a3c03fc2a9686179902658a4e3d02946 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-1.0 summary: 'Pathifier is an algorithm that infers pathway deregulation scores for each tumor sample on the basis of expression data. This score is determined, in a context-specific manner, for every particular dataset and type of cancer that is being investigated. The algorithm transforms gene-level information into pathway-level information, generating a compact and biologically relevant representation of each sample.' extra: identifiers: - biotools:pathifier - doi:10.1073/pnas.1219651110 + parent_recipe: + name: bioconductor-pathifier + path: recipes/bioconductor-pathifier + version: 1.20.0 + diff --git a/recipes/bioconductor-pathnet/build.sh b/recipes/bioconductor-pathnet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathnet/build.sh +++ b/recipes/bioconductor-pathnet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathnet/meta.yaml b/recipes/bioconductor-pathnet/meta.yaml index e56237366a638..b4bd6fff988be 100644 --- a/recipes/bioconductor-pathnet/meta.yaml +++ b/recipes/bioconductor-pathnet/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "PathNet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8a3ab66135f274c44fc6415f51f48140b376bcde385faa498712e051a5676e70 + md5: b7ba6c5f1e0cec5a3b1d5c820345b02a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: PathNetData, RUnit, BiocGenerics requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'PathNet uses topological information present in pathways and differential expression levels of genes (obtained from microarray experiment) to identify pathways that are 1) significantly enriched and 2) associated with each other in the context of differential expression. The algorithm is described in: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J. Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' extra: identifiers: - biotools:pathnet + parent_recipe: + name: bioconductor-pathnet + path: recipes/bioconductor-pathnet + version: 1.20.0 + diff --git a/recipes/bioconductor-pathnetdata/meta.yaml b/recipes/bioconductor-pathnetdata/meta.yaml new file mode 100644 index 0000000000000..5d48436e4f880 --- /dev/null +++ b/recipes/bioconductor-pathnetdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "PathNetData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: baad9f77b8914d21f84963e3b19f67ed +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This package contains the data employed in the vignette of the PathNet package. These data belong to the following publication: PathNet: A tool for pathway analysis using topological information. Dutta B, Wallqvist A, and Reifman J., Source Code for Biology and Medicine 2012 Sep 24;7(1):10.' + diff --git a/recipes/bioconductor-pathnetdata/post-link.sh b/recipes/bioconductor-pathnetdata/post-link.sh new file mode 100644 index 0000000000000..49f82e32a03a6 --- /dev/null +++ b/recipes/bioconductor-pathnetdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PathNetData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PathNetData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/PathNetData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pathnetdata/bioconductor-pathnetdata_1.18.0_src_all.tar.gz" +) +MD5="baad9f77b8914d21f84963e3b19f67ed" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pathnetdata/pre-unlink.sh b/recipes/bioconductor-pathnetdata/pre-unlink.sh new file mode 100644 index 0000000000000..6559a40a168f5 --- /dev/null +++ b/recipes/bioconductor-pathnetdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PathNetData diff --git a/recipes/bioconductor-pathostat/build.sh b/recipes/bioconductor-pathostat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathostat/build.sh +++ b/recipes/bioconductor-pathostat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathostat/meta.yaml b/recipes/bioconductor-pathostat/meta.yaml index a45e4314e362d..6210339c749e9 100644 --- a/recipes/bioconductor-pathostat/meta.yaml +++ b/recipes/bioconductor-pathostat/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.4" %} {% set name = "PathoStat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2a097c072861423bcf6e498d6a10a2c847ace11a464f45ecbc702de9352410d3 + md5: 385833d81ba649fab612821f5f0fad55 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: rmarkdown, testthat requirements: host: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-ape - r-base - r-corpcor @@ -49,12 +51,12 @@ requirements: - r-webshot - r-xml run: - - 'bioconductor-biocstyle >=2.8.2,<2.10.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-ape - r-base - r-corpcor @@ -83,10 +85,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The purpose of this package is to perform Statistical Microbiome Analysis on metagenomics results from sequencing data samples. In particular, it supports analyses on the PathoScope generated report files. PathoStat provides various functionalities including Relative Abundance charts, Diversity estimates and plots, tests of Differential Abundance, Time Series visualization, and Core OTU analysis.' extra: identifiers: - biotools:pathostat - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pathostat + path: recipes/bioconductor-pathostat + version: 1.6.1 + diff --git a/recipes/bioconductor-pathprint/build.sh b/recipes/bioconductor-pathprint/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathprint/build.sh +++ b/recipes/bioconductor-pathprint/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathprint/meta.yaml b/recipes/bioconductor-pathprint/meta.yaml index ef2af2e84229d..f7b0a8544209c 100644 --- a/recipes/bioconductor-pathprint/meta.yaml +++ b/recipes/bioconductor-pathprint/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.4" %} +{% set version = "1.12.0" %} {% set name = "pathprint" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 911d04eafc4c71721fa1a65d7c74389d05a2e54710902004e7c6caa05ab113e8 + md5: 4fa4f3fecafee2af2d62766f6affa9fa build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, GEOquery, pathprintGEOData, SummarizedExperiment requirements: host: - r-base @@ -25,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Algorithms to convert a gene expression array provided as an expression table or a GEO reference to a ''pathway fingerprint'', a vector of discrete ternary scores representing high (1), low(-1) or insignificant (0) expression in a suite of pathways.' - +extra: + parent_recipe: + name: bioconductor-pathprint + path: recipes/bioconductor-pathprint + version: 1.10.4 diff --git a/recipes/bioconductor-pathprintgeodata/meta.yaml b/recipes/bioconductor-pathprintgeodata/meta.yaml new file mode 100644 index 0000000000000..8bb2c5a056a94 --- /dev/null +++ b/recipes/bioconductor-pathprintgeodata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "pathprintGEOData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ad2f10bec6bb16df90e3e9ad1e193563 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pathprint, SummarizedExperiment +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Pathway Fingerprint vectors that have been pre-calculated for ~390,000 publicly available arrays from the GEO corpus, spanning 6 species and 31 platforms. All data are accompanied by their associated metadata.' + diff --git a/recipes/bioconductor-pathprintgeodata/post-link.sh b/recipes/bioconductor-pathprintgeodata/post-link.sh new file mode 100644 index 0000000000000..582c94b134d86 --- /dev/null +++ b/recipes/bioconductor-pathprintgeodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pathprintGEOData_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pathprintGEOData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pathprintGEOData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pathprintgeodata/bioconductor-pathprintgeodata_1.12.0_src_all.tar.gz" +) +MD5="ad2f10bec6bb16df90e3e9ad1e193563" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pathprintgeodata/pre-unlink.sh b/recipes/bioconductor-pathprintgeodata/pre-unlink.sh new file mode 100644 index 0000000000000..e3bc803e809e7 --- /dev/null +++ b/recipes/bioconductor-pathprintgeodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pathprintGEOData diff --git a/recipes/bioconductor-pathrender/build.sh b/recipes/bioconductor-pathrender/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathrender/build.sh +++ b/recipes/bioconductor-pathrender/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathrender/meta.yaml b/recipes/bioconductor-pathrender/meta.yaml index 8c4c270af1968..3dc5825cf9802 100644 --- a/recipes/bioconductor-pathrender/meta.yaml +++ b/recipes/bioconductor-pathrender/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "pathRender" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 329a09681d89938ae629526b3e80766af254482844a0e9e1d92d6144199607ee + md5: 91a194d410a75cfcd81136ccce3496e7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-cmap >=1.15.1,<1.17.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-cmap >=1.15.0,<1.16.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-rcolorbrewer run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-cmap >=1.15.1,<1.17.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-cmap >=1.15.0,<1.16.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-rcolorbrewer test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'build graphs from pathway databases, render them by Rgraphviz.' extra: identifiers: - biotools:pathrender - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pathrender + path: recipes/bioconductor-pathrender + version: 1.48.0 + diff --git a/recipes/bioconductor-pathvar/build.sh b/recipes/bioconductor-pathvar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathvar/build.sh +++ b/recipes/bioconductor-pathvar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathvar/meta.yaml b/recipes/bioconductor-pathvar/meta.yaml index 2082e9ddc4886..46d799cca0508 100644 --- a/recipes/bioconductor-pathvar/meta.yaml +++ b/recipes/bioconductor-pathvar/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "pathVar" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4eb965ee2da7dfd2407bf8dccfbee333c970c44d46ebf2020f522b9b75bd8f19 + md5: 6a0e4fc15f3b005a5d188b3242149420 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package contains the functions to find the pathways that have significantly different variability than a reference gene set. It also finds the categories from this pathway that are significant where each category is a cluster of genes. The genes are separated into clusters by their level of variability.' extra: identifiers: - biotools:pathvar - doi:10.7717/peerj.3334 + parent_recipe: + name: bioconductor-pathvar + path: recipes/bioconductor-pathvar + version: 1.10.0 + diff --git a/recipes/bioconductor-pathview/build.sh b/recipes/bioconductor-pathview/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pathview/build.sh +++ b/recipes/bioconductor-pathview/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathview/meta.yaml b/recipes/bioconductor-pathview/meta.yaml index 109c89458ca90..d46b16e2dee60 100644 --- a/recipes/bioconductor-pathview/meta.yaml +++ b/recipes/bioconductor-pathview/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pathview" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5381d31827aac6b05bf084c06350fc2ecf29bb280243347f800498d891a56bf4 + md5: e11c9047d1053c360d828e5312684f39 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: gage, org.Mm.eg.db, RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-png - r-xml run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-png - r-xml @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3.0)' summary: 'Pathview is a tool set for pathway based data integration and visualization. It maps and renders a wide variety of biological data on relevant pathway graphs. All users need is to supply their data and specify the target pathway. Pathview automatically downloads the pathway graph data, parses the data file, maps user data to the pathway, and render pathway graph with the mapped data. In addition, Pathview also seamlessly integrates with pathway and gene set (enrichment) analysis tools for large-scale and fully automated analysis.' extra: identifiers: - biotools:pathview + parent_recipe: + name: bioconductor-pathview + path: recipes/bioconductor-pathview + version: 1.20.0 + diff --git a/recipes/bioconductor-pathwaysplice/build.sh b/recipes/bioconductor-pathwaysplice/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pathwaysplice/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pathwaysplice/meta.yaml b/recipes/bioconductor-pathwaysplice/meta.yaml new file mode 100644 index 0000000000000..b53be9e5274f6 --- /dev/null +++ b/recipes/bioconductor-pathwaysplice/meta.yaml @@ -0,0 +1,93 @@ +{% set version = "1.6.0" %} +{% set name = "PathwaySplice" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5f7e8982f76c5513f7194ed91beef545 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-junctionseq >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biasedurn + - r-dplyr + - r-gdata + - r-gplots + - r-gridextra + - r-htmlwidgets + - r-igraph + - r-mgcv + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-tibble + - r-venndiagram + - r-webshot + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichmentbrowser >=2.12.0,<2.13.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-junctionseq >=1.12.0,<1.13.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biasedurn + - r-dplyr + - r-gdata + - r-gplots + - r-gridextra + - r-htmlwidgets + - r-igraph + - r-mgcv + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-tibble + - r-venndiagram + - r-webshot +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL(>=2) + summary: 'Pathway analysis of alternative splicing would be biased without accounting for the different number of exons associated with each gene, because genes with higher number of exons are more likely to be included in the ''significant'' gene list in alternative splicing. PathwaySplice is an R package that: (1) performs pathway analysis that explicitly adjusts for the number of exons associated with each gene (2) visualizes selection bias due to different number of exons for each gene (3) formally tests for presence of bias using logistic regression (4) supports gene sets based on the Gene Ontology terms, as well as more broadly defined gene sets (e.g. MSigDB) or user defined gene sets (5) identifies the significant genes driving pathway significance (6) organizes significant pathways with an enrichment map, where pathways with large number of overlapping genes are grouped together in a network graph' + diff --git a/recipes/bioconductor-paxtoolsr/build.sh b/recipes/bioconductor-paxtoolsr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-paxtoolsr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-paxtoolsr/meta.yaml b/recipes/bioconductor-paxtoolsr/meta.yaml new file mode 100644 index 0000000000000..589efcb21308b --- /dev/null +++ b/recipes/bioconductor-paxtoolsr/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.16.0" %} +{% set name = "paxtoolsr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8394eb60eeaee13886d8934e67581e7d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, BiocStyle, rmarkdown, RColorBrewer, biomaRt, estrogen, affy, hgu95av2, hgu95av2cdf, limma, foreach, doSNOW, parallel, org.Hs.eg.db +# SystemRequirements: Java (>= 1.6) +requirements: + host: + - r-base + - r-httr + - r-igraph + - r-jsonlite + - r-plyr + - r-r.utils + - r-readr + - 'r-rjava >=0.9-8' + - r-rjson + - r-xml + run: + - r-base + - r-httr + - r-igraph + - r-jsonlite + - r-plyr + - r-r.utils + - r-readr + - 'r-rjava >=0.9-8' + - r-rjson + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'The package provides a set of R functions for interacting with BioPAX OWL files using Paxtools and the querying Pathway Commons (PC) molecular interaction database that are hosted by the Computational Biology Center at Memorial Sloan-Kettering Cancer Center (MSKCC). Pathway Commons databases include: BIND, BioGRID, CORUM, CTD, DIP, DrugBank, HPRD, HumanCyc, IntAct, KEGG, MirTarBase, Panther, PhosphoSitePlus, Reactome, RECON, TRANSFAC.' + diff --git a/recipes/bioconductor-pbase/build.sh b/recipes/bioconductor-pbase/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pbase/build.sh +++ b/recipes/bioconductor-pbase/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pbase/meta.yaml b/recipes/bioconductor-pbase/meta.yaml index 16d7c020c6c5f..456e824776867 100644 --- a/recipes/bioconductor-pbase/meta.yaml +++ b/recipes/bioconductor-pbase/meta.yaml @@ -1,60 +1,61 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "Pbase" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8c458b8265aa425b8edf715eaab650e31eea4ce90c56b1b18490052d0d24b9b2 + md5: 8e2040630fe615962eabbf6bcd1c9e65 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat (>= 0.8), ggplot2, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationHub, knitr, rmarkdown, BiocStyle, EnsDb.Hsapiens.v86 (>= 2.0.0) requirements: host: - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-cleaver >=1.18.0,<1.20.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-pviz >=1.14.0,<1.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-cleaver >=1.20.0,<1.21.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-pviz >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcpp run: - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-cleaver >=1.18.0,<1.20.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzid >=1.18.0,<1.20.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-pviz >=1.14.0,<1.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-cleaver >=1.20.0,<1.21.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzid >=1.20.0,<1.21.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-pviz >=1.16.0,<1.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-rcpp build: @@ -64,10 +65,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A set of classes and functions to investigate and understand protein sequence data in the context of a proteomics experiment.' extra: identifiers: - biotools:pbase - doi:10.1002/pmic.201400392 + parent_recipe: + name: bioconductor-pbase + path: recipes/bioconductor-pbase + version: 0.20.0 + diff --git a/recipes/bioconductor-pcaexplorer/build.sh b/recipes/bioconductor-pcaexplorer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcaexplorer/build.sh +++ b/recipes/bioconductor-pcaexplorer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcaexplorer/meta.yaml b/recipes/bioconductor-pcaexplorer/meta.yaml index 23fdc7a21634d..46d59f859c4bf 100644 --- a/recipes/bioconductor-pcaexplorer/meta.yaml +++ b/recipes/bioconductor-pcaexplorer/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "2.6.0" %} +{% set version = "2.8.0" %} {% set name = "pcaExplorer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f2231a38edffb178860aeac9af51f026e57914ff688ea68b9d5fe2455a9a7e6b + md5: dd19f6f70e9b1cc4a09ec19d725bc2ca build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, airway, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-d3heatmap - r-dt @@ -48,18 +50,18 @@ requirements: - r-threejs - r-tidyr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-d3heatmap - r-dt @@ -81,10 +83,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'This package provides functionality for interactive visualization of RNA-seq datasets based on Principal Components Analysis. The methods provided allow for quick information extraction and effective data exploration. A Shiny application encapsulates the whole analysis.' extra: identifiers: - biotools:pcaexplorer - doi:10.18547/gcb.2017.vol3.iss1.e39 + parent_recipe: + name: bioconductor-pcaexplorer + path: recipes/bioconductor-pcaexplorer + version: 2.6.0 + diff --git a/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml b/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml new file mode 100644 index 0000000000000..44a88b2b48ca9 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.hs.hg19/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "pcaGoPromoter.Hs.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4cc30df25e7ebdcfda9a818e51a58a5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Contains the data for transciption factors analysis of organism Homo Sapiens with package pcaGoPromoter' + diff --git a/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh b/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh new file mode 100644 index 0000000000000..d5e7b80871515 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.hs.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Hs.hg19_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.hs.hg19/bioconductor-pcagopromoter.hs.hg19_1.18.0_src_all.tar.gz" +) +MD5="4cc30df25e7ebdcfda9a818e51a58a5d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pcagopromoter.hs.hg19/pre-unlink.sh b/recipes/bioconductor-pcagopromoter.hs.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..054de0ec281be --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.hs.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pcaGoPromoter.Hs.hg19 diff --git a/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml b/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml new file mode 100644 index 0000000000000..c1e13d279fea4 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.mm.mm9/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "pcaGoPromoter.Mm.mm9" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 33379deaeaa464ca75ad1b86a737c8dd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Contains the data for transciption factors analysis of organism Mus musculus with package pcaGoPromoter' + diff --git a/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh b/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh new file mode 100644 index 0000000000000..468977784b6c9 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.mm.mm9/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Mm.mm9_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.mm.mm9/bioconductor-pcagopromoter.mm.mm9_1.18.0_src_all.tar.gz" +) +MD5="33379deaeaa464ca75ad1b86a737c8dd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pcagopromoter.mm.mm9/pre-unlink.sh b/recipes/bioconductor-pcagopromoter.mm.mm9/pre-unlink.sh new file mode 100644 index 0000000000000..6b3d9b4ac26cd --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.mm.mm9/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pcaGoPromoter.Mm.mm9 diff --git a/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml b/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml new file mode 100644 index 0000000000000..27a42bf27dc26 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.rn.rn4/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "pcaGoPromoter.Rn.rn4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8d3ddf814343009ddddecc7082f971c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Contains the data for transciption factors analysis of organism Rattus norvegicus with package pcaGoPromoter' + diff --git a/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh b/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh new file mode 100644 index 0000000000000..da56d49bcce68 --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.rn.rn4/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcaGoPromoter.Rn.rn4_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcagopromoter.rn.rn4/bioconductor-pcagopromoter.rn.rn4_1.18.0_src_all.tar.gz" +) +MD5="8d3ddf814343009ddddecc7082f971c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pcagopromoter.rn.rn4/pre-unlink.sh b/recipes/bioconductor-pcagopromoter.rn.rn4/pre-unlink.sh new file mode 100644 index 0000000000000..1104e882f6cda --- /dev/null +++ b/recipes/bioconductor-pcagopromoter.rn.rn4/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pcaGoPromoter.Rn.rn4 diff --git a/recipes/bioconductor-pcagopromoter/build.sh b/recipes/bioconductor-pcagopromoter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcagopromoter/build.sh +++ b/recipes/bioconductor-pcagopromoter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcagopromoter/meta.yaml b/recipes/bioconductor-pcagopromoter/meta.yaml index fb49ac4b94e23..1b21df4afe96a 100644 --- a/recipes/bioconductor-pcagopromoter/meta.yaml +++ b/recipes/bioconductor-pcagopromoter/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "pcaGoPromoter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 54f59073eed0031d6b2d73f43394e25b76784b0b9618588153850626c76af622 + md5: 4e977c7652ab79cdbc1f34bb9f2e69e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz, GO.db, hgu133plus2.db, mouse4302.db, rat2302.db, hugene10sttranscriptcluster.db, mogene10sttranscriptcluster.db, pcaGoPromoter.Hs.hg19, pcaGoPromoter.Mm.mm9, pcaGoPromoter.Rn.rn4, serumStimulation, parallel requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-ellipse run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-ellipse test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains functions to ease the analyses of DNA micro arrays. It utilizes principal component analysis as the initial multivariate analysis, followed by functional interpretation of the principal component dimensions with overrepresentation analysis for GO terms and regulatory interpretations using overrepresentation analysis of predicted transcription factor binding sites with the primo algorithm.' extra: identifiers: - biotools:pcagopromoter + parent_recipe: + name: bioconductor-pcagopromoter + path: recipes/bioconductor-pcagopromoter + version: 1.24.0 + diff --git a/recipes/bioconductor-pcamethods/build.sh b/recipes/bioconductor-pcamethods/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcamethods/build.sh +++ b/recipes/bioconductor-pcamethods/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcamethods/meta.yaml b/recipes/bioconductor-pcamethods/meta.yaml index 811d94c09934e..4e7e44b982aa2 100644 --- a/recipes/bioconductor-pcamethods/meta.yaml +++ b/recipes/bioconductor-pcamethods/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.72.0" %} +{% set version = "1.74.0" %} {% set name = "pcaMethods" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 07284d96b9049f95280b31e06057c18c3aebf07d0ffc91c137d0e75391f3296d + md5: 6a9c216fb47845695f034c5a8d76a804 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: matrixStats, lattice, ggplot2 +# SystemRequirements: Rcpp requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - 'r-rcpp >=0.11.3' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - 'r-rcpp >=0.11.3' @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Provides Bayesian PCA, Probabilistic PCA, Nipals PCA, Inverse Non-Linear PCA and the conventional SVD PCA. A cluster based method for missing value estimation is included for comparison. BPCA, PPCA and NipalsPCA may be used to perform PCA on incomplete data as well as for accurate missing value estimation. A set of methods for printing and plotting the results is also provided. All PCA methods make use of the same data structure (pcaRes) to provide a common interface to the PCA results. Initiated at the Max-Planck Institute for Molecular Plant Physiology, Golm, Germany.' extra: identifiers: - biotools:pcamethods - doi:10.1093/bioinformatics/btm069 + parent_recipe: + name: bioconductor-pcamethods + path: recipes/bioconductor-pcamethods + version: 1.72.0 + diff --git a/recipes/bioconductor-pcan/build.sh b/recipes/bioconductor-pcan/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcan/build.sh +++ b/recipes/bioconductor-pcan/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcan/meta.yaml b/recipes/bioconductor-pcan/meta.yaml index d1830658226be..f8d372eda7cc9 100644 --- a/recipes/bioconductor-pcan/meta.yaml +++ b/recipes/bioconductor-pcan/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PCAN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4cdf96ce949fbb33f14ae1736efcf76dd780412a29c90e1d5e70b6f4dce48e43 + md5: 07f2255c8748a0a112ff3870d63e63ed build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, reactome.db, STRINGdb requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0' summary: 'Phenotypes comparison based on a pathway consensus approach. Assess the relationship between candidate genes and a set of phenotypes based on additional genes related to the candidate (e.g. Pathways or network neighbors).' extra: identifiers: - biotools:pcan + parent_recipe: + name: bioconductor-pcan + path: recipes/bioconductor-pcan + version: 1.8.0 + diff --git a/recipes/bioconductor-pchicdata/meta.yaml b/recipes/bioconductor-pchicdata/meta.yaml index da374f8f7ab4b..0207c513f4aff 100644 --- a/recipes/bioconductor-pchicdata/meta.yaml +++ b/recipes/bioconductor-pchicdata/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "PCHiCdata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1ffb05620d982bd57421d20e535fce5aa8fea5ee86dda375b8d3f23ae6957d2e + md5: 8e3da1443273ed288b35b8fd0cdf1d1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-chicago >=1.8.0,<1.10.0' + - 'bioconductor-chicago >=1.10.0,<1.11.0' - r-base run: - - 'bioconductor-chicago >=1.8.0,<1.10.0' + - 'bioconductor-chicago >=1.10.0,<1.11.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'Subsets of Promoter Capture Hi-C data conveniently packaged for Chicago users. Data includes interactions detected for chromosomes 20 and 21 in GM12878 cells and for chromosomes 18 and 19 in mESC.' - +extra: + parent_recipe: + name: bioconductor-pchicdata + path: recipes/bioconductor-pchicdata + version: 1.8.0 diff --git a/recipes/bioconductor-pchicdata/post-link.sh b/recipes/bioconductor-pchicdata/post-link.sh index 1ab160ae7bce8..2bef2d25f70c0 100644 --- a/recipes/bioconductor-pchicdata/post-link.sh +++ b/recipes/bioconductor-pchicdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PCHiCdata_1.8.0.tar.gz" +FN="PCHiCdata_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/PCHiCdata_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/PCHiCdata_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PCHiCdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/PCHiCdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pchicdata/bioconductor-pchicdata_1.10.0_src_all.tar.gz" ) -MD5="e2f47759614488314cbae936a38b7330" +MD5="8e3da1443273ed288b35b8fd0cdf1d1d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-pcot2/build.sh b/recipes/bioconductor-pcot2/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcot2/build.sh +++ b/recipes/bioconductor-pcot2/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcot2/meta.yaml b/recipes/bioconductor-pcot2/meta.yaml index 5646b95e33abf..6c043f1799c65 100644 --- a/recipes/bioconductor-pcot2/meta.yaml +++ b/recipes/bioconductor-pcot2/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "pcot2" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dfcf06e36e80cbb3ab85d2cc7786612512c3f1b84a78c7d0d2ef928046dfb4bb + md5: aa57791e2f80a012910aba04f449bf80 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: multtest, hu6800.db, KEGG.db, mvtnorm requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-amap - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-amap - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'PCOT2 is a permutation-based method for investigating changes in the activity of multi-gene networks. It utilizes inter-gene correlation information to detect significant alterations in gene network activities. Currently it can be applied to two-sample comparisons.' extra: identifiers: - biotools:pcot2 - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pcot2 + path: recipes/bioconductor-pcot2 + version: 1.48.0 + diff --git a/recipes/bioconductor-pcpheno/build.sh b/recipes/bioconductor-pcpheno/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pcpheno/build.sh +++ b/recipes/bioconductor-pcpheno/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcpheno/meta.yaml b/recipes/bioconductor-pcpheno/meta.yaml index b15da47f2a2fb..c252adf4b43eb 100644 --- a/recipes/bioconductor-pcpheno/meta.yaml +++ b/recipes/bioconductor-pcpheno/meta.yaml @@ -1,58 +1,65 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "PCpheno" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c1a90074a87604403e642e7dface19f9b3edfb71e538a82b61f020c9f5f2dcb3 + md5: 145f9f7d83b7405cb42e5949fae540e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: KEGG.db, GO.db, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-ppidata >=0.18.0,<0.20.0' - - 'bioconductor-ppistats >=1.46.0,<1.48.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' - - 'bioconductor-slgi >=1.40.0,<1.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-ppidata >=0.20.0,<0.21.0' + - 'bioconductor-ppistats >=1.48.0,<1.49.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-slgi >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-ppidata >=0.18.0,<0.20.0' - - 'bioconductor-ppistats >=1.46.0,<1.48.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' - - 'bioconductor-slgi >=1.40.0,<1.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-ppidata >=0.20.0,<0.21.0' + - 'bioconductor-ppistats >=1.48.0,<1.49.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' + - 'bioconductor-slgi >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to integrate, annotate, and link phenotypes to cellular organizational units such as protein complexes and pathways.' extra: identifiers: - biotools:pcpheno - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pcpheno + path: recipes/bioconductor-pcpheno + version: 1.42.0 + diff --git a/recipes/bioconductor-pcxn/build.sh b/recipes/bioconductor-pcxn/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pcxn/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pcxn/meta.yaml b/recipes/bioconductor-pcxn/meta.yaml new file mode 100644 index 0000000000000..c197a164dec83 --- /dev/null +++ b/recipes/bioconductor-pcxn/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.4.0" %} +{% set name = "pcxn" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3945e77826c7917f07557d39f5d7af19 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: igraph, annotate, org.Hs.eg.db +requirements: + host: + - 'bioconductor-pcxndata >=2.4.0,<2.5.0' + - r-base + - r-pheatmap + run: + - 'bioconductor-pcxndata >=2.4.0,<2.5.0' + - r-base + - r-pheatmap +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Discover the correlated pathways/gene sets of a single pathway/gene set or discover correlation relationships among multiple pathways/gene sets. Draw a heatmap or create a network of your query and extract members of each pathway/gene set found in the available collections (MSigDB H hallmark, MSigDB C2 Canonical pathways, MSigDB C5 GO BP and Pathprint).' + diff --git a/recipes/bioconductor-pcxndata/meta.yaml b/recipes/bioconductor-pcxndata/meta.yaml new file mode 100644 index 0000000000000..af51782dc3961 --- /dev/null +++ b/recipes/bioconductor-pcxndata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "2.4.0" %} +{% set name = "pcxnData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b5c348c5e4f36193ef30afef989fdc49 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pcxn +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'PCxN database contains correlation coefficients and p values between pre-defined gene sets within MSigDB H hallmark gene sets, MSigDB C2 CP (Canonical pathways), MSigDB C5 GO BP gene sets and Pathprint respectively, as well as adjusted pathway correlations to account for the shared genes between pathway pairs.' + diff --git a/recipes/bioconductor-pcxndata/post-link.sh b/recipes/bioconductor-pcxndata/post-link.sh new file mode 100644 index 0000000000000..7b6caddf8403b --- /dev/null +++ b/recipes/bioconductor-pcxndata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pcxnData_2.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pcxnData_2.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/pcxnData_2.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pcxndata/bioconductor-pcxndata_2.4.0_src_all.tar.gz" +) +MD5="b5c348c5e4f36193ef30afef989fdc49" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pcxndata/pre-unlink.sh b/recipes/bioconductor-pcxndata/pre-unlink.sh new file mode 100644 index 0000000000000..27590429fab8d --- /dev/null +++ b/recipes/bioconductor-pcxndata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pcxnData diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml new file mode 100644 index 0000000000000..afd3959f107df --- /dev/null +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.4" %} +{% set name = "pd.081229.hg18.promoter.medip.hx1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f3c240fa0d4503e94047be5ee323856b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen 081229_hg18_promoter_medip_hx1' + diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh new file mode 100644 index 0000000000000..a97e49c395d65 --- /dev/null +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" + "https://bioarchive.galaxyproject.org/pd.081229.hg18.promoter.medip.hx1_0.99.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.081229.hg18.promoter.medip.hx1/bioconductor-pd.081229.hg18.promoter.medip.hx1_0.99.4_src_all.tar.gz" +) +MD5="f3c240fa0d4503e94047be5ee323856b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/pre-unlink.sh b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/pre-unlink.sh new file mode 100644 index 0000000000000..1769c4db85e98 --- /dev/null +++ b/recipes/bioconductor-pd.081229.hg18.promoter.medip.hx1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.081229.hg18.promoter.medip.hx1 diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml new file mode 100644 index 0000000000000..dc253cdc85c9a --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.8.1" %} +{% set name = "pd.2006.07.18.hg18.refseq.promoter" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 00838332d75b82d212078a9957f495df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.11.1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.11.1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen 2006-07-18_hg18_refseq_promoter' + diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh new file mode 100644 index 0000000000000..a9a4cae8b2b5e --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.2006.07.18.hg18.refseq.promoter_1.8.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.hg18.refseq.promoter/bioconductor-pd.2006.07.18.hg18.refseq.promoter_1.8.1_src_all.tar.gz" +) +MD5="00838332d75b82d212078a9957f495df" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/pre-unlink.sh b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/pre-unlink.sh new file mode 100644 index 0000000000000..80236f4f7b0aa --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.hg18.refseq.promoter/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.2006.07.18.hg18.refseq.promoter diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml new file mode 100644 index 0000000000000..7fcf628c1b03e --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.3" %} +{% set name = "pd.2006.07.18.mm8.refseq.promoter" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 084b0a6759fd96d1bc775dd4c66c42b0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen 2006-07-18_mm8_refseq_promoter' + diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh new file mode 100644 index 0000000000000..7a8f98f7a8306 --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" + "https://bioarchive.galaxyproject.org/pd.2006.07.18.mm8.refseq.promoter_0.99.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.07.18.mm8.refseq.promoter/bioconductor-pd.2006.07.18.mm8.refseq.promoter_0.99.3_src_all.tar.gz" +) +MD5="084b0a6759fd96d1bc775dd4c66c42b0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/pre-unlink.sh b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/pre-unlink.sh new file mode 100644 index 0000000000000..b0a4da1419bf2 --- /dev/null +++ b/recipes/bioconductor-pd.2006.07.18.mm8.refseq.promoter/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.2006.07.18.mm8.refseq.promoter diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml new file mode 100644 index 0000000000000..5e1b85e231cef --- /dev/null +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.3" %} +{% set name = "pd.2006.10.31.rn34.refseq.promoter" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ab5bb767ad29b213e5a969a5fc51ee7d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen 2006-10-31_rn34_refseq_promoter' + diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh new file mode 100644 index 0000000000000..0e2e8d679287c --- /dev/null +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" + "https://bioarchive.galaxyproject.org/pd.2006.10.31.rn34.refseq.promoter_0.99.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.2006.10.31.rn34.refseq.promoter/bioconductor-pd.2006.10.31.rn34.refseq.promoter_0.99.3_src_all.tar.gz" +) +MD5="ab5bb767ad29b213e5a969a5fc51ee7d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/pre-unlink.sh b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/pre-unlink.sh new file mode 100644 index 0000000000000..e1ae37d9819c8 --- /dev/null +++ b/recipes/bioconductor-pd.2006.10.31.rn34.refseq.promoter/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.2006.10.31.rn34.refseq.promoter diff --git a/recipes/bioconductor-pd.ag/meta.yaml b/recipes/bioconductor-pd.ag/meta.yaml new file mode 100644 index 0000000000000..6fa58b284314f --- /dev/null +++ b/recipes/bioconductor-pd.ag/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ag" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 21fb288536568ff010ad4847b671f9d6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name AG' + diff --git a/recipes/bioconductor-pd.ag/post-link.sh b/recipes/bioconductor-pd.ag/post-link.sh new file mode 100644 index 0000000000000..cfbe50a58e4a7 --- /dev/null +++ b/recipes/bioconductor-pd.ag/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ag_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ag_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ag_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ag/bioconductor-pd.ag_3.12.0_src_all.tar.gz" +) +MD5="21fb288536568ff010ad4847b671f9d6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ag/pre-unlink.sh b/recipes/bioconductor-pd.ag/pre-unlink.sh new file mode 100644 index 0000000000000..69f8a6cf5c6f3 --- /dev/null +++ b/recipes/bioconductor-pd.ag/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ag diff --git a/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..e2f53d9fa8a9b --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.aragene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ff87a0793fd4b713c4a45b6c1d4a4977 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix AraGene-1_0-st' + diff --git a/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh b/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..1e1e430c19a22 --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.aragene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.aragene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.aragene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.0.st/bioconductor-pd.aragene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="ff87a0793fd4b713c4a45b6c1d4a4977" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.aragene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.aragene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..c4c7c765036f3 --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.aragene.1.0.st diff --git a/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..1c20130332728 --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.aragene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 828ad790eb2495e396d7fcd9bcbf9133 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix AraGene-1_1-st' + diff --git a/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh b/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..60cd0ad3dd936 --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.aragene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.aragene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.aragene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.aragene.1.1.st/bioconductor-pd.aragene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="828ad790eb2495e396d7fcd9bcbf9133" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.aragene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.aragene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..d072635bdc61f --- /dev/null +++ b/recipes/bioconductor-pd.aragene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.aragene.1.1.st diff --git a/recipes/bioconductor-pd.atdschip.tiling/meta.yaml b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml new file mode 100644 index 0000000000000..881041cbba7cc --- /dev/null +++ b/recipes/bioconductor-pd.atdschip.tiling/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "0.20.0" %} +{% set name = "pd.atdschip.tiling" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4e8b33dcee82491454fb2954983fab60 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.10.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.10.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Atdschip_tiling' + diff --git a/recipes/bioconductor-pd.atdschip.tiling/post-link.sh b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh new file mode 100644 index 0000000000000..541cfc4ee9997 --- /dev/null +++ b/recipes/bioconductor-pd.atdschip.tiling/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.atdschip.tiling_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pd.atdschip.tiling_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.atdschip.tiling_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.atdschip.tiling/bioconductor-pd.atdschip.tiling_0.20.0_src_all.tar.gz" +) +MD5="4e8b33dcee82491454fb2954983fab60" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.atdschip.tiling/pre-unlink.sh b/recipes/bioconductor-pd.atdschip.tiling/pre-unlink.sh new file mode 100644 index 0000000000000..fb7f4ba2c3757 --- /dev/null +++ b/recipes/bioconductor-pd.atdschip.tiling/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.atdschip.tiling diff --git a/recipes/bioconductor-pd.ath1.121501/meta.yaml b/recipes/bioconductor-pd.ath1.121501/meta.yaml new file mode 100644 index 0000000000000..ea30ac5c3bfbd --- /dev/null +++ b/recipes/bioconductor-pd.ath1.121501/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ath1.121501" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d7ed8640f0deac552e0083a091e72a72 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name ATH1-121501' + diff --git a/recipes/bioconductor-pd.ath1.121501/post-link.sh b/recipes/bioconductor-pd.ath1.121501/post-link.sh new file mode 100644 index 0000000000000..b477843bccb4c --- /dev/null +++ b/recipes/bioconductor-pd.ath1.121501/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ath1.121501_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ath1.121501_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ath1.121501_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ath1.121501/bioconductor-pd.ath1.121501_3.12.0_src_all.tar.gz" +) +MD5="d7ed8640f0deac552e0083a091e72a72" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ath1.121501/pre-unlink.sh b/recipes/bioconductor-pd.ath1.121501/pre-unlink.sh new file mode 100644 index 0000000000000..f405c1bf4e255 --- /dev/null +++ b/recipes/bioconductor-pd.ath1.121501/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ath1.121501 diff --git a/recipes/bioconductor-pd.barley1/meta.yaml b/recipes/bioconductor-pd.barley1/meta.yaml new file mode 100644 index 0000000000000..b5474e854377c --- /dev/null +++ b/recipes/bioconductor-pd.barley1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.barley1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b8d11f5ad42e75f7a91931b46d449c1a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Barley1' + diff --git a/recipes/bioconductor-pd.barley1/post-link.sh b/recipes/bioconductor-pd.barley1/post-link.sh new file mode 100644 index 0000000000000..6131b0b8f131b --- /dev/null +++ b/recipes/bioconductor-pd.barley1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.barley1_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.barley1_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.barley1_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.barley1/bioconductor-pd.barley1_3.12.0_src_all.tar.gz" +) +MD5="b8d11f5ad42e75f7a91931b46d449c1a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.barley1/pre-unlink.sh b/recipes/bioconductor-pd.barley1/pre-unlink.sh new file mode 100644 index 0000000000000..0a502ffc4d069 --- /dev/null +++ b/recipes/bioconductor-pd.barley1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.barley1 diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..1c9905891496e --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.bovgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6e9747d13aee7825722562ccc49ad35f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix BovGene-1_0-st' + diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..a40737e3f522f --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.bovgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.bovgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.0.st/bioconductor-pd.bovgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="6e9747d13aee7825722562ccc49ad35f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.bovgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.bovgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..7a6f1964a4da8 --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.bovgene.1.0.st diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..fb0f79bfdc981 --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.bovgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 342246c0a76755fcca458cd723b3e98e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix BovGene-1_1-st' + diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..3252f7266567e --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.bovgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.bovgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovgene.1.1.st/bioconductor-pd.bovgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="342246c0a76755fcca458cd723b3e98e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.bovgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.bovgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..b736bbf2900a7 --- /dev/null +++ b/recipes/bioconductor-pd.bovgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.bovgene.1.1.st diff --git a/recipes/bioconductor-pd.bovine/meta.yaml b/recipes/bioconductor-pd.bovine/meta.yaml new file mode 100644 index 0000000000000..f59f5bb25b11e --- /dev/null +++ b/recipes/bioconductor-pd.bovine/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.bovine" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6c7026dba53b54b547b1f1e135d043b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Bovine' + diff --git a/recipes/bioconductor-pd.bovine/post-link.sh b/recipes/bioconductor-pd.bovine/post-link.sh new file mode 100644 index 0000000000000..c3ecdb3d4d996 --- /dev/null +++ b/recipes/bioconductor-pd.bovine/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.bovine_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bovine_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.bovine_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bovine/bioconductor-pd.bovine_3.12.0_src_all.tar.gz" +) +MD5="6c7026dba53b54b547b1f1e135d043b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.bovine/pre-unlink.sh b/recipes/bioconductor-pd.bovine/pre-unlink.sh new file mode 100644 index 0000000000000..acf7081228db4 --- /dev/null +++ b/recipes/bioconductor-pd.bovine/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.bovine diff --git a/recipes/bioconductor-pd.bsubtilis/meta.yaml b/recipes/bioconductor-pd.bsubtilis/meta.yaml new file mode 100644 index 0000000000000..f7f4a21a6a514 --- /dev/null +++ b/recipes/bioconductor-pd.bsubtilis/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.bsubtilis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2261d8b0ec178beb432d71eafd90ec9a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Bsubtilis' + diff --git a/recipes/bioconductor-pd.bsubtilis/post-link.sh b/recipes/bioconductor-pd.bsubtilis/post-link.sh new file mode 100644 index 0000000000000..4b54ebd9a4914 --- /dev/null +++ b/recipes/bioconductor-pd.bsubtilis/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.bsubtilis_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.bsubtilis_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.bsubtilis_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.bsubtilis/bioconductor-pd.bsubtilis_3.12.0_src_all.tar.gz" +) +MD5="2261d8b0ec178beb432d71eafd90ec9a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.bsubtilis/pre-unlink.sh b/recipes/bioconductor-pd.bsubtilis/pre-unlink.sh new file mode 100644 index 0000000000000..b6895b648ba62 --- /dev/null +++ b/recipes/bioconductor-pd.bsubtilis/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.bsubtilis diff --git a/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..a4d9804405d91 --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cangene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0a39d6378193e3f7d31a7210f6766eaf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CanGene-1_0-st' + diff --git a/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..123e44e3148ba --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cangene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cangene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cangene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.0.st/bioconductor-pd.cangene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="0a39d6378193e3f7d31a7210f6766eaf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cangene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.cangene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..448376410c2fd --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cangene.1.0.st diff --git a/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..37dda7d173e73 --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cangene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 946074601e7bee72f3b3dd6ae6b3bc33 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CanGene-1_1-st' + diff --git a/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..e4ed2b3049373 --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cangene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cangene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cangene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cangene.1.1.st/bioconductor-pd.cangene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="946074601e7bee72f3b3dd6ae6b3bc33" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cangene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.cangene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..e00ec2659ed5d --- /dev/null +++ b/recipes/bioconductor-pd.cangene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cangene.1.1.st diff --git a/recipes/bioconductor-pd.canine.2/meta.yaml b/recipes/bioconductor-pd.canine.2/meta.yaml new file mode 100644 index 0000000000000..0df7c79a2a4e7 --- /dev/null +++ b/recipes/bioconductor-pd.canine.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.canine.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bc918d1953a3c7ac7168b60a53405a93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Canine_2' + diff --git a/recipes/bioconductor-pd.canine.2/post-link.sh b/recipes/bioconductor-pd.canine.2/post-link.sh new file mode 100644 index 0000000000000..63cedc9a36867 --- /dev/null +++ b/recipes/bioconductor-pd.canine.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.canine.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.canine.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.canine.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.canine.2/bioconductor-pd.canine.2_3.12.0_src_all.tar.gz" +) +MD5="bc918d1953a3c7ac7168b60a53405a93" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.canine.2/pre-unlink.sh b/recipes/bioconductor-pd.canine.2/pre-unlink.sh new file mode 100644 index 0000000000000..d7b7d6eac3ef5 --- /dev/null +++ b/recipes/bioconductor-pd.canine.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.canine.2 diff --git a/recipes/bioconductor-pd.canine/meta.yaml b/recipes/bioconductor-pd.canine/meta.yaml new file mode 100644 index 0000000000000..02a986f7f1b16 --- /dev/null +++ b/recipes/bioconductor-pd.canine/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.canine" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5b40fe9e40d0b7f36d338e413d121ba7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Canine' + diff --git a/recipes/bioconductor-pd.canine/post-link.sh b/recipes/bioconductor-pd.canine/post-link.sh new file mode 100644 index 0000000000000..e818fc076d2f4 --- /dev/null +++ b/recipes/bioconductor-pd.canine/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.canine_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.canine_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.canine_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.canine/bioconductor-pd.canine_3.12.0_src_all.tar.gz" +) +MD5="5b40fe9e40d0b7f36d338e413d121ba7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.canine/pre-unlink.sh b/recipes/bioconductor-pd.canine/pre-unlink.sh new file mode 100644 index 0000000000000..5e1579fe22280 --- /dev/null +++ b/recipes/bioconductor-pd.canine/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.canine diff --git a/recipes/bioconductor-pd.celegans/meta.yaml b/recipes/bioconductor-pd.celegans/meta.yaml new file mode 100644 index 0000000000000..17cf2f64068de --- /dev/null +++ b/recipes/bioconductor-pd.celegans/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.celegans" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b90ea2e071522bb340c103a1c8270205 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Celegans' + diff --git a/recipes/bioconductor-pd.celegans/post-link.sh b/recipes/bioconductor-pd.celegans/post-link.sh new file mode 100644 index 0000000000000..3ba6718567f3f --- /dev/null +++ b/recipes/bioconductor-pd.celegans/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.celegans_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.celegans_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.celegans_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.celegans/bioconductor-pd.celegans_3.12.0_src_all.tar.gz" +) +MD5="b90ea2e071522bb340c103a1c8270205" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.celegans/pre-unlink.sh b/recipes/bioconductor-pd.celegans/pre-unlink.sh new file mode 100644 index 0000000000000..3e19a21926e14 --- /dev/null +++ b/recipes/bioconductor-pd.celegans/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.celegans diff --git a/recipes/bioconductor-pd.charm.hg18.example/meta.yaml b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml new file mode 100644 index 0000000000000..8350d307c75af --- /dev/null +++ b/recipes/bioconductor-pd.charm.hg18.example/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.4" %} +{% set name = "pd.charm.hg18.example" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e201d4281a23c202f57bae1135e226b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen charm_hg18_example' + diff --git a/recipes/bioconductor-pd.charm.hg18.example/post-link.sh b/recipes/bioconductor-pd.charm.hg18.example/post-link.sh new file mode 100644 index 0000000000000..3899ce0b754c7 --- /dev/null +++ b/recipes/bioconductor-pd.charm.hg18.example/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.charm.hg18.example_0.99.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.charm.hg18.example_0.99.4.tar.gz" + "https://bioarchive.galaxyproject.org/pd.charm.hg18.example_0.99.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.charm.hg18.example/bioconductor-pd.charm.hg18.example_0.99.4_src_all.tar.gz" +) +MD5="e201d4281a23c202f57bae1135e226b4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.charm.hg18.example/pre-unlink.sh b/recipes/bioconductor-pd.charm.hg18.example/pre-unlink.sh new file mode 100644 index 0000000000000..1faa7283a3c84 --- /dev/null +++ b/recipes/bioconductor-pd.charm.hg18.example/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.charm.hg18.example diff --git a/recipes/bioconductor-pd.chicken/meta.yaml b/recipes/bioconductor-pd.chicken/meta.yaml new file mode 100644 index 0000000000000..83ebac8bf942b --- /dev/null +++ b/recipes/bioconductor-pd.chicken/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.chicken" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: af79b6d0910621910e72ea374499e5eb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Chicken' + diff --git a/recipes/bioconductor-pd.chicken/post-link.sh b/recipes/bioconductor-pd.chicken/post-link.sh new file mode 100644 index 0000000000000..8553edad6657b --- /dev/null +++ b/recipes/bioconductor-pd.chicken/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.chicken_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chicken_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.chicken_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chicken/bioconductor-pd.chicken_3.12.0_src_all.tar.gz" +) +MD5="af79b6d0910621910e72ea374499e5eb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.chicken/pre-unlink.sh b/recipes/bioconductor-pd.chicken/pre-unlink.sh new file mode 100644 index 0000000000000..7203a53ac13b6 --- /dev/null +++ b/recipes/bioconductor-pd.chicken/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.chicken diff --git a/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..3483dfba62d97 --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.chigene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e37cb047678fabb1801109d4efd16773 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix ChiGene-1_0-st' + diff --git a/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..b08755291502d --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.chigene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chigene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.chigene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.0.st/bioconductor-pd.chigene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="e37cb047678fabb1801109d4efd16773" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.chigene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.chigene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..c0085f8aeba10 --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.chigene.1.0.st diff --git a/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..b4123160acea7 --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.chigene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bec602b45961607f5a4571977d54e015 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix ChiGene-1_1-st' + diff --git a/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..b6a57f582b114 --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.chigene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chigene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.chigene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chigene.1.1.st/bioconductor-pd.chigene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="bec602b45961607f5a4571977d54e015" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.chigene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.chigene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..d2d03a7f0f6cf --- /dev/null +++ b/recipes/bioconductor-pd.chigene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.chigene.1.1.st diff --git a/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml new file mode 100644 index 0000000000000..0a62763efd2c4 --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.chogene.2.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 641718e3d172838185a200bac3d32433 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CHOGene-2_0-st' + diff --git a/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh b/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh new file mode 100644 index 0000000000000..57a7516fad3a2 --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.chogene.2.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chogene.2.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.chogene.2.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.0.st/bioconductor-pd.chogene.2.0.st_3.12.0_src_all.tar.gz" +) +MD5="641718e3d172838185a200bac3d32433" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.chogene.2.0.st/pre-unlink.sh b/recipes/bioconductor-pd.chogene.2.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..ca52a83a29c39 --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.chogene.2.0.st diff --git a/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml new file mode 100644 index 0000000000000..5131123b0501c --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.chogene.2.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ed25825e58a514cdde70b961bce9b4d7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CHOGene-2_1-st' + diff --git a/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh b/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh new file mode 100644 index 0000000000000..266636f0809ca --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.chogene.2.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.chogene.2.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.chogene.2.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.chogene.2.1.st/bioconductor-pd.chogene.2.1.st_3.12.0_src_all.tar.gz" +) +MD5="ed25825e58a514cdde70b961bce9b4d7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.chogene.2.1.st/pre-unlink.sh b/recipes/bioconductor-pd.chogene.2.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..59082a49f21f8 --- /dev/null +++ b/recipes/bioconductor-pd.chogene.2.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.chogene.2.1.st diff --git a/recipes/bioconductor-pd.citrus/meta.yaml b/recipes/bioconductor-pd.citrus/meta.yaml new file mode 100644 index 0000000000000..f483b8d9c3067 --- /dev/null +++ b/recipes/bioconductor-pd.citrus/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.citrus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dee9b3298b84e7dd5152f48ad449b15a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Citrus' + diff --git a/recipes/bioconductor-pd.citrus/post-link.sh b/recipes/bioconductor-pd.citrus/post-link.sh new file mode 100644 index 0000000000000..46f0e2e7d2bc4 --- /dev/null +++ b/recipes/bioconductor-pd.citrus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.citrus_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.citrus_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.citrus_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.citrus/bioconductor-pd.citrus_3.12.0_src_all.tar.gz" +) +MD5="dee9b3298b84e7dd5152f48ad449b15a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.citrus/pre-unlink.sh b/recipes/bioconductor-pd.citrus/pre-unlink.sh new file mode 100644 index 0000000000000..4ce55eb9d929f --- /dev/null +++ b/recipes/bioconductor-pd.citrus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.citrus diff --git a/recipes/bioconductor-pd.clariom.d.human/meta.yaml b/recipes/bioconductor-pd.clariom.d.human/meta.yaml new file mode 100644 index 0000000000000..ea5ee3c88bab4 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.d.human/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.d.human" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9d3505af53cc7c99980f29c527f0f37d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_D_Human' + diff --git a/recipes/bioconductor-pd.clariom.d.human/post-link.sh b/recipes/bioconductor-pd.clariom.d.human/post-link.sh new file mode 100644 index 0000000000000..eb290145c606e --- /dev/null +++ b/recipes/bioconductor-pd.clariom.d.human/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.d.human_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.d.human_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.d.human_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.d.human/bioconductor-pd.clariom.d.human_3.14.1_src_all.tar.gz" +) +MD5="9d3505af53cc7c99980f29c527f0f37d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.d.human/pre-unlink.sh b/recipes/bioconductor-pd.clariom.d.human/pre-unlink.sh new file mode 100644 index 0000000000000..d64c3ef2f98ce --- /dev/null +++ b/recipes/bioconductor-pd.clariom.d.human/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.d.human diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml new file mode 100644 index 0000000000000..84d15b4917bbb --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human.ht/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.human.ht" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 90f910bea1b1aeb550a3f1bdd91d1a06 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Human_HT' + diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh new file mode 100644 index 0000000000000..89cfd9968a5db --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human.ht/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.human.ht_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.human.ht_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.human.ht_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human.ht/bioconductor-pd.clariom.s.human.ht_3.14.1_src_all.tar.gz" +) +MD5="90f910bea1b1aeb550a3f1bdd91d1a06" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.human.ht/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.human.ht/pre-unlink.sh new file mode 100644 index 0000000000000..8209abf78fcb1 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human.ht/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.human.ht diff --git a/recipes/bioconductor-pd.clariom.s.human/meta.yaml b/recipes/bioconductor-pd.clariom.s.human/meta.yaml new file mode 100644 index 0000000000000..18652019a287e --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.human" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 797afe8a6a8041453a34ced3cce34884 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Human' + diff --git a/recipes/bioconductor-pd.clariom.s.human/post-link.sh b/recipes/bioconductor-pd.clariom.s.human/post-link.sh new file mode 100644 index 0000000000000..ff48c5e4f1fe2 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.human_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.human_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.human_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.human/bioconductor-pd.clariom.s.human_3.14.1_src_all.tar.gz" +) +MD5="797afe8a6a8041453a34ced3cce34884" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.human/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.human/pre-unlink.sh new file mode 100644 index 0000000000000..f968ec413c922 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.human/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.human diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml new file mode 100644 index 0000000000000..0bb1e39afa69b --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.mouse.ht" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9cb6f77cf9666a0d54e1eacb904fd57c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Mouse_HT' + diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh new file mode 100644 index 0000000000000..3880ba9a16daf --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.mouse.ht_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.mouse.ht_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse.ht_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse.ht/bioconductor-pd.clariom.s.mouse.ht_3.14.1_src_all.tar.gz" +) +MD5="9cb6f77cf9666a0d54e1eacb904fd57c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.mouse.ht/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.mouse.ht/pre-unlink.sh new file mode 100644 index 0000000000000..c777366ba67a6 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse.ht/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.mouse.ht diff --git a/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml new file mode 100644 index 0000000000000..05510e9f3d4dd --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.mouse" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e3e4ce2b22a78faf525dd6c0c0b2a42d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Mouse' + diff --git a/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh b/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh new file mode 100644 index 0000000000000..21bcc2011163a --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.mouse_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.mouse_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.mouse_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.mouse/bioconductor-pd.clariom.s.mouse_3.14.1_src_all.tar.gz" +) +MD5="e3e4ce2b22a78faf525dd6c0c0b2a42d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.mouse/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.mouse/pre-unlink.sh new file mode 100644 index 0000000000000..e5f186446447e --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.mouse/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.mouse diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml new file mode 100644 index 0000000000000..60fb604a31b06 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.rat.ht" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be901eb9e8830f3e5bedf154189a3743 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Rat_HT' + diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh b/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh new file mode 100644 index 0000000000000..1887053fd7dac --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.rat.ht_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.rat.ht_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.rat.ht_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat.ht/bioconductor-pd.clariom.s.rat.ht_3.14.1_src_all.tar.gz" +) +MD5="be901eb9e8830f3e5bedf154189a3743" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.rat.ht/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.rat.ht/pre-unlink.sh new file mode 100644 index 0000000000000..dc8065582b528 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat.ht/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.rat.ht diff --git a/recipes/bioconductor-pd.clariom.s.rat/meta.yaml b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml new file mode 100644 index 0000000000000..dd432e9a4ae29 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.clariom.s.rat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be464b3eaea8eb8bdbcca6047fce4dea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Clariom_S_Rat' + diff --git a/recipes/bioconductor-pd.clariom.s.rat/post-link.sh b/recipes/bioconductor-pd.clariom.s.rat/post-link.sh new file mode 100644 index 0000000000000..e817dad8b19ae --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.clariom.s.rat_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.clariom.s.rat_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.clariom.s.rat_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.clariom.s.rat/bioconductor-pd.clariom.s.rat_3.14.1_src_all.tar.gz" +) +MD5="be464b3eaea8eb8bdbcca6047fce4dea" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.clariom.s.rat/pre-unlink.sh b/recipes/bioconductor-pd.clariom.s.rat/pre-unlink.sh new file mode 100644 index 0000000000000..e58c873251f21 --- /dev/null +++ b/recipes/bioconductor-pd.clariom.s.rat/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.clariom.s.rat diff --git a/recipes/bioconductor-pd.cotton/meta.yaml b/recipes/bioconductor-pd.cotton/meta.yaml new file mode 100644 index 0000000000000..0d24b4d76f1b2 --- /dev/null +++ b/recipes/bioconductor-pd.cotton/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cotton" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 78c408902bcefb8c695119767534b393 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Cotton' + diff --git a/recipes/bioconductor-pd.cotton/post-link.sh b/recipes/bioconductor-pd.cotton/post-link.sh new file mode 100644 index 0000000000000..1dea45c247502 --- /dev/null +++ b/recipes/bioconductor-pd.cotton/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cotton_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cotton_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cotton_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cotton/bioconductor-pd.cotton_3.12.0_src_all.tar.gz" +) +MD5="78c408902bcefb8c695119767534b393" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cotton/pre-unlink.sh b/recipes/bioconductor-pd.cotton/pre-unlink.sh new file mode 100644 index 0000000000000..446fc78b00e8f --- /dev/null +++ b/recipes/bioconductor-pd.cotton/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cotton diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..e664de6b79cf3 --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cyngene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 784fac6cc92a0fe46dae32c9b737812a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CynGene-1_0-st' + diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..27fee7fe4f45a --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cyngene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyngene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cyngene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.0.st/bioconductor-pd.cyngene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="784fac6cc92a0fe46dae32c9b737812a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cyngene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.cyngene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..28a323a5c01a1 --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cyngene.1.0.st diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..9da5ef3f1911e --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cyngene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a6217267e3e08a15f70c600918c7d4f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CynGene-1_1-st' + diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..ec1fcdea905da --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cyngene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyngene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cyngene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyngene.1.1.st/bioconductor-pd.cyngene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="a6217267e3e08a15f70c600918c7d4f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cyngene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.cyngene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..7dff56fb703a7 --- /dev/null +++ b/recipes/bioconductor-pd.cyngene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cyngene.1.1.st diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..2fc72014bb125 --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cyrgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 63228c07d3d16d6c62e9c0e83f10a855 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CyRGene-1_0-st' + diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..b1fd50f92c43a --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cyrgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyrgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cyrgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.0.st/bioconductor-pd.cyrgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="63228c07d3d16d6c62e9c0e83f10a855" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cyrgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.cyrgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..dc260dec82b3e --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cyrgene.1.0.st diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..48417e813630c --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cyrgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dbe3bb580b96aaddcc597de45159320d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix CyRGene-1_1-st' + diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..e656b3b1acc05 --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cyrgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cyrgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cyrgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cyrgene.1.1.st/bioconductor-pd.cyrgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="dbe3bb580b96aaddcc597de45159320d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cyrgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.cyrgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..d04d5a32321dc --- /dev/null +++ b/recipes/bioconductor-pd.cyrgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cyrgene.1.1.st diff --git a/recipes/bioconductor-pd.cytogenetics.array/meta.yaml b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml new file mode 100644 index 0000000000000..99936587debd1 --- /dev/null +++ b/recipes/bioconductor-pd.cytogenetics.array/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.cytogenetics.array" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8c359ff56a9a558d370dc9a6a54218e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Cytogenetics_Array' + diff --git a/recipes/bioconductor-pd.cytogenetics.array/post-link.sh b/recipes/bioconductor-pd.cytogenetics.array/post-link.sh new file mode 100644 index 0000000000000..831860ad70750 --- /dev/null +++ b/recipes/bioconductor-pd.cytogenetics.array/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.cytogenetics.array_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.cytogenetics.array_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.cytogenetics.array_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.cytogenetics.array/bioconductor-pd.cytogenetics.array_3.12.0_src_all.tar.gz" +) +MD5="8c359ff56a9a558d370dc9a6a54218e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.cytogenetics.array/pre-unlink.sh b/recipes/bioconductor-pd.cytogenetics.array/pre-unlink.sh new file mode 100644 index 0000000000000..301fc97fa1643 --- /dev/null +++ b/recipes/bioconductor-pd.cytogenetics.array/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.cytogenetics.array diff --git a/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..981e995c7ad76 --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.drogene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 67f92a97a5b78a95693edfdd32b67e93 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix DroGene-1_0-st' + diff --git a/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh b/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..e6aba7fd5c973 --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.drogene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drogene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.drogene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.0.st/bioconductor-pd.drogene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="67f92a97a5b78a95693edfdd32b67e93" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.drogene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.drogene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..64e99aaf08cff --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.drogene.1.0.st diff --git a/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..84a1aa8ee8c82 --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.drogene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5c63236ea91390d49dbabea63a48f0a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix DroGene-1_1-st' + diff --git a/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh b/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..06600c1985315 --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.drogene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drogene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.drogene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drogene.1.1.st/bioconductor-pd.drogene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="5c63236ea91390d49dbabea63a48f0a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.drogene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.drogene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..73bd8df6ef660 --- /dev/null +++ b/recipes/bioconductor-pd.drogene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.drogene.1.1.st diff --git a/recipes/bioconductor-pd.drosgenome1/meta.yaml b/recipes/bioconductor-pd.drosgenome1/meta.yaml new file mode 100644 index 0000000000000..8f92379750aab --- /dev/null +++ b/recipes/bioconductor-pd.drosgenome1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.drosgenome1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 59c1a37a7d6a43fc70ff8756bf1195ef +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name DrosGenome1' + diff --git a/recipes/bioconductor-pd.drosgenome1/post-link.sh b/recipes/bioconductor-pd.drosgenome1/post-link.sh new file mode 100644 index 0000000000000..8cb838a5ebf40 --- /dev/null +++ b/recipes/bioconductor-pd.drosgenome1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.drosgenome1_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drosgenome1_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.drosgenome1_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drosgenome1/bioconductor-pd.drosgenome1_3.12.0_src_all.tar.gz" +) +MD5="59c1a37a7d6a43fc70ff8756bf1195ef" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.drosgenome1/pre-unlink.sh b/recipes/bioconductor-pd.drosgenome1/pre-unlink.sh new file mode 100644 index 0000000000000..eff0f1a242067 --- /dev/null +++ b/recipes/bioconductor-pd.drosgenome1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.drosgenome1 diff --git a/recipes/bioconductor-pd.drosophila.2/meta.yaml b/recipes/bioconductor-pd.drosophila.2/meta.yaml new file mode 100644 index 0000000000000..532ef5e05999b --- /dev/null +++ b/recipes/bioconductor-pd.drosophila.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.drosophila.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ddb821e35e722af8dcf0807c6da4fac1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Drosophila_2' + diff --git a/recipes/bioconductor-pd.drosophila.2/post-link.sh b/recipes/bioconductor-pd.drosophila.2/post-link.sh new file mode 100644 index 0000000000000..1df4b0a76f7b9 --- /dev/null +++ b/recipes/bioconductor-pd.drosophila.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.drosophila.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.drosophila.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.drosophila.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.drosophila.2/bioconductor-pd.drosophila.2_3.12.0_src_all.tar.gz" +) +MD5="ddb821e35e722af8dcf0807c6da4fac1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.drosophila.2/pre-unlink.sh b/recipes/bioconductor-pd.drosophila.2/pre-unlink.sh new file mode 100644 index 0000000000000..d15db207a78c3 --- /dev/null +++ b/recipes/bioconductor-pd.drosophila.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.drosophila.2 diff --git a/recipes/bioconductor-pd.e.coli.2/meta.yaml b/recipes/bioconductor-pd.e.coli.2/meta.yaml new file mode 100644 index 0000000000000..2596518c7ecd3 --- /dev/null +++ b/recipes/bioconductor-pd.e.coli.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.e.coli.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9176faa60a0c252a815b2a74d2f63dd4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name E_coli_2' + diff --git a/recipes/bioconductor-pd.e.coli.2/post-link.sh b/recipes/bioconductor-pd.e.coli.2/post-link.sh new file mode 100644 index 0000000000000..2200e5e2443a1 --- /dev/null +++ b/recipes/bioconductor-pd.e.coli.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.e.coli.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.e.coli.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.e.coli.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.e.coli.2/bioconductor-pd.e.coli.2_3.12.0_src_all.tar.gz" +) +MD5="9176faa60a0c252a815b2a74d2f63dd4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.e.coli.2/pre-unlink.sh b/recipes/bioconductor-pd.e.coli.2/pre-unlink.sh new file mode 100644 index 0000000000000..05203dcf5e70f --- /dev/null +++ b/recipes/bioconductor-pd.e.coli.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.e.coli.2 diff --git a/recipes/bioconductor-pd.ecoli.asv2/meta.yaml b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml new file mode 100644 index 0000000000000..44ad5eb0fadd6 --- /dev/null +++ b/recipes/bioconductor-pd.ecoli.asv2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ecoli.asv2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d789ddf5a178a9a50c5587ee3ab294a4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Ecoli_ASv2' + diff --git a/recipes/bioconductor-pd.ecoli.asv2/post-link.sh b/recipes/bioconductor-pd.ecoli.asv2/post-link.sh new file mode 100644 index 0000000000000..0fd3583bcd5ee --- /dev/null +++ b/recipes/bioconductor-pd.ecoli.asv2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ecoli.asv2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ecoli.asv2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ecoli.asv2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli.asv2/bioconductor-pd.ecoli.asv2_3.12.0_src_all.tar.gz" +) +MD5="d789ddf5a178a9a50c5587ee3ab294a4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ecoli.asv2/pre-unlink.sh b/recipes/bioconductor-pd.ecoli.asv2/pre-unlink.sh new file mode 100644 index 0000000000000..ed724593638be --- /dev/null +++ b/recipes/bioconductor-pd.ecoli.asv2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ecoli.asv2 diff --git a/recipes/bioconductor-pd.ecoli/meta.yaml b/recipes/bioconductor-pd.ecoli/meta.yaml new file mode 100644 index 0000000000000..5df2ad1927929 --- /dev/null +++ b/recipes/bioconductor-pd.ecoli/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ecoli" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 077e91b2567a32780305f0fb6b126fe9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Ecoli' + diff --git a/recipes/bioconductor-pd.ecoli/post-link.sh b/recipes/bioconductor-pd.ecoli/post-link.sh new file mode 100644 index 0000000000000..6c965575707d7 --- /dev/null +++ b/recipes/bioconductor-pd.ecoli/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ecoli_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ecoli_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ecoli_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ecoli/bioconductor-pd.ecoli_3.12.0_src_all.tar.gz" +) +MD5="077e91b2567a32780305f0fb6b126fe9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ecoli/pre-unlink.sh b/recipes/bioconductor-pd.ecoli/pre-unlink.sh new file mode 100644 index 0000000000000..629348b9b17f9 --- /dev/null +++ b/recipes/bioconductor-pd.ecoli/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ecoli diff --git a/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..73b38012c45aa --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.elegene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b6110c58d5964703c7117e5e0668c901 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix EleGene-1_0-st' + diff --git a/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh b/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..f43b260f75e59 --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.elegene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.elegene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.elegene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.0.st/bioconductor-pd.elegene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="b6110c58d5964703c7117e5e0668c901" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.elegene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.elegene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..8fb33dfa2eda1 --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.elegene.1.0.st diff --git a/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..84e7b1a37ba53 --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.elegene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1dbe166ea347a5a7e240db925d2081c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix EleGene-1_1-st' + diff --git a/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh b/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..5a7a686c1639e --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.elegene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.elegene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.elegene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.elegene.1.1.st/bioconductor-pd.elegene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="1dbe166ea347a5a7e240db925d2081c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.elegene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.elegene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..1c19f4130ed71 --- /dev/null +++ b/recipes/bioconductor-pd.elegene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.elegene.1.1.st diff --git a/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..2ce1c9c7caea3 --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.equgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3448f36fdb899f04702be37ffab4c4c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix EquGene-1_0-st' + diff --git a/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..7a4502a6b4c8b --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.equgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.equgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.equgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.0.st/bioconductor-pd.equgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="3448f36fdb899f04702be37ffab4c4c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.equgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.equgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..8821e1b1b6113 --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.equgene.1.0.st diff --git a/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..84bdbe4e0fc01 --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.equgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bed32525513ce25f14d433ce805e7d6c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix EquGene-1_1-st' + diff --git a/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..db87d4d745e85 --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.equgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.equgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.equgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.equgene.1.1.st/bioconductor-pd.equgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="bed32525513ce25f14d433ce805e7d6c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.equgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.equgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..7d9c2b94f7b13 --- /dev/null +++ b/recipes/bioconductor-pd.equgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.equgene.1.1.st diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml new file mode 100644 index 0000000000000..f096ba5520db5 --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.3" %} +{% set name = "pd.feinberg.hg18.me.hx1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b6eeaf79671bab6f597965009516ce57 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen feinberg_hg18_me_hx1' + diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh new file mode 100644 index 0000000000000..c87c99640012f --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" + "https://bioarchive.galaxyproject.org/pd.feinberg.hg18.me.hx1_0.99.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.hg18.me.hx1/bioconductor-pd.feinberg.hg18.me.hx1_0.99.3_src_all.tar.gz" +) +MD5="b6eeaf79671bab6f597965009516ce57" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.feinberg.hg18.me.hx1/pre-unlink.sh b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/pre-unlink.sh new file mode 100644 index 0000000000000..a52cd1ce2457f --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.hg18.me.hx1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.feinberg.hg18.me.hx1 diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml new file mode 100644 index 0000000000000..e2a6a6fc7e6e9 --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.99.3" %} +{% set name = "pd.feinberg.mm8.me.hx1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7332102b69fc9ee087f52d3cdc311d00 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.7-1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen feinberg_mm8_me_hx1' + diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh new file mode 100644 index 0000000000000..280587ed11eaf --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" + "https://bioarchive.galaxyproject.org/pd.feinberg.mm8.me.hx1_0.99.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.feinberg.mm8.me.hx1/bioconductor-pd.feinberg.mm8.me.hx1_0.99.3_src_all.tar.gz" +) +MD5="7332102b69fc9ee087f52d3cdc311d00" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.feinberg.mm8.me.hx1/pre-unlink.sh b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/pre-unlink.sh new file mode 100644 index 0000000000000..ef4bd79ef3b85 --- /dev/null +++ b/recipes/bioconductor-pd.feinberg.mm8.me.hx1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.feinberg.mm8.me.hx1 diff --git a/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..d39e3885d27ad --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.felgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b7ac0a5cbde5f248aac5d0a7422bd88d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix FelGene-1_0-st' + diff --git a/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..f03580f8ecaf9 --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.felgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.felgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.felgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.0.st/bioconductor-pd.felgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="b7ac0a5cbde5f248aac5d0a7422bd88d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.felgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.felgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..995d154a3c4da --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.felgene.1.0.st diff --git a/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..5309cae021ad0 --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.felgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 734807a7f3608f6c44c76df7eee04c99 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix FelGene-1_1-st' + diff --git a/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..54221bf99ce9d --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.felgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.felgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.felgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.felgene.1.1.st/bioconductor-pd.felgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="734807a7f3608f6c44c76df7eee04c99" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.felgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.felgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..ee8add3b99c88 --- /dev/null +++ b/recipes/bioconductor-pd.felgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.felgene.1.1.st diff --git a/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..7d7f124e88b7f --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.fingene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b79e4f8a52cad3b62e32401bbe74603d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix FinGene-1_0-st' + diff --git a/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh b/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..3eaab1bffc31b --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.fingene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.fingene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.fingene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.0.st/bioconductor-pd.fingene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="b79e4f8a52cad3b62e32401bbe74603d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.fingene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.fingene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..e6d3f7180f45a --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.fingene.1.0.st diff --git a/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..6675c46159c45 --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.fingene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 29030b14a0e8f8073874fb694a8c0c09 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix FinGene-1_1-st' + diff --git a/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh b/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..f372ffd255515 --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.fingene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.fingene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.fingene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.fingene.1.1.st/bioconductor-pd.fingene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="29030b14a0e8f8073874fb694a8c0c09" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.fingene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.fingene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..4d37af75e879f --- /dev/null +++ b/recipes/bioconductor-pd.fingene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.fingene.1.1.st diff --git a/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml new file mode 100644 index 0000000000000..e0ca4764fa82f --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.5/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.genomewidesnp.5" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d02255c861e82fca6a7445ada0c69e5d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix GenomeWideSNP_5' + diff --git a/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh b/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh new file mode 100644 index 0000000000000..c375c3508fecc --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.5/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.genomewidesnp.5_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.genomewidesnp.5_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.genomewidesnp.5_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.5/bioconductor-pd.genomewidesnp.5_3.14.1_src_all.tar.gz" +) +MD5="d02255c861e82fca6a7445ada0c69e5d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.genomewidesnp.5/pre-unlink.sh b/recipes/bioconductor-pd.genomewidesnp.5/pre-unlink.sh new file mode 100644 index 0000000000000..a60517e021975 --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.5/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.genomewidesnp.5 diff --git a/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml new file mode 100644 index 0000000000000..31d01a87aa181 --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.6/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.genomewidesnp.6" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6e5369234e251c763f4f6c0220fbcb0c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix GenomeWideSNP_6' + diff --git a/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh b/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh new file mode 100644 index 0000000000000..0102fa0221f65 --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.6/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.genomewidesnp.6_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.genomewidesnp.6_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.genomewidesnp.6_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.genomewidesnp.6/bioconductor-pd.genomewidesnp.6_3.14.1_src_all.tar.gz" +) +MD5="6e5369234e251c763f4f6c0220fbcb0c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.genomewidesnp.6/pre-unlink.sh b/recipes/bioconductor-pd.genomewidesnp.6/pre-unlink.sh new file mode 100644 index 0000000000000..fbfb859d9f4fe --- /dev/null +++ b/recipes/bioconductor-pd.genomewidesnp.6/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.genomewidesnp.6 diff --git a/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..70a23e632291d --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.guigene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 29fe31499931836af72ddd0c7d06acfa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix GuiGene-1_0-st' + diff --git a/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..3d4f555fa42ba --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.guigene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.guigene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.guigene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.0.st/bioconductor-pd.guigene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="29fe31499931836af72ddd0c7d06acfa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.guigene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.guigene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..18a0df0bb88a8 --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.guigene.1.0.st diff --git a/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..b41b1b441ca0f --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.guigene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: aa3e0389c596a3676322104de5ad2358 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix GuiGene-1_1-st' + diff --git a/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..ffa298288dd39 --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.guigene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.guigene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.guigene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.guigene.1.1.st/bioconductor-pd.guigene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="aa3e0389c596a3676322104de5ad2358" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.guigene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.guigene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..de551675bd667 --- /dev/null +++ b/recipes/bioconductor-pd.guigene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.guigene.1.1.st diff --git a/recipes/bioconductor-pd.hc.g110/meta.yaml b/recipes/bioconductor-pd.hc.g110/meta.yaml new file mode 100644 index 0000000000000..bcf46a6f68877 --- /dev/null +++ b/recipes/bioconductor-pd.hc.g110/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hc.g110" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5c5418c588ed28e2fa088c7952c48b91 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HC_G110' + diff --git a/recipes/bioconductor-pd.hc.g110/post-link.sh b/recipes/bioconductor-pd.hc.g110/post-link.sh new file mode 100644 index 0000000000000..9137af9411e05 --- /dev/null +++ b/recipes/bioconductor-pd.hc.g110/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hc.g110_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hc.g110_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hc.g110_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hc.g110/bioconductor-pd.hc.g110_3.12.0_src_all.tar.gz" +) +MD5="5c5418c588ed28e2fa088c7952c48b91" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hc.g110/pre-unlink.sh b/recipes/bioconductor-pd.hc.g110/pre-unlink.sh new file mode 100644 index 0000000000000..02a9e0f1fd9a9 --- /dev/null +++ b/recipes/bioconductor-pd.hc.g110/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hc.g110 diff --git a/recipes/bioconductor-pd.hg.focus/meta.yaml b/recipes/bioconductor-pd.hg.focus/meta.yaml new file mode 100644 index 0000000000000..d8f0a81a7cf85 --- /dev/null +++ b/recipes/bioconductor-pd.hg.focus/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.focus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a89f344ae7ff8061a8e7968f155f4bcf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-Focus' + diff --git a/recipes/bioconductor-pd.hg.focus/post-link.sh b/recipes/bioconductor-pd.hg.focus/post-link.sh new file mode 100644 index 0000000000000..b459c1c819b82 --- /dev/null +++ b/recipes/bioconductor-pd.hg.focus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.focus_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.focus_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.focus_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.focus/bioconductor-pd.hg.focus_3.12.0_src_all.tar.gz" +) +MD5="a89f344ae7ff8061a8e7968f155f4bcf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.focus/pre-unlink.sh b/recipes/bioconductor-pd.hg.focus/pre-unlink.sh new file mode 100644 index 0000000000000..1792c801fc8c8 --- /dev/null +++ b/recipes/bioconductor-pd.hg.focus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.focus diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml new file mode 100644 index 0000000000000..78adae80ac122 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133.plus.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u133.plus.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8a87aa63c04e84266962bdde5226c06c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U133_Plus_2' + diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh b/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh new file mode 100644 index 0000000000000..a25d5c7815f34 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133.plus.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u133.plus.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133.plus.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u133.plus.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133.plus.2/bioconductor-pd.hg.u133.plus.2_3.12.0_src_all.tar.gz" +) +MD5="8a87aa63c04e84266962bdde5226c06c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u133.plus.2/pre-unlink.sh b/recipes/bioconductor-pd.hg.u133.plus.2/pre-unlink.sh new file mode 100644 index 0000000000000..f0e2c54868234 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133.plus.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u133.plus.2 diff --git a/recipes/bioconductor-pd.hg.u133a.2/meta.yaml b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml new file mode 100644 index 0000000000000..671580261d468 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u133a.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a7941473bf081831fad4f4412023d9ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A_2' + diff --git a/recipes/bioconductor-pd.hg.u133a.2/post-link.sh b/recipes/bioconductor-pd.hg.u133a.2/post-link.sh new file mode 100644 index 0000000000000..f9948b8a72d3f --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u133a.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u133a.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.2/bioconductor-pd.hg.u133a.2_3.12.0_src_all.tar.gz" +) +MD5="a7941473bf081831fad4f4412023d9ee" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u133a.2/pre-unlink.sh b/recipes/bioconductor-pd.hg.u133a.2/pre-unlink.sh new file mode 100644 index 0000000000000..4253b5e8696c9 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u133a.2 diff --git a/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml new file mode 100644 index 0000000000000..3ae9c2cc9d075 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.tag/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u133a.tag" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e090383098d6e1062b290889fba065d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A_tag' + diff --git a/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh b/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh new file mode 100644 index 0000000000000..f79e46beee695 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.tag/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u133a.tag_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a.tag_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u133a.tag_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a.tag/bioconductor-pd.hg.u133a.tag_3.12.0_src_all.tar.gz" +) +MD5="e090383098d6e1062b290889fba065d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u133a.tag/pre-unlink.sh b/recipes/bioconductor-pd.hg.u133a.tag/pre-unlink.sh new file mode 100644 index 0000000000000..c91ff83cd0082 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a.tag/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u133a.tag diff --git a/recipes/bioconductor-pd.hg.u133a/meta.yaml b/recipes/bioconductor-pd.hg.u133a/meta.yaml new file mode 100644 index 0000000000000..0c3b21de43fa9 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u133a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 05b4521f65ab294a5040a0c60198d22c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U133A' + diff --git a/recipes/bioconductor-pd.hg.u133a/post-link.sh b/recipes/bioconductor-pd.hg.u133a/post-link.sh new file mode 100644 index 0000000000000..cb30da469c283 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u133a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u133a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133a/bioconductor-pd.hg.u133a_3.12.0_src_all.tar.gz" +) +MD5="05b4521f65ab294a5040a0c60198d22c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u133a/pre-unlink.sh b/recipes/bioconductor-pd.hg.u133a/pre-unlink.sh new file mode 100644 index 0000000000000..71696f60ed5bd --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u133a diff --git a/recipes/bioconductor-pd.hg.u133b/meta.yaml b/recipes/bioconductor-pd.hg.u133b/meta.yaml new file mode 100644 index 0000000000000..e583674f2c5a7 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u133b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c5eac82ad7480571b9f2b442b4a8faa6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U133B' + diff --git a/recipes/bioconductor-pd.hg.u133b/post-link.sh b/recipes/bioconductor-pd.hg.u133b/post-link.sh new file mode 100644 index 0000000000000..9d3f10b09a49c --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u133b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u133b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u133b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u133b/bioconductor-pd.hg.u133b_3.12.0_src_all.tar.gz" +) +MD5="c5eac82ad7480571b9f2b442b4a8faa6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u133b/pre-unlink.sh b/recipes/bioconductor-pd.hg.u133b/pre-unlink.sh new file mode 100644 index 0000000000000..3e34de87e7a05 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u133b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u133b diff --git a/recipes/bioconductor-pd.hg.u219/meta.yaml b/recipes/bioconductor-pd.hg.u219/meta.yaml new file mode 100644 index 0000000000000..71afd04fa8078 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u219/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u219" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dab073d315af47ff3001c72a6d1e7972 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG-U219' + diff --git a/recipes/bioconductor-pd.hg.u219/post-link.sh b/recipes/bioconductor-pd.hg.u219/post-link.sh new file mode 100644 index 0000000000000..568dc042368e9 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u219/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u219_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u219_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u219_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u219/bioconductor-pd.hg.u219_3.12.0_src_all.tar.gz" +) +MD5="dab073d315af47ff3001c72a6d1e7972" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u219/pre-unlink.sh b/recipes/bioconductor-pd.hg.u219/pre-unlink.sh new file mode 100644 index 0000000000000..1811d84238f87 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u219/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u219 diff --git a/recipes/bioconductor-pd.hg.u95a/meta.yaml b/recipes/bioconductor-pd.hg.u95a/meta.yaml new file mode 100644 index 0000000000000..a0e7b7a5a45f8 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a9ad7d6a085e0e3ed7623902e7810da0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95A' + diff --git a/recipes/bioconductor-pd.hg.u95a/post-link.sh b/recipes/bioconductor-pd.hg.u95a/post-link.sh new file mode 100644 index 0000000000000..b7b663d097dd3 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95a/bioconductor-pd.hg.u95a_3.12.0_src_all.tar.gz" +) +MD5="a9ad7d6a085e0e3ed7623902e7810da0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95a/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95a/pre-unlink.sh new file mode 100644 index 0000000000000..02d239e1edd5c --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95a diff --git a/recipes/bioconductor-pd.hg.u95av2/meta.yaml b/recipes/bioconductor-pd.hg.u95av2/meta.yaml new file mode 100644 index 0000000000000..cab257d09afad --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95av2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95av2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3a4182b529bc07ec91277a95b1462468 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95Av2' + diff --git a/recipes/bioconductor-pd.hg.u95av2/post-link.sh b/recipes/bioconductor-pd.hg.u95av2/post-link.sh new file mode 100644 index 0000000000000..9e7d9913d7b5b --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95av2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95av2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95av2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95av2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95av2/bioconductor-pd.hg.u95av2_3.12.0_src_all.tar.gz" +) +MD5="3a4182b529bc07ec91277a95b1462468" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95av2/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95av2/pre-unlink.sh new file mode 100644 index 0000000000000..5e84b63d94b27 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95av2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95av2 diff --git a/recipes/bioconductor-pd.hg.u95b/meta.yaml b/recipes/bioconductor-pd.hg.u95b/meta.yaml new file mode 100644 index 0000000000000..a8b20f16bfcee --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a7f10f91e920e191c5009fac8ca79c24 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95B' + diff --git a/recipes/bioconductor-pd.hg.u95b/post-link.sh b/recipes/bioconductor-pd.hg.u95b/post-link.sh new file mode 100644 index 0000000000000..31329bba8a115 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95b/bioconductor-pd.hg.u95b_3.12.0_src_all.tar.gz" +) +MD5="a7f10f91e920e191c5009fac8ca79c24" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95b/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95b/pre-unlink.sh new file mode 100644 index 0000000000000..bce2cc3778e5e --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95b diff --git a/recipes/bioconductor-pd.hg.u95c/meta.yaml b/recipes/bioconductor-pd.hg.u95c/meta.yaml new file mode 100644 index 0000000000000..1197616ee4bf0 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95c/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95c" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 85655bf7a9ecd7aaa867e05899c5e3e4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95C' + diff --git a/recipes/bioconductor-pd.hg.u95c/post-link.sh b/recipes/bioconductor-pd.hg.u95c/post-link.sh new file mode 100644 index 0000000000000..37f08145fbbbf --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95c/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95c_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95c_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95c_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95c/bioconductor-pd.hg.u95c_3.12.0_src_all.tar.gz" +) +MD5="85655bf7a9ecd7aaa867e05899c5e3e4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95c/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95c/pre-unlink.sh new file mode 100644 index 0000000000000..4b168e4858f7a --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95c/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95c diff --git a/recipes/bioconductor-pd.hg.u95d/meta.yaml b/recipes/bioconductor-pd.hg.u95d/meta.yaml new file mode 100644 index 0000000000000..854904b189322 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95d/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95d" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 946701ecfc9cccb46aaeb57a4d6fe1c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95D' + diff --git a/recipes/bioconductor-pd.hg.u95d/post-link.sh b/recipes/bioconductor-pd.hg.u95d/post-link.sh new file mode 100644 index 0000000000000..4481a3b1e83f0 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95d/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95d_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95d_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95d_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95d/bioconductor-pd.hg.u95d_3.12.0_src_all.tar.gz" +) +MD5="946701ecfc9cccb46aaeb57a4d6fe1c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95d/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95d/pre-unlink.sh new file mode 100644 index 0000000000000..6190175cc04f1 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95d/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95d diff --git a/recipes/bioconductor-pd.hg.u95e/meta.yaml b/recipes/bioconductor-pd.hg.u95e/meta.yaml new file mode 100644 index 0000000000000..ca1efd9e89962 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95e/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg.u95e" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9295e2fd1b4be6ff58477ea5a5de45ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HG U95E' + diff --git a/recipes/bioconductor-pd.hg.u95e/post-link.sh b/recipes/bioconductor-pd.hg.u95e/post-link.sh new file mode 100644 index 0000000000000..0cc7e31503076 --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95e/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg.u95e_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg.u95e_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg.u95e_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg.u95e/bioconductor-pd.hg.u95e_3.12.0_src_all.tar.gz" +) +MD5="9295e2fd1b4be6ff58477ea5a5de45ee" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg.u95e/pre-unlink.sh b/recipes/bioconductor-pd.hg.u95e/pre-unlink.sh new file mode 100644 index 0000000000000..69d8a8f8e8a2b --- /dev/null +++ b/recipes/bioconductor-pd.hg.u95e/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg.u95e diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml new file mode 100644 index 0000000000000..1c90f86056a36 --- /dev/null +++ b/recipes/bioconductor-pd.hg18.60mer.expr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hg18.60mer.expr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ee8d3813f74edce4e796933aa63999fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for NimbleGen hg18_60mer_expr' + diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh b/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh new file mode 100644 index 0000000000000..3921c9d1a6f2a --- /dev/null +++ b/recipes/bioconductor-pd.hg18.60mer.expr/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hg18.60mer.expr_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hg18.60mer.expr_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hg18.60mer.expr_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hg18.60mer.expr/bioconductor-pd.hg18.60mer.expr_3.12.0_src_all.tar.gz" +) +MD5="ee8d3813f74edce4e796933aa63999fb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hg18.60mer.expr/pre-unlink.sh b/recipes/bioconductor-pd.hg18.60mer.expr/pre-unlink.sh new file mode 100644 index 0000000000000..7402dd7121654 --- /dev/null +++ b/recipes/bioconductor-pd.hg18.60mer.expr/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hg18.60mer.expr diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml new file mode 100644 index 0000000000000..be2bbe27053b3 --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ht.hg.u133.plus.pm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5b1c3dd0ab3f8b21154982c197512a7c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133_Plus_PM' + diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh new file mode 100644 index 0000000000000..cd9e2bfda9a6f --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ht.hg.u133.plus.pm_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133.plus.pm/bioconductor-pd.ht.hg.u133.plus.pm_3.12.0_src_all.tar.gz" +) +MD5="5b1c3dd0ab3f8b21154982c197512a7c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ht.hg.u133.plus.pm/pre-unlink.sh b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/pre-unlink.sh new file mode 100644 index 0000000000000..25d51498c0871 --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133.plus.pm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ht.hg.u133.plus.pm diff --git a/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml new file mode 100644 index 0000000000000..1f30b170f4240 --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ht.hg.u133a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 80a82f43083f95e1e9f5e2e2da2e288e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HT_HG-U133A' + diff --git a/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh b/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh new file mode 100644 index 0000000000000..c15cfd5c6df0b --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ht.hg.u133a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.hg.u133a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ht.hg.u133a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.hg.u133a/bioconductor-pd.ht.hg.u133a_3.12.0_src_all.tar.gz" +) +MD5="80a82f43083f95e1e9f5e2e2da2e288e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ht.hg.u133a/pre-unlink.sh b/recipes/bioconductor-pd.ht.hg.u133a/pre-unlink.sh new file mode 100644 index 0000000000000..412c07aba87c1 --- /dev/null +++ b/recipes/bioconductor-pd.ht.hg.u133a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ht.hg.u133a diff --git a/recipes/bioconductor-pd.ht.mg.430a/meta.yaml b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml new file mode 100644 index 0000000000000..7fef8da9d1497 --- /dev/null +++ b/recipes/bioconductor-pd.ht.mg.430a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ht.mg.430a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 65ea4fae22d21ad70998ba3ea034dcc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name HT_MG-430A' + diff --git a/recipes/bioconductor-pd.ht.mg.430a/post-link.sh b/recipes/bioconductor-pd.ht.mg.430a/post-link.sh new file mode 100644 index 0000000000000..fb26eeb510fde --- /dev/null +++ b/recipes/bioconductor-pd.ht.mg.430a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ht.mg.430a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ht.mg.430a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ht.mg.430a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ht.mg.430a/bioconductor-pd.ht.mg.430a_3.12.0_src_all.tar.gz" +) +MD5="65ea4fae22d21ad70998ba3ea034dcc0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ht.mg.430a/pre-unlink.sh b/recipes/bioconductor-pd.ht.mg.430a/pre-unlink.sh new file mode 100644 index 0000000000000..538854e663ea7 --- /dev/null +++ b/recipes/bioconductor-pd.ht.mg.430a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ht.mg.430a diff --git a/recipes/bioconductor-pd.hta.2.0/meta.yaml b/recipes/bioconductor-pd.hta.2.0/meta.yaml new file mode 100644 index 0000000000000..22fd2e74bbc83 --- /dev/null +++ b/recipes/bioconductor-pd.hta.2.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.2" %} +{% set name = "pd.hta.2.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8e13f85ece49c38da73eaf7b2247f5f0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HTA-2_0' + diff --git a/recipes/bioconductor-pd.hta.2.0/post-link.sh b/recipes/bioconductor-pd.hta.2.0/post-link.sh new file mode 100644 index 0000000000000..f344df59892aa --- /dev/null +++ b/recipes/bioconductor-pd.hta.2.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hta.2.0_3.12.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hta.2.0_3.12.2.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hta.2.0_3.12.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hta.2.0/bioconductor-pd.hta.2.0_3.12.2_src_all.tar.gz" +) +MD5="8e13f85ece49c38da73eaf7b2247f5f0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hta.2.0/pre-unlink.sh b/recipes/bioconductor-pd.hta.2.0/pre-unlink.sh new file mode 100644 index 0000000000000..d38d0816f68dc --- /dev/null +++ b/recipes/bioconductor-pd.hta.2.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hta.2.0 diff --git a/recipes/bioconductor-pd.hu6800/meta.yaml b/recipes/bioconductor-pd.hu6800/meta.yaml new file mode 100644 index 0000000000000..1f61fa9012872 --- /dev/null +++ b/recipes/bioconductor-pd.hu6800/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.hu6800" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9a3a3edde6d6f31b9e90dc32aa68875d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Hu6800' + diff --git a/recipes/bioconductor-pd.hu6800/post-link.sh b/recipes/bioconductor-pd.hu6800/post-link.sh new file mode 100644 index 0000000000000..804544b0486c9 --- /dev/null +++ b/recipes/bioconductor-pd.hu6800/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hu6800_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hu6800_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hu6800_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hu6800/bioconductor-pd.hu6800_3.12.0_src_all.tar.gz" +) +MD5="9a3a3edde6d6f31b9e90dc32aa68875d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hu6800/pre-unlink.sh b/recipes/bioconductor-pd.hu6800/pre-unlink.sh new file mode 100644 index 0000000000000..c5322fb8cccb8 --- /dev/null +++ b/recipes/bioconductor-pd.hu6800/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hu6800 diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml new file mode 100644 index 0000000000000..c7c78ec2b31ac --- /dev/null +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.huex.1.0.st.v2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f4c4836c53447890b75b012efbdef3e9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HuEx-1_0-st-v2' + diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh b/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh new file mode 100644 index 0000000000000..23d37dc1adba3 --- /dev/null +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.huex.1.0.st.v2_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.huex.1.0.st.v2_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.huex.1.0.st.v2_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.huex.1.0.st.v2/bioconductor-pd.huex.1.0.st.v2_3.14.1_src_all.tar.gz" +) +MD5="f4c4836c53447890b75b012efbdef3e9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.huex.1.0.st.v2/pre-unlink.sh b/recipes/bioconductor-pd.huex.1.0.st.v2/pre-unlink.sh new file mode 100644 index 0000000000000..ea1fe6dd52d9b --- /dev/null +++ b/recipes/bioconductor-pd.huex.1.0.st.v2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.huex.1.0.st.v2 diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml new file mode 100644 index 0000000000000..9f01db74671ee --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.hugene.1.0.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8cb24c351aee5bf216180e4b19742506 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HuGene-1_0-st-v1' + diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh new file mode 100644 index 0000000000000..c58169067d1e4 --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hugene.1.0.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.0.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hugene.1.0.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.0.st.v1/bioconductor-pd.hugene.1.0.st.v1_3.14.1_src_all.tar.gz" +) +MD5="8cb24c351aee5bf216180e4b19742506" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hugene.1.0.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.hugene.1.0.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..9faacc68a32ec --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.0.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hugene.1.0.st.v1 diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml new file mode 100644 index 0000000000000..089ace99adb3e --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.hugene.1.1.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7a17ee4f7d258792be1d21be7d03deb0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HuGene-1_1-st-v1' + diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh new file mode 100644 index 0000000000000..a474fb42bbf0e --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hugene.1.1.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.1.1.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hugene.1.1.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.1.1.st.v1/bioconductor-pd.hugene.1.1.st.v1_3.14.1_src_all.tar.gz" +) +MD5="7a17ee4f7d258792be1d21be7d03deb0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hugene.1.1.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.hugene.1.1.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..4f572c16c1b6a --- /dev/null +++ b/recipes/bioconductor-pd.hugene.1.1.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hugene.1.1.st.v1 diff --git a/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml new file mode 100644 index 0000000000000..45a8dd6e0abdb --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.hugene.2.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e484209aa0c2a839c3445d91c1a799ce +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HuGene-2_0-st' + diff --git a/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh b/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh new file mode 100644 index 0000000000000..4ef0d6c6405c8 --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hugene.2.0.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.2.0.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hugene.2.0.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.0.st/bioconductor-pd.hugene.2.0.st_3.14.1_src_all.tar.gz" +) +MD5="e484209aa0c2a839c3445d91c1a799ce" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hugene.2.0.st/pre-unlink.sh b/recipes/bioconductor-pd.hugene.2.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..79fd7155bb7fc --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hugene.2.0.st diff --git a/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml new file mode 100644 index 0000000000000..3c469087ecb8f --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.hugene.2.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 164227f10b87f87059e4ae27b40f5238 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix HuGene-2_1-st' + diff --git a/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh b/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh new file mode 100644 index 0000000000000..22b5fe3db8493 --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.hugene.2.1.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.hugene.2.1.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.hugene.2.1.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.hugene.2.1.st/bioconductor-pd.hugene.2.1.st_3.14.1_src_all.tar.gz" +) +MD5="164227f10b87f87059e4ae27b40f5238" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.hugene.2.1.st/pre-unlink.sh b/recipes/bioconductor-pd.hugene.2.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..e9e5ce7ba7fce --- /dev/null +++ b/recipes/bioconductor-pd.hugene.2.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.hugene.2.1.st diff --git a/recipes/bioconductor-pd.maize/meta.yaml b/recipes/bioconductor-pd.maize/meta.yaml new file mode 100644 index 0000000000000..b023717c7fdb4 --- /dev/null +++ b/recipes/bioconductor-pd.maize/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.maize" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a1689518c8525d3dfa97e870f90b7a7b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Maize' + diff --git a/recipes/bioconductor-pd.maize/post-link.sh b/recipes/bioconductor-pd.maize/post-link.sh new file mode 100644 index 0000000000000..af49bbd2cbd2c --- /dev/null +++ b/recipes/bioconductor-pd.maize/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.maize_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.maize_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.maize_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.maize/bioconductor-pd.maize_3.12.0_src_all.tar.gz" +) +MD5="a1689518c8525d3dfa97e870f90b7a7b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.maize/pre-unlink.sh b/recipes/bioconductor-pd.maize/pre-unlink.sh new file mode 100644 index 0000000000000..ad74452a858a1 --- /dev/null +++ b/recipes/bioconductor-pd.maize/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.maize diff --git a/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml new file mode 100644 index 0000000000000..04c36cec81448 --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.nsp/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mapping250k.nsp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2786d00e1d621a9c415a599b4afe838b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Mapping250K_Nsp' + diff --git a/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh b/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh new file mode 100644 index 0000000000000..0919d44f63b4a --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.nsp/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mapping250k.nsp_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping250k.nsp_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mapping250k.nsp_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.nsp/bioconductor-pd.mapping250k.nsp_3.12.0_src_all.tar.gz" +) +MD5="2786d00e1d621a9c415a599b4afe838b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mapping250k.nsp/pre-unlink.sh b/recipes/bioconductor-pd.mapping250k.nsp/pre-unlink.sh new file mode 100644 index 0000000000000..bf09b77566f9e --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.nsp/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mapping250k.nsp diff --git a/recipes/bioconductor-pd.mapping250k.sty/meta.yaml b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml new file mode 100644 index 0000000000000..b6538eae6d40e --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.sty/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mapping250k.sty" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0db5992855eaf9b8f61f8bc2e57ef347 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Mapping250K_Sty' + diff --git a/recipes/bioconductor-pd.mapping250k.sty/post-link.sh b/recipes/bioconductor-pd.mapping250k.sty/post-link.sh new file mode 100644 index 0000000000000..dd68cb1b2fc42 --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.sty/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mapping250k.sty_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping250k.sty_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mapping250k.sty_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping250k.sty/bioconductor-pd.mapping250k.sty_3.12.0_src_all.tar.gz" +) +MD5="0db5992855eaf9b8f61f8bc2e57ef347" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mapping250k.sty/pre-unlink.sh b/recipes/bioconductor-pd.mapping250k.sty/pre-unlink.sh new file mode 100644 index 0000000000000..1a70feaf16926 --- /dev/null +++ b/recipes/bioconductor-pd.mapping250k.sty/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mapping250k.sty diff --git a/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml new file mode 100644 index 0000000000000..a20f1c299ae2e --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.hind240/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mapping50k.hind240" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 83615dcb01eb381f0c69e07504809094 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Mapping50K_Hind240' + diff --git a/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh b/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh new file mode 100644 index 0000000000000..85866da94c21e --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.hind240/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mapping50k.hind240_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping50k.hind240_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mapping50k.hind240_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.hind240/bioconductor-pd.mapping50k.hind240_3.12.0_src_all.tar.gz" +) +MD5="83615dcb01eb381f0c69e07504809094" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mapping50k.hind240/pre-unlink.sh b/recipes/bioconductor-pd.mapping50k.hind240/pre-unlink.sh new file mode 100644 index 0000000000000..252639aba0a9a --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.hind240/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mapping50k.hind240 diff --git a/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml new file mode 100644 index 0000000000000..2af765f8663e5 --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.xba240/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mapping50k.xba240" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eb0f9250fe0d7b590ca9938fee88f2e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix Mapping50K_Xba240' + diff --git a/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh b/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh new file mode 100644 index 0000000000000..fc37c8c7f2f64 --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.xba240/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mapping50k.xba240_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mapping50k.xba240_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mapping50k.xba240_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mapping50k.xba240/bioconductor-pd.mapping50k.xba240_3.12.0_src_all.tar.gz" +) +MD5="eb0f9250fe0d7b590ca9938fee88f2e7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mapping50k.xba240/pre-unlink.sh b/recipes/bioconductor-pd.mapping50k.xba240/pre-unlink.sh new file mode 100644 index 0000000000000..c672dbfbc5004 --- /dev/null +++ b/recipes/bioconductor-pd.mapping50k.xba240/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mapping50k.xba240 diff --git a/recipes/bioconductor-pd.margene.1.0.st/meta.yaml b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..418f148f0ede8 --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.margene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f670b192e4b453f13bb7cae154b5de42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MarGene-1_0-st' + diff --git a/recipes/bioconductor-pd.margene.1.0.st/post-link.sh b/recipes/bioconductor-pd.margene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..ece1638b37566 --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.margene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.margene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.margene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.0.st/bioconductor-pd.margene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="f670b192e4b453f13bb7cae154b5de42" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.margene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.margene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..d0f22bd3ae5d2 --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.margene.1.0.st diff --git a/recipes/bioconductor-pd.margene.1.1.st/meta.yaml b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..be6c3a466e56f --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.margene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: efd71aeb9c5ab36c2ddeccf9cb66ddec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MarGene-1_1-st' + diff --git a/recipes/bioconductor-pd.margene.1.1.st/post-link.sh b/recipes/bioconductor-pd.margene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..61578f865a0ea --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.margene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.margene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.margene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.margene.1.1.st/bioconductor-pd.margene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="efd71aeb9c5ab36c2ddeccf9cb66ddec" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.margene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.margene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..67e98c870fa9a --- /dev/null +++ b/recipes/bioconductor-pd.margene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.margene.1.1.st diff --git a/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..0f915d68abbd9 --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.medgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2a0048ccd5310ec5c45bb691f3c25885 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MedGene-1_0-st' + diff --git a/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..c3f35fe410253 --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.medgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.medgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.0.st/bioconductor-pd.medgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="2a0048ccd5310ec5c45bb691f3c25885" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.medgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.medgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..e82f07b7cd33d --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.medgene.1.0.st diff --git a/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..afd6294028a17 --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.medgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d96894cfea509734af62110311100142 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MedGene-1_1-st' + diff --git a/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..b53d4d2b555af --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.medgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.medgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medgene.1.1.st/bioconductor-pd.medgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="d96894cfea509734af62110311100142" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.medgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.medgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..a95d76aca455b --- /dev/null +++ b/recipes/bioconductor-pd.medgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.medgene.1.1.st diff --git a/recipes/bioconductor-pd.medicago/meta.yaml b/recipes/bioconductor-pd.medicago/meta.yaml new file mode 100644 index 0000000000000..17010967cb4fa --- /dev/null +++ b/recipes/bioconductor-pd.medicago/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.medicago" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0e3f00777919374619a9dc8244167068 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Medicago' + diff --git a/recipes/bioconductor-pd.medicago/post-link.sh b/recipes/bioconductor-pd.medicago/post-link.sh new file mode 100644 index 0000000000000..7792f916f1355 --- /dev/null +++ b/recipes/bioconductor-pd.medicago/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.medicago_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.medicago_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.medicago_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.medicago/bioconductor-pd.medicago_3.12.0_src_all.tar.gz" +) +MD5="0e3f00777919374619a9dc8244167068" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.medicago/pre-unlink.sh b/recipes/bioconductor-pd.medicago/pre-unlink.sh new file mode 100644 index 0000000000000..0affc15636c31 --- /dev/null +++ b/recipes/bioconductor-pd.medicago/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.medicago diff --git a/recipes/bioconductor-pd.mg.u74a/meta.yaml b/recipes/bioconductor-pd.mg.u74a/meta.yaml new file mode 100644 index 0000000000000..932b8798fe557 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a855c7d2b80e9b8f9bbc1a3f83aca799 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74A' + diff --git a/recipes/bioconductor-pd.mg.u74a/post-link.sh b/recipes/bioconductor-pd.mg.u74a/post-link.sh new file mode 100644 index 0000000000000..b339624cb27ec --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74a/bioconductor-pd.mg.u74a_3.12.0_src_all.tar.gz" +) +MD5="a855c7d2b80e9b8f9bbc1a3f83aca799" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74a/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74a/pre-unlink.sh new file mode 100644 index 0000000000000..c41b539ea2da2 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74a diff --git a/recipes/bioconductor-pd.mg.u74av2/meta.yaml b/recipes/bioconductor-pd.mg.u74av2/meta.yaml new file mode 100644 index 0000000000000..4ac48a298231b --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74av2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74av2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 01c6e4da9c2ad0f1939482284dd5b421 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Av2' + diff --git a/recipes/bioconductor-pd.mg.u74av2/post-link.sh b/recipes/bioconductor-pd.mg.u74av2/post-link.sh new file mode 100644 index 0000000000000..be3e7994073e8 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74av2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74av2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74av2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74av2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74av2/bioconductor-pd.mg.u74av2_3.12.0_src_all.tar.gz" +) +MD5="01c6e4da9c2ad0f1939482284dd5b421" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74av2/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74av2/pre-unlink.sh new file mode 100644 index 0000000000000..421cefdc4b450 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74av2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74av2 diff --git a/recipes/bioconductor-pd.mg.u74b/meta.yaml b/recipes/bioconductor-pd.mg.u74b/meta.yaml new file mode 100644 index 0000000000000..5222e0cfeda99 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 47bb81abaceba6dfaab3e0987f28706c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74B' + diff --git a/recipes/bioconductor-pd.mg.u74b/post-link.sh b/recipes/bioconductor-pd.mg.u74b/post-link.sh new file mode 100644 index 0000000000000..810c4114af8ee --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74b/bioconductor-pd.mg.u74b_3.12.0_src_all.tar.gz" +) +MD5="47bb81abaceba6dfaab3e0987f28706c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74b/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74b/pre-unlink.sh new file mode 100644 index 0000000000000..5c7a51902c9dc --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74b diff --git a/recipes/bioconductor-pd.mg.u74bv2/meta.yaml b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml new file mode 100644 index 0000000000000..d7a1e53040633 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74bv2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74bv2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dbb6cd5b16bd5cafbf654744bc2d5c5c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Bv2' + diff --git a/recipes/bioconductor-pd.mg.u74bv2/post-link.sh b/recipes/bioconductor-pd.mg.u74bv2/post-link.sh new file mode 100644 index 0000000000000..67c7398120e56 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74bv2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74bv2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74bv2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74bv2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74bv2/bioconductor-pd.mg.u74bv2_3.12.0_src_all.tar.gz" +) +MD5="dbb6cd5b16bd5cafbf654744bc2d5c5c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74bv2/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74bv2/pre-unlink.sh new file mode 100644 index 0000000000000..007986d5d7312 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74bv2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74bv2 diff --git a/recipes/bioconductor-pd.mg.u74c/meta.yaml b/recipes/bioconductor-pd.mg.u74c/meta.yaml new file mode 100644 index 0000000000000..a53f367ca6a64 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74c/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74c" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 01f10eae99481f03d1d5a6a2c2f01733 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74C' + diff --git a/recipes/bioconductor-pd.mg.u74c/post-link.sh b/recipes/bioconductor-pd.mg.u74c/post-link.sh new file mode 100644 index 0000000000000..0d9ab5aa829a8 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74c/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74c_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74c_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74c_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74c/bioconductor-pd.mg.u74c_3.12.0_src_all.tar.gz" +) +MD5="01f10eae99481f03d1d5a6a2c2f01733" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74c/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74c/pre-unlink.sh new file mode 100644 index 0000000000000..c40592d2a021d --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74c/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74c diff --git a/recipes/bioconductor-pd.mg.u74cv2/meta.yaml b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml new file mode 100644 index 0000000000000..5db33c5231782 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74cv2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mg.u74cv2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b60943b90b95a24fcf93f8c245fd88be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MG_U74Cv2' + diff --git a/recipes/bioconductor-pd.mg.u74cv2/post-link.sh b/recipes/bioconductor-pd.mg.u74cv2/post-link.sh new file mode 100644 index 0000000000000..bdf367a6701b0 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74cv2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mg.u74cv2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mg.u74cv2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mg.u74cv2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mg.u74cv2/bioconductor-pd.mg.u74cv2_3.12.0_src_all.tar.gz" +) +MD5="b60943b90b95a24fcf93f8c245fd88be" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mg.u74cv2/pre-unlink.sh b/recipes/bioconductor-pd.mg.u74cv2/pre-unlink.sh new file mode 100644 index 0000000000000..08b353111ec06 --- /dev/null +++ b/recipes/bioconductor-pd.mg.u74cv2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mg.u74cv2 diff --git a/recipes/bioconductor-pd.mirna.1.0/meta.yaml b/recipes/bioconductor-pd.mirna.1.0/meta.yaml new file mode 100644 index 0000000000000..fbaf0a3953983 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.1.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mirna.1.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8dfeb82a9da6d6f73e5fb716a2867a34 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name miRNA-1_0' + diff --git a/recipes/bioconductor-pd.mirna.1.0/post-link.sh b/recipes/bioconductor-pd.mirna.1.0/post-link.sh new file mode 100644 index 0000000000000..6c0b22f2eedb1 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.1.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mirna.1.0_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.1.0_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mirna.1.0_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.1.0/bioconductor-pd.mirna.1.0_3.12.0_src_all.tar.gz" +) +MD5="8dfeb82a9da6d6f73e5fb716a2867a34" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mirna.1.0/pre-unlink.sh b/recipes/bioconductor-pd.mirna.1.0/pre-unlink.sh new file mode 100644 index 0000000000000..efded7d3965c9 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.1.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mirna.1.0 diff --git a/recipes/bioconductor-pd.mirna.2.0/meta.yaml b/recipes/bioconductor-pd.mirna.2.0/meta.yaml new file mode 100644 index 0000000000000..5a2ba95b1f343 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.2.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mirna.2.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: aab53cbc62fbd7727ca0303aeb1dca13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix miRNA-2_0' + diff --git a/recipes/bioconductor-pd.mirna.2.0/post-link.sh b/recipes/bioconductor-pd.mirna.2.0/post-link.sh new file mode 100644 index 0000000000000..c621a45ce9712 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.2.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mirna.2.0_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.2.0_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mirna.2.0_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.2.0/bioconductor-pd.mirna.2.0_3.12.0_src_all.tar.gz" +) +MD5="aab53cbc62fbd7727ca0303aeb1dca13" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mirna.2.0/pre-unlink.sh b/recipes/bioconductor-pd.mirna.2.0/pre-unlink.sh new file mode 100644 index 0000000000000..09944380e9eaf --- /dev/null +++ b/recipes/bioconductor-pd.mirna.2.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mirna.2.0 diff --git a/recipes/bioconductor-pd.mirna.3.0/meta.yaml b/recipes/bioconductor-pd.mirna.3.0/meta.yaml new file mode 100644 index 0000000000000..198938b3fcf7d --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mirna.3.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1265f1969c618b3b5121e6a77ba57009 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix miRNA-3_0' + diff --git a/recipes/bioconductor-pd.mirna.3.0/post-link.sh b/recipes/bioconductor-pd.mirna.3.0/post-link.sh new file mode 100644 index 0000000000000..085739a23bf46 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mirna.3.0_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.3.0_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mirna.3.0_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.0/bioconductor-pd.mirna.3.0_3.12.0_src_all.tar.gz" +) +MD5="1265f1969c618b3b5121e6a77ba57009" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mirna.3.0/pre-unlink.sh b/recipes/bioconductor-pd.mirna.3.0/pre-unlink.sh new file mode 100644 index 0000000000000..c15e9839ed8b0 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mirna.3.0 diff --git a/recipes/bioconductor-pd.mirna.3.1/meta.yaml b/recipes/bioconductor-pd.mirna.3.1/meta.yaml new file mode 100644 index 0000000000000..b9d0f495c2ab3 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.1/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.8.1" %} +{% set name = "pd.mirna.3.1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 296b3584ee5e9416c9018353d3e29c6c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.11.1' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - r-base + - r-dbi + - 'r-rsqlite >=0.11.1' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix miRNA-3_1' + diff --git a/recipes/bioconductor-pd.mirna.3.1/post-link.sh b/recipes/bioconductor-pd.mirna.3.1/post-link.sh new file mode 100644 index 0000000000000..557d67ff2d640 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mirna.3.1_3.8.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.3.1_3.8.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mirna.3.1_3.8.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.3.1/bioconductor-pd.mirna.3.1_3.8.1_src_all.tar.gz" +) +MD5="296b3584ee5e9416c9018353d3e29c6c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mirna.3.1/pre-unlink.sh b/recipes/bioconductor-pd.mirna.3.1/pre-unlink.sh new file mode 100644 index 0000000000000..5e678fa32bee3 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.3.1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mirna.3.1 diff --git a/recipes/bioconductor-pd.mirna.4.0/meta.yaml b/recipes/bioconductor-pd.mirna.4.0/meta.yaml new file mode 100644 index 0000000000000..19e6ddfdcd07b --- /dev/null +++ b/recipes/bioconductor-pd.mirna.4.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mirna.4.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cae1a18c02aaa20a2f05172103e9d938 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix miRNA-4_0' + diff --git a/recipes/bioconductor-pd.mirna.4.0/post-link.sh b/recipes/bioconductor-pd.mirna.4.0/post-link.sh new file mode 100644 index 0000000000000..910d53d8cda5c --- /dev/null +++ b/recipes/bioconductor-pd.mirna.4.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mirna.4.0_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mirna.4.0_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mirna.4.0_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mirna.4.0/bioconductor-pd.mirna.4.0_3.12.0_src_all.tar.gz" +) +MD5="cae1a18c02aaa20a2f05172103e9d938" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mirna.4.0/pre-unlink.sh b/recipes/bioconductor-pd.mirna.4.0/pre-unlink.sh new file mode 100644 index 0000000000000..e58ae8a84aaa8 --- /dev/null +++ b/recipes/bioconductor-pd.mirna.4.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mirna.4.0 diff --git a/recipes/bioconductor-pd.moe430a/meta.yaml b/recipes/bioconductor-pd.moe430a/meta.yaml new file mode 100644 index 0000000000000..d9a84110fd774 --- /dev/null +++ b/recipes/bioconductor-pd.moe430a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.moe430a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f9a7cb62140e42c2a82177548a1c73fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MOE430A' + diff --git a/recipes/bioconductor-pd.moe430a/post-link.sh b/recipes/bioconductor-pd.moe430a/post-link.sh new file mode 100644 index 0000000000000..5904b6d4634f3 --- /dev/null +++ b/recipes/bioconductor-pd.moe430a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.moe430a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moe430a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.moe430a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moe430a/bioconductor-pd.moe430a_3.12.0_src_all.tar.gz" +) +MD5="f9a7cb62140e42c2a82177548a1c73fb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.moe430a/pre-unlink.sh b/recipes/bioconductor-pd.moe430a/pre-unlink.sh new file mode 100644 index 0000000000000..0f441f35a6eab --- /dev/null +++ b/recipes/bioconductor-pd.moe430a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.moe430a diff --git a/recipes/bioconductor-pd.moe430b/meta.yaml b/recipes/bioconductor-pd.moe430b/meta.yaml new file mode 100644 index 0000000000000..16e03b2be047d --- /dev/null +++ b/recipes/bioconductor-pd.moe430b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.moe430b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c19d2ee5e7e87703cf73afa33a5f3156 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name MOE430B' + diff --git a/recipes/bioconductor-pd.moe430b/post-link.sh b/recipes/bioconductor-pd.moe430b/post-link.sh new file mode 100644 index 0000000000000..e5c1d9176a24f --- /dev/null +++ b/recipes/bioconductor-pd.moe430b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.moe430b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moe430b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.moe430b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moe430b/bioconductor-pd.moe430b_3.12.0_src_all.tar.gz" +) +MD5="c19d2ee5e7e87703cf73afa33a5f3156" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.moe430b/pre-unlink.sh b/recipes/bioconductor-pd.moe430b/pre-unlink.sh new file mode 100644 index 0000000000000..0cf296326b21e --- /dev/null +++ b/recipes/bioconductor-pd.moe430b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.moe430b diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml new file mode 100644 index 0000000000000..18fccfc1ceb43 --- /dev/null +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.moex.1.0.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 57427e63b2d44258c12d796eada1897b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MoEx-1_0-st-v1' + diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh new file mode 100644 index 0000000000000..01b472f139f86 --- /dev/null +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.moex.1.0.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.moex.1.0.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.moex.1.0.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.moex.1.0.st.v1/bioconductor-pd.moex.1.0.st.v1_3.14.1_src_all.tar.gz" +) +MD5="57427e63b2d44258c12d796eada1897b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.moex.1.0.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.moex.1.0.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..c723a9eb9a5c6 --- /dev/null +++ b/recipes/bioconductor-pd.moex.1.0.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.moex.1.0.st.v1 diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml new file mode 100644 index 0000000000000..118dd521ebd39 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.mogene.1.0.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c3767385af3b9a120c777adb6d6e3364 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MoGene-1_0-st-v1' + diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh new file mode 100644 index 0000000000000..e78faef855e72 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mogene.1.0.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.1.0.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mogene.1.0.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.0.st.v1/bioconductor-pd.mogene.1.0.st.v1_3.14.1_src_all.tar.gz" +) +MD5="c3767385af3b9a120c777adb6d6e3364" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mogene.1.0.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.mogene.1.0.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..456625d011295 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.0.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mogene.1.0.st.v1 diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml new file mode 100644 index 0000000000000..b3918ef7c394e --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.mogene.1.1.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3d6c5d29e4d8a0b0152e109b68f82c37 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MoGene-1_1-st-v1' + diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh new file mode 100644 index 0000000000000..a55e6aef3c943 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mogene.1.1.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.1.1.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mogene.1.1.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.1.1.st.v1/bioconductor-pd.mogene.1.1.st.v1_3.14.1_src_all.tar.gz" +) +MD5="3d6c5d29e4d8a0b0152e109b68f82c37" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mogene.1.1.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.mogene.1.1.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..11601147aff03 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.1.1.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mogene.1.1.st.v1 diff --git a/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml new file mode 100644 index 0000000000000..9266d76840128 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.mogene.2.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 71326d6bd85de02490171696f923d053 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MoGene-2_0-st' + diff --git a/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh b/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh new file mode 100644 index 0000000000000..8c0457f0f5cb9 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mogene.2.0.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.2.0.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mogene.2.0.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.0.st/bioconductor-pd.mogene.2.0.st_3.14.1_src_all.tar.gz" +) +MD5="71326d6bd85de02490171696f923d053" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mogene.2.0.st/pre-unlink.sh b/recipes/bioconductor-pd.mogene.2.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..6f5f83a07a1b5 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mogene.2.0.st diff --git a/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml new file mode 100644 index 0000000000000..4ae0c5ef48ee4 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.mogene.2.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2c7fc5644eae98359cb945ff16d072a2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MoGene-2_1-st' + diff --git a/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh b/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh new file mode 100644 index 0000000000000..5cf42e83de2fc --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mogene.2.1.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mogene.2.1.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mogene.2.1.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mogene.2.1.st/bioconductor-pd.mogene.2.1.st_3.14.1_src_all.tar.gz" +) +MD5="2c7fc5644eae98359cb945ff16d072a2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mogene.2.1.st/pre-unlink.sh b/recipes/bioconductor-pd.mogene.2.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..b5ef0718be0c3 --- /dev/null +++ b/recipes/bioconductor-pd.mogene.2.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mogene.2.1.st diff --git a/recipes/bioconductor-pd.mouse430.2/meta.yaml b/recipes/bioconductor-pd.mouse430.2/meta.yaml new file mode 100644 index 0000000000000..c1f7e8ef7cee3 --- /dev/null +++ b/recipes/bioconductor-pd.mouse430.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mouse430.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7f37397a57b06d15101ef86fa6242ca4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Mouse430_2' + diff --git a/recipes/bioconductor-pd.mouse430.2/post-link.sh b/recipes/bioconductor-pd.mouse430.2/post-link.sh new file mode 100644 index 0000000000000..c0e23c2942155 --- /dev/null +++ b/recipes/bioconductor-pd.mouse430.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mouse430.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mouse430.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mouse430.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430.2/bioconductor-pd.mouse430.2_3.12.0_src_all.tar.gz" +) +MD5="7f37397a57b06d15101ef86fa6242ca4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mouse430.2/pre-unlink.sh b/recipes/bioconductor-pd.mouse430.2/pre-unlink.sh new file mode 100644 index 0000000000000..16b24faba5a5e --- /dev/null +++ b/recipes/bioconductor-pd.mouse430.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mouse430.2 diff --git a/recipes/bioconductor-pd.mouse430a.2/meta.yaml b/recipes/bioconductor-pd.mouse430a.2/meta.yaml new file mode 100644 index 0000000000000..5efa51f441a3f --- /dev/null +++ b/recipes/bioconductor-pd.mouse430a.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mouse430a.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0c28f564a1fa23f59c936d42c156796d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Mouse430A_2' + diff --git a/recipes/bioconductor-pd.mouse430a.2/post-link.sh b/recipes/bioconductor-pd.mouse430a.2/post-link.sh new file mode 100644 index 0000000000000..08adb1187962e --- /dev/null +++ b/recipes/bioconductor-pd.mouse430a.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mouse430a.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mouse430a.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mouse430a.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mouse430a.2/bioconductor-pd.mouse430a.2_3.12.0_src_all.tar.gz" +) +MD5="0c28f564a1fa23f59c936d42c156796d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mouse430a.2/pre-unlink.sh b/recipes/bioconductor-pd.mouse430a.2/pre-unlink.sh new file mode 100644 index 0000000000000..718b8e910f7a6 --- /dev/null +++ b/recipes/bioconductor-pd.mouse430a.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mouse430a.2 diff --git a/recipes/bioconductor-pd.mta.1.0/meta.yaml b/recipes/bioconductor-pd.mta.1.0/meta.yaml new file mode 100644 index 0000000000000..4cc68033ac38b --- /dev/null +++ b/recipes/bioconductor-pd.mta.1.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mta.1.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0f737b4f1f1353733e56e2df637f554b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix MTA-1_0' + diff --git a/recipes/bioconductor-pd.mta.1.0/post-link.sh b/recipes/bioconductor-pd.mta.1.0/post-link.sh new file mode 100644 index 0000000000000..d7bb9fe6f4352 --- /dev/null +++ b/recipes/bioconductor-pd.mta.1.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mta.1.0_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mta.1.0_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mta.1.0_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mta.1.0/bioconductor-pd.mta.1.0_3.12.0_src_all.tar.gz" +) +MD5="0f737b4f1f1353733e56e2df637f554b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mta.1.0/pre-unlink.sh b/recipes/bioconductor-pd.mta.1.0/pre-unlink.sh new file mode 100644 index 0000000000000..0183c3f386ecc --- /dev/null +++ b/recipes/bioconductor-pd.mta.1.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mta.1.0 diff --git a/recipes/bioconductor-pd.mu11ksuba/meta.yaml b/recipes/bioconductor-pd.mu11ksuba/meta.yaml new file mode 100644 index 0000000000000..1813fad5bfa3f --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksuba/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mu11ksuba" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 56be58b3f444ccb9572dc4c3882964b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Mu11KsubA' + diff --git a/recipes/bioconductor-pd.mu11ksuba/post-link.sh b/recipes/bioconductor-pd.mu11ksuba/post-link.sh new file mode 100644 index 0000000000000..bc09886823b82 --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksuba/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mu11ksuba_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mu11ksuba_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mu11ksuba_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksuba/bioconductor-pd.mu11ksuba_3.12.0_src_all.tar.gz" +) +MD5="56be58b3f444ccb9572dc4c3882964b2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mu11ksuba/pre-unlink.sh b/recipes/bioconductor-pd.mu11ksuba/pre-unlink.sh new file mode 100644 index 0000000000000..67863396fc439 --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksuba/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mu11ksuba diff --git a/recipes/bioconductor-pd.mu11ksubb/meta.yaml b/recipes/bioconductor-pd.mu11ksubb/meta.yaml new file mode 100644 index 0000000000000..5f04ea5c23082 --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksubb/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.mu11ksubb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c45b0ebe777b99cec38499826cc1b457 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Mu11KsubB' + diff --git a/recipes/bioconductor-pd.mu11ksubb/post-link.sh b/recipes/bioconductor-pd.mu11ksubb/post-link.sh new file mode 100644 index 0000000000000..59bfa000e0a0d --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksubb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.mu11ksubb_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.mu11ksubb_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.mu11ksubb_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.mu11ksubb/bioconductor-pd.mu11ksubb_3.12.0_src_all.tar.gz" +) +MD5="c45b0ebe777b99cec38499826cc1b457" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.mu11ksubb/pre-unlink.sh b/recipes/bioconductor-pd.mu11ksubb/pre-unlink.sh new file mode 100644 index 0000000000000..913fc1e851938 --- /dev/null +++ b/recipes/bioconductor-pd.mu11ksubb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.mu11ksubb diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml new file mode 100644 index 0000000000000..cf6a439e1a443 --- /dev/null +++ b/recipes/bioconductor-pd.nugo.hs1a520180/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.4.0" %} +{% set name = "pd.nugo.hs1a520180" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 88a836472f0f9aab2e1d54e4bad7d6af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name NuGO_Hs1a520180' + diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh b/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh new file mode 100644 index 0000000000000..0ab9093b71c05 --- /dev/null +++ b/recipes/bioconductor-pd.nugo.hs1a520180/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.nugo.hs1a520180_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.nugo.hs1a520180_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.nugo.hs1a520180_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.hs1a520180/bioconductor-pd.nugo.hs1a520180_3.4.0_src_all.tar.gz" +) +MD5="88a836472f0f9aab2e1d54e4bad7d6af" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.nugo.hs1a520180/pre-unlink.sh b/recipes/bioconductor-pd.nugo.hs1a520180/pre-unlink.sh new file mode 100644 index 0000000000000..18f987e2f1e58 --- /dev/null +++ b/recipes/bioconductor-pd.nugo.hs1a520180/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.nugo.hs1a520180 diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml new file mode 100644 index 0000000000000..4e9d7cf7d3f4e --- /dev/null +++ b/recipes/bioconductor-pd.nugo.mm1a520177/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.4.0" %} +{% set name = "pd.nugo.mm1a520177" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5cd64895eaddaf4cae1c48db9468c079 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name NuGO_Mm1a520177' + diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh b/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh new file mode 100644 index 0000000000000..40a3fe068d44f --- /dev/null +++ b/recipes/bioconductor-pd.nugo.mm1a520177/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.nugo.mm1a520177_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.nugo.mm1a520177_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.nugo.mm1a520177_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.nugo.mm1a520177/bioconductor-pd.nugo.mm1a520177_3.4.0_src_all.tar.gz" +) +MD5="5cd64895eaddaf4cae1c48db9468c079" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.nugo.mm1a520177/pre-unlink.sh b/recipes/bioconductor-pd.nugo.mm1a520177/pre-unlink.sh new file mode 100644 index 0000000000000..ac7ad1ca2ccb8 --- /dev/null +++ b/recipes/bioconductor-pd.nugo.mm1a520177/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.nugo.mm1a520177 diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..4626ef43efed3 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ovigene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 88cfedfe10dd357539305051a69d31a1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix OviGene-1_0-st' + diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh b/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..36b5a01b46781 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ovigene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ovigene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ovigene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.0.st/bioconductor-pd.ovigene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="88cfedfe10dd357539305051a69d31a1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ovigene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.ovigene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..92d5c81cc2989 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ovigene.1.0.st diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..d8ca32c874ca9 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.ovigene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d6158cacd32a1892975fddd8dc8bb3f2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix OviGene-1_1-st' + diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh b/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..73944815fb6b7 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ovigene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ovigene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ovigene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ovigene.1.1.st/bioconductor-pd.ovigene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="d6158cacd32a1892975fddd8dc8bb3f2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ovigene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.ovigene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..741c05cbc58f0 --- /dev/null +++ b/recipes/bioconductor-pd.ovigene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ovigene.1.1.st diff --git a/recipes/bioconductor-pd.pae.g1a/meta.yaml b/recipes/bioconductor-pd.pae.g1a/meta.yaml new file mode 100644 index 0000000000000..3dc92fdfa84a9 --- /dev/null +++ b/recipes/bioconductor-pd.pae.g1a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.pae.g1a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d96462eb35c63b30772bccae2a27a8cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Pae_G1a' + diff --git a/recipes/bioconductor-pd.pae.g1a/post-link.sh b/recipes/bioconductor-pd.pae.g1a/post-link.sh new file mode 100644 index 0000000000000..d95e014b5a3d0 --- /dev/null +++ b/recipes/bioconductor-pd.pae.g1a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.pae.g1a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.pae.g1a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.pae.g1a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.pae.g1a/bioconductor-pd.pae.g1a_3.12.0_src_all.tar.gz" +) +MD5="d96462eb35c63b30772bccae2a27a8cd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.pae.g1a/pre-unlink.sh b/recipes/bioconductor-pd.pae.g1a/pre-unlink.sh new file mode 100644 index 0000000000000..ce942be4696aa --- /dev/null +++ b/recipes/bioconductor-pd.pae.g1a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.pae.g1a diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml new file mode 100644 index 0000000000000..0d72c4b87af78 --- /dev/null +++ b/recipes/bioconductor-pd.plasmodium.anopheles/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.plasmodium.anopheles" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ae55b1451ceaed951f68213c0433f3d0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Plasmodium_Anopheles' + diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh b/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh new file mode 100644 index 0000000000000..1b0416d2e97a5 --- /dev/null +++ b/recipes/bioconductor-pd.plasmodium.anopheles/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.plasmodium.anopheles_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.plasmodium.anopheles_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.plasmodium.anopheles_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.plasmodium.anopheles/bioconductor-pd.plasmodium.anopheles_3.12.0_src_all.tar.gz" +) +MD5="ae55b1451ceaed951f68213c0433f3d0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.plasmodium.anopheles/pre-unlink.sh b/recipes/bioconductor-pd.plasmodium.anopheles/pre-unlink.sh new file mode 100644 index 0000000000000..9d1f374d230a7 --- /dev/null +++ b/recipes/bioconductor-pd.plasmodium.anopheles/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.plasmodium.anopheles diff --git a/recipes/bioconductor-pd.poplar/meta.yaml b/recipes/bioconductor-pd.poplar/meta.yaml new file mode 100644 index 0000000000000..ea17481d19759 --- /dev/null +++ b/recipes/bioconductor-pd.poplar/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.poplar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9c33b7528e5a47654aeacf61b71058a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Poplar' + diff --git a/recipes/bioconductor-pd.poplar/post-link.sh b/recipes/bioconductor-pd.poplar/post-link.sh new file mode 100644 index 0000000000000..e312b76ac2e30 --- /dev/null +++ b/recipes/bioconductor-pd.poplar/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.poplar_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.poplar_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.poplar_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.poplar/bioconductor-pd.poplar_3.12.0_src_all.tar.gz" +) +MD5="9c33b7528e5a47654aeacf61b71058a8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.poplar/pre-unlink.sh b/recipes/bioconductor-pd.poplar/pre-unlink.sh new file mode 100644 index 0000000000000..418535312165c --- /dev/null +++ b/recipes/bioconductor-pd.poplar/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.poplar diff --git a/recipes/bioconductor-pd.porcine/meta.yaml b/recipes/bioconductor-pd.porcine/meta.yaml new file mode 100644 index 0000000000000..298b44ccf9970 --- /dev/null +++ b/recipes/bioconductor-pd.porcine/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.porcine" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5df404babadb1d6faef73e249c819a72 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Porcine' + diff --git a/recipes/bioconductor-pd.porcine/post-link.sh b/recipes/bioconductor-pd.porcine/post-link.sh new file mode 100644 index 0000000000000..f46533e1d4001 --- /dev/null +++ b/recipes/bioconductor-pd.porcine/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.porcine_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porcine_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.porcine_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porcine/bioconductor-pd.porcine_3.12.0_src_all.tar.gz" +) +MD5="5df404babadb1d6faef73e249c819a72" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.porcine/pre-unlink.sh b/recipes/bioconductor-pd.porcine/pre-unlink.sh new file mode 100644 index 0000000000000..7598b8e82ea2d --- /dev/null +++ b/recipes/bioconductor-pd.porcine/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.porcine diff --git a/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..34c1c5cc82dc5 --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.porgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 203fc56b0e2904fa7063c4a325e038f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix PorGene-1_0-st' + diff --git a/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..8e2d4a333becd --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.porgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.porgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.0.st/bioconductor-pd.porgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="203fc56b0e2904fa7063c4a325e038f1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.porgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.porgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..9f65815ae7ed7 --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.porgene.1.0.st diff --git a/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..762ee9eff28a8 --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.porgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3a31d325861925a7428241207c461a1d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix PorGene-1_1-st' + diff --git a/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..259b6afddf79b --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.porgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.porgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.porgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.porgene.1.1.st/bioconductor-pd.porgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="3a31d325861925a7428241207c461a1d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.porgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.porgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..066b5e78f2150 --- /dev/null +++ b/recipes/bioconductor-pd.porgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.porgene.1.1.st diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..1add7d7362342 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rabgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7f1e33f4767a4c4653bdaff2b79989a0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RabGene-1_0-st' + diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..5c1066d6e2c47 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rabgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rabgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rabgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.0.st/bioconductor-pd.rabgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="7f1e33f4767a4c4653bdaff2b79989a0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rabgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.rabgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..8cc6cce578e67 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rabgene.1.0.st diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..dc1075fb37315 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rabgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2492695661309f5e6628612685460ee5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RabGene-1_1-st' + diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..6de544b2644d5 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rabgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rabgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rabgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rabgene.1.1.st/bioconductor-pd.rabgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="2492695661309f5e6628612685460ee5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rabgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.rabgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..81ecfa2f04019 --- /dev/null +++ b/recipes/bioconductor-pd.rabgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rabgene.1.1.st diff --git a/recipes/bioconductor-pd.rae230a/meta.yaml b/recipes/bioconductor-pd.rae230a/meta.yaml new file mode 100644 index 0000000000000..693724c087a3e --- /dev/null +++ b/recipes/bioconductor-pd.rae230a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rae230a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fa4a1c29d3457b1db82b1010c5f72412 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RAE230A' + diff --git a/recipes/bioconductor-pd.rae230a/post-link.sh b/recipes/bioconductor-pd.rae230a/post-link.sh new file mode 100644 index 0000000000000..9890ffc859cf5 --- /dev/null +++ b/recipes/bioconductor-pd.rae230a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rae230a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rae230a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rae230a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rae230a/bioconductor-pd.rae230a_3.12.0_src_all.tar.gz" +) +MD5="fa4a1c29d3457b1db82b1010c5f72412" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rae230a/pre-unlink.sh b/recipes/bioconductor-pd.rae230a/pre-unlink.sh new file mode 100644 index 0000000000000..cd6dcabe10809 --- /dev/null +++ b/recipes/bioconductor-pd.rae230a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rae230a diff --git a/recipes/bioconductor-pd.rae230b/meta.yaml b/recipes/bioconductor-pd.rae230b/meta.yaml new file mode 100644 index 0000000000000..8cc778f198afa --- /dev/null +++ b/recipes/bioconductor-pd.rae230b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rae230b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 10e2e70bb7538119127cd65f636f93b6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RAE230B' + diff --git a/recipes/bioconductor-pd.rae230b/post-link.sh b/recipes/bioconductor-pd.rae230b/post-link.sh new file mode 100644 index 0000000000000..15d2035239b82 --- /dev/null +++ b/recipes/bioconductor-pd.rae230b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rae230b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rae230b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rae230b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rae230b/bioconductor-pd.rae230b_3.12.0_src_all.tar.gz" +) +MD5="10e2e70bb7538119127cd65f636f93b6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rae230b/pre-unlink.sh b/recipes/bioconductor-pd.rae230b/pre-unlink.sh new file mode 100644 index 0000000000000..fbb73cffc61b9 --- /dev/null +++ b/recipes/bioconductor-pd.rae230b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rae230b diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml new file mode 100644 index 0000000000000..a402c2d258b37 --- /dev/null +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.raex.1.0.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e2160b549f63ffcc9222d88d82d4d393 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RaEx-1_0-st-v1' + diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh new file mode 100644 index 0000000000000..2d1bfbbd97b7a --- /dev/null +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.raex.1.0.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.raex.1.0.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.raex.1.0.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.raex.1.0.st.v1/bioconductor-pd.raex.1.0.st.v1_3.14.1_src_all.tar.gz" +) +MD5="e2160b549f63ffcc9222d88d82d4d393" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.raex.1.0.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.raex.1.0.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..372ff8514756b --- /dev/null +++ b/recipes/bioconductor-pd.raex.1.0.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.raex.1.0.st.v1 diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml new file mode 100644 index 0000000000000..abb26f7641121 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.ragene.1.0.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 122cb69603e705218d01d70f48e90cad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RaGene-1_0-st-v1' + diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh b/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh new file mode 100644 index 0000000000000..2dff263cadfb0 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ragene.1.0.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.1.0.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ragene.1.0.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.0.st.v1/bioconductor-pd.ragene.1.0.st.v1_3.14.1_src_all.tar.gz" +) +MD5="122cb69603e705218d01d70f48e90cad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ragene.1.0.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.ragene.1.0.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..4551cb95c8556 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.0.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ragene.1.0.st.v1 diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml new file mode 100644 index 0000000000000..ee0370bed7bfd --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.ragene.1.1.st.v1" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7301ab6472849395ccb800c39807e969 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RaGene-1_1-st-v1' + diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh b/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh new file mode 100644 index 0000000000000..54d407613f244 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ragene.1.1.st.v1_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.1.1.st.v1_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ragene.1.1.st.v1_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.1.1.st.v1/bioconductor-pd.ragene.1.1.st.v1_3.14.1_src_all.tar.gz" +) +MD5="7301ab6472849395ccb800c39807e969" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ragene.1.1.st.v1/pre-unlink.sh b/recipes/bioconductor-pd.ragene.1.1.st.v1/pre-unlink.sh new file mode 100644 index 0000000000000..1dfec15ac9e6d --- /dev/null +++ b/recipes/bioconductor-pd.ragene.1.1.st.v1/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ragene.1.1.st.v1 diff --git a/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml new file mode 100644 index 0000000000000..c7eb78697e2f3 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.ragene.2.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 37157b09f009fef368b54e47711c313b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RaGene-2_0-st' + diff --git a/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh b/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh new file mode 100644 index 0000000000000..de1980207e6ad --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ragene.2.0.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.2.0.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ragene.2.0.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.0.st/bioconductor-pd.ragene.2.0.st_3.14.1_src_all.tar.gz" +) +MD5="37157b09f009fef368b54e47711c313b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ragene.2.0.st/pre-unlink.sh b/recipes/bioconductor-pd.ragene.2.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..d8cf4051a2ee2 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ragene.2.0.st diff --git a/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml new file mode 100644 index 0000000000000..f541a6e0b6036 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.14.1" %} +{% set name = "pd.ragene.2.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 53adfa5ff2c7e466da83b807dbc7b237 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RaGene-2_1-st' + diff --git a/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh b/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh new file mode 100644 index 0000000000000..e1f72d156d6a3 --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.ragene.2.1.st_3.14.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.ragene.2.1.st_3.14.1.tar.gz" + "https://bioarchive.galaxyproject.org/pd.ragene.2.1.st_3.14.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.ragene.2.1.st/bioconductor-pd.ragene.2.1.st_3.14.1_src_all.tar.gz" +) +MD5="53adfa5ff2c7e466da83b807dbc7b237" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.ragene.2.1.st/pre-unlink.sh b/recipes/bioconductor-pd.ragene.2.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..f0eb90d8306ec --- /dev/null +++ b/recipes/bioconductor-pd.ragene.2.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.ragene.2.1.st diff --git a/recipes/bioconductor-pd.rat230.2/meta.yaml b/recipes/bioconductor-pd.rat230.2/meta.yaml new file mode 100644 index 0000000000000..4ab1361705c55 --- /dev/null +++ b/recipes/bioconductor-pd.rat230.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rat230.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 286b1a7868ef6c795ebeb6dd8a5d5920 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Rat230_2' + diff --git a/recipes/bioconductor-pd.rat230.2/post-link.sh b/recipes/bioconductor-pd.rat230.2/post-link.sh new file mode 100644 index 0000000000000..cbd826be87d39 --- /dev/null +++ b/recipes/bioconductor-pd.rat230.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rat230.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rat230.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rat230.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rat230.2/bioconductor-pd.rat230.2_3.12.0_src_all.tar.gz" +) +MD5="286b1a7868ef6c795ebeb6dd8a5d5920" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rat230.2/pre-unlink.sh b/recipes/bioconductor-pd.rat230.2/pre-unlink.sh new file mode 100644 index 0000000000000..5373ae17cd689 --- /dev/null +++ b/recipes/bioconductor-pd.rat230.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rat230.2 diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..ee73766158a5a --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rcngene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9c7c5ef4d4f5ed92d9130d77a99a0685 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RCnGene-1_0-st' + diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..7abc8c8915f5d --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rcngene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rcngene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rcngene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.0.st/bioconductor-pd.rcngene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="9c7c5ef4d4f5ed92d9130d77a99a0685" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rcngene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.rcngene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..507fc960eafc0 --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rcngene.1.0.st diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..d2196c6d86ae2 --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rcngene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9781549447d90b5423e820fff5cc6273 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RCnGene-1_1-st' + diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..f43c70696ada1 --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rcngene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rcngene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rcngene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rcngene.1.1.st/bioconductor-pd.rcngene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="9781549447d90b5423e820fff5cc6273" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rcngene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.rcngene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..36deb966f874d --- /dev/null +++ b/recipes/bioconductor-pd.rcngene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rcngene.1.1.st diff --git a/recipes/bioconductor-pd.rg.u34a/meta.yaml b/recipes/bioconductor-pd.rg.u34a/meta.yaml new file mode 100644 index 0000000000000..849e610981ed7 --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34a/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rg.u34a" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ac3a6cc203dabb8faab85b97f1a7ae3c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RG_U34A' + diff --git a/recipes/bioconductor-pd.rg.u34a/post-link.sh b/recipes/bioconductor-pd.rg.u34a/post-link.sh new file mode 100644 index 0000000000000..8dd25d5de44f2 --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34a/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rg.u34a_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34a_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rg.u34a_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34a/bioconductor-pd.rg.u34a_3.12.0_src_all.tar.gz" +) +MD5="ac3a6cc203dabb8faab85b97f1a7ae3c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rg.u34a/pre-unlink.sh b/recipes/bioconductor-pd.rg.u34a/pre-unlink.sh new file mode 100644 index 0000000000000..dadda0757a4fc --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34a/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rg.u34a diff --git a/recipes/bioconductor-pd.rg.u34b/meta.yaml b/recipes/bioconductor-pd.rg.u34b/meta.yaml new file mode 100644 index 0000000000000..7f9fc6818b199 --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34b/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rg.u34b" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 757966b66795d388c7169816d31977ad +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RG_U34B' + diff --git a/recipes/bioconductor-pd.rg.u34b/post-link.sh b/recipes/bioconductor-pd.rg.u34b/post-link.sh new file mode 100644 index 0000000000000..adc9803bda966 --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34b/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rg.u34b_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34b_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rg.u34b_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34b/bioconductor-pd.rg.u34b_3.12.0_src_all.tar.gz" +) +MD5="757966b66795d388c7169816d31977ad" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rg.u34b/pre-unlink.sh b/recipes/bioconductor-pd.rg.u34b/pre-unlink.sh new file mode 100644 index 0000000000000..1144faa56f81d --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34b/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rg.u34b diff --git a/recipes/bioconductor-pd.rg.u34c/meta.yaml b/recipes/bioconductor-pd.rg.u34c/meta.yaml new file mode 100644 index 0000000000000..6c89b0ad42db4 --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34c/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rg.u34c" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bc9cb7b208972ac2901235bdabdee5b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RG_U34C' + diff --git a/recipes/bioconductor-pd.rg.u34c/post-link.sh b/recipes/bioconductor-pd.rg.u34c/post-link.sh new file mode 100644 index 0000000000000..b7be3908cb2bf --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34c/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rg.u34c_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rg.u34c_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rg.u34c_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rg.u34c/bioconductor-pd.rg.u34c_3.12.0_src_all.tar.gz" +) +MD5="bc9cb7b208972ac2901235bdabdee5b2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rg.u34c/pre-unlink.sh b/recipes/bioconductor-pd.rg.u34c/pre-unlink.sh new file mode 100644 index 0000000000000..d67921a05c86c --- /dev/null +++ b/recipes/bioconductor-pd.rg.u34c/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rg.u34c diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..c9907fcbafdd9 --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rhegene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6469add6928e663529df4df98fcdd7a8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RheGene-1_0-st' + diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..e44422059d24a --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rhegene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhegene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rhegene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.0.st/bioconductor-pd.rhegene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="6469add6928e663529df4df98fcdd7a8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rhegene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.rhegene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..d6b5c1755745c --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rhegene.1.0.st diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..28d58fd1c675c --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rhegene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4f63424ab52283a95731767dce6623cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RheGene-1_1-st' + diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..44c1bd5e13eb4 --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rhegene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhegene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rhegene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhegene.1.1.st/bioconductor-pd.rhegene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="4f63424ab52283a95731767dce6623cd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rhegene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.rhegene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..5045fa077ea65 --- /dev/null +++ b/recipes/bioconductor-pd.rhegene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rhegene.1.1.st diff --git a/recipes/bioconductor-pd.rhesus/meta.yaml b/recipes/bioconductor-pd.rhesus/meta.yaml new file mode 100644 index 0000000000000..808950302c055 --- /dev/null +++ b/recipes/bioconductor-pd.rhesus/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rhesus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 51efcfe1384ac956ff93bf0530965054 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Rhesus' + diff --git a/recipes/bioconductor-pd.rhesus/post-link.sh b/recipes/bioconductor-pd.rhesus/post-link.sh new file mode 100644 index 0000000000000..aff35e4f01495 --- /dev/null +++ b/recipes/bioconductor-pd.rhesus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rhesus_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rhesus_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rhesus_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rhesus/bioconductor-pd.rhesus_3.12.0_src_all.tar.gz" +) +MD5="51efcfe1384ac956ff93bf0530965054" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rhesus/pre-unlink.sh b/recipes/bioconductor-pd.rhesus/pre-unlink.sh new file mode 100644 index 0000000000000..64818545d7dba --- /dev/null +++ b/recipes/bioconductor-pd.rhesus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rhesus diff --git a/recipes/bioconductor-pd.rice/meta.yaml b/recipes/bioconductor-pd.rice/meta.yaml new file mode 100644 index 0000000000000..2af44cf17a7d4 --- /dev/null +++ b/recipes/bioconductor-pd.rice/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rice" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9c456981b3d0b99a96ac6c71e3eb7c8a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Rice' + diff --git a/recipes/bioconductor-pd.rice/post-link.sh b/recipes/bioconductor-pd.rice/post-link.sh new file mode 100644 index 0000000000000..93be3e525b029 --- /dev/null +++ b/recipes/bioconductor-pd.rice/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rice_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rice_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rice_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rice/bioconductor-pd.rice_3.12.0_src_all.tar.gz" +) +MD5="9c456981b3d0b99a96ac6c71e3eb7c8a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rice/pre-unlink.sh b/recipes/bioconductor-pd.rice/pre-unlink.sh new file mode 100644 index 0000000000000..0cbc7ee9dfb80 --- /dev/null +++ b/recipes/bioconductor-pd.rice/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rice diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..7a2c16a9bc4a2 --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rjpgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 066f5dbacc1110e42ce4d457ad3b9306 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RJpGene-1_0-st' + diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..e4c1e667cc79d --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rjpgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rjpgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rjpgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.0.st/bioconductor-pd.rjpgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="066f5dbacc1110e42ce4d457ad3b9306" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rjpgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.rjpgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..4270e9578a4d2 --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rjpgene.1.0.st diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..3e3f56eb9f463 --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rjpgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 265503774b15e0f4e71ac53a276a80f2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RJpGene-1_1-st' + diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..c09a977871521 --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rjpgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rjpgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rjpgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rjpgene.1.1.st/bioconductor-pd.rjpgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="265503774b15e0f4e71ac53a276a80f2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rjpgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.rjpgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..eb476e4a8c285 --- /dev/null +++ b/recipes/bioconductor-pd.rjpgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rjpgene.1.1.st diff --git a/recipes/bioconductor-pd.rn.u34/meta.yaml b/recipes/bioconductor-pd.rn.u34/meta.yaml new file mode 100644 index 0000000000000..a7fd5de75dc3c --- /dev/null +++ b/recipes/bioconductor-pd.rn.u34/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rn.u34" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1728c547f1383bffab330796505119ec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name RN_U34' + diff --git a/recipes/bioconductor-pd.rn.u34/post-link.sh b/recipes/bioconductor-pd.rn.u34/post-link.sh new file mode 100644 index 0000000000000..1c9920cb6d093 --- /dev/null +++ b/recipes/bioconductor-pd.rn.u34/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rn.u34_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rn.u34_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rn.u34_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rn.u34/bioconductor-pd.rn.u34_3.12.0_src_all.tar.gz" +) +MD5="1728c547f1383bffab330796505119ec" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rn.u34/pre-unlink.sh b/recipes/bioconductor-pd.rn.u34/pre-unlink.sh new file mode 100644 index 0000000000000..45b16e7ec2a72 --- /dev/null +++ b/recipes/bioconductor-pd.rn.u34/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rn.u34 diff --git a/recipes/bioconductor-pd.rta.1.0/meta.yaml b/recipes/bioconductor-pd.rta.1.0/meta.yaml new file mode 100644 index 0000000000000..a0418e6bf4499 --- /dev/null +++ b/recipes/bioconductor-pd.rta.1.0/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.2" %} +{% set name = "pd.rta.1.0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 90752a892a103c7fe4cd6c86e61a61db +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RTA-1_0' + diff --git a/recipes/bioconductor-pd.rta.1.0/post-link.sh b/recipes/bioconductor-pd.rta.1.0/post-link.sh new file mode 100644 index 0000000000000..013a09f092237 --- /dev/null +++ b/recipes/bioconductor-pd.rta.1.0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rta.1.0_3.12.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rta.1.0_3.12.2.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rta.1.0_3.12.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rta.1.0/bioconductor-pd.rta.1.0_3.12.2_src_all.tar.gz" +) +MD5="90752a892a103c7fe4cd6c86e61a61db" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rta.1.0/pre-unlink.sh b/recipes/bioconductor-pd.rta.1.0/pre-unlink.sh new file mode 100644 index 0000000000000..e4c5e5ee8cf78 --- /dev/null +++ b/recipes/bioconductor-pd.rta.1.0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rta.1.0 diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..f0f99b78f0634 --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rusgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0b9b00fee58ef211e041395052344483 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RUSGene-1_0-st' + diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..7a192701bce8a --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rusgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rusgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rusgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.0.st/bioconductor-pd.rusgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="0b9b00fee58ef211e041395052344483" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rusgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.rusgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..c0e7dc03fe422 --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rusgene.1.0.st diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..4513e18f66d31 --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.rusgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 228837c2de4a4b106806cb7f384564fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix RUSGene-1_1-st' + diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..29b4dd017bf4e --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.rusgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.rusgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.rusgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.rusgene.1.1.st/bioconductor-pd.rusgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="228837c2de4a4b106806cb7f384564fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.rusgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.rusgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..03ca612a5b2e2 --- /dev/null +++ b/recipes/bioconductor-pd.rusgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.rusgene.1.1.st diff --git a/recipes/bioconductor-pd.s.aureus/meta.yaml b/recipes/bioconductor-pd.s.aureus/meta.yaml new file mode 100644 index 0000000000000..d7334ebd4f7de --- /dev/null +++ b/recipes/bioconductor-pd.s.aureus/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.s.aureus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f173ae6e4316aaa2eafbde92d5868a5a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name S_aureus' + diff --git a/recipes/bioconductor-pd.s.aureus/post-link.sh b/recipes/bioconductor-pd.s.aureus/post-link.sh new file mode 100644 index 0000000000000..8ad18e28ccca6 --- /dev/null +++ b/recipes/bioconductor-pd.s.aureus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.s.aureus_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.s.aureus_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.s.aureus_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.s.aureus/bioconductor-pd.s.aureus_3.12.0_src_all.tar.gz" +) +MD5="f173ae6e4316aaa2eafbde92d5868a5a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.s.aureus/pre-unlink.sh b/recipes/bioconductor-pd.s.aureus/pre-unlink.sh new file mode 100644 index 0000000000000..4a27382226b47 --- /dev/null +++ b/recipes/bioconductor-pd.s.aureus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.s.aureus diff --git a/recipes/bioconductor-pd.soybean/meta.yaml b/recipes/bioconductor-pd.soybean/meta.yaml new file mode 100644 index 0000000000000..3455db067e1c8 --- /dev/null +++ b/recipes/bioconductor-pd.soybean/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.soybean" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6dbe167be9d40c1d9096485afb4525f0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Soybean' + diff --git a/recipes/bioconductor-pd.soybean/post-link.sh b/recipes/bioconductor-pd.soybean/post-link.sh new file mode 100644 index 0000000000000..a6d22d34e6336 --- /dev/null +++ b/recipes/bioconductor-pd.soybean/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.soybean_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soybean_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.soybean_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soybean/bioconductor-pd.soybean_3.12.0_src_all.tar.gz" +) +MD5="6dbe167be9d40c1d9096485afb4525f0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.soybean/pre-unlink.sh b/recipes/bioconductor-pd.soybean/pre-unlink.sh new file mode 100644 index 0000000000000..fe9cb3dfb7351 --- /dev/null +++ b/recipes/bioconductor-pd.soybean/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.soybean diff --git a/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..bc932a8cef225 --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.soygene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b264df0648ec35d04f91e0ef8e26ac95 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix SoyGene-1_0-st' + diff --git a/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh b/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..f470e1244acee --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.soygene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soygene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.soygene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.0.st/bioconductor-pd.soygene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="b264df0648ec35d04f91e0ef8e26ac95" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.soygene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.soygene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..e533326b0d37c --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.soygene.1.0.st diff --git a/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..9d88114b187ba --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.soygene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4a911a4a4b5de927fe6239e500a2993f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix SoyGene-1_1-st' + diff --git a/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh b/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..bb2b8935bd98e --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.soygene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.soygene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.soygene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.soygene.1.1.st/bioconductor-pd.soygene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="4a911a4a4b5de927fe6239e500a2993f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.soygene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.soygene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..988ef0ee46d60 --- /dev/null +++ b/recipes/bioconductor-pd.soygene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.soygene.1.1.st diff --git a/recipes/bioconductor-pd.sugar.cane/meta.yaml b/recipes/bioconductor-pd.sugar.cane/meta.yaml new file mode 100644 index 0000000000000..41fc8801affa5 --- /dev/null +++ b/recipes/bioconductor-pd.sugar.cane/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.sugar.cane" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bd7eb8b1a1c9ac77359358a5347330fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Sugar_Cane' + diff --git a/recipes/bioconductor-pd.sugar.cane/post-link.sh b/recipes/bioconductor-pd.sugar.cane/post-link.sh new file mode 100644 index 0000000000000..e63846ab1c367 --- /dev/null +++ b/recipes/bioconductor-pd.sugar.cane/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.sugar.cane_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.sugar.cane_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.sugar.cane_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.sugar.cane/bioconductor-pd.sugar.cane_3.12.0_src_all.tar.gz" +) +MD5="bd7eb8b1a1c9ac77359358a5347330fb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.sugar.cane/pre-unlink.sh b/recipes/bioconductor-pd.sugar.cane/pre-unlink.sh new file mode 100644 index 0000000000000..23320f44d6733 --- /dev/null +++ b/recipes/bioconductor-pd.sugar.cane/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.sugar.cane diff --git a/recipes/bioconductor-pd.tomato/meta.yaml b/recipes/bioconductor-pd.tomato/meta.yaml new file mode 100644 index 0000000000000..be349c4cc439d --- /dev/null +++ b/recipes/bioconductor-pd.tomato/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.tomato" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ce78f6ee43d72e017608413dd4d50580 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Tomato' + diff --git a/recipes/bioconductor-pd.tomato/post-link.sh b/recipes/bioconductor-pd.tomato/post-link.sh new file mode 100644 index 0000000000000..59a43d012ec00 --- /dev/null +++ b/recipes/bioconductor-pd.tomato/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.tomato_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.tomato_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.tomato_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.tomato/bioconductor-pd.tomato_3.12.0_src_all.tar.gz" +) +MD5="ce78f6ee43d72e017608413dd4d50580" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.tomato/pre-unlink.sh b/recipes/bioconductor-pd.tomato/pre-unlink.sh new file mode 100644 index 0000000000000..d1978dfc0371d --- /dev/null +++ b/recipes/bioconductor-pd.tomato/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.tomato diff --git a/recipes/bioconductor-pd.u133.x3p/meta.yaml b/recipes/bioconductor-pd.u133.x3p/meta.yaml new file mode 100644 index 0000000000000..90dfdeca57bde --- /dev/null +++ b/recipes/bioconductor-pd.u133.x3p/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.u133.x3p" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e3f343e32273667f851e26d7b8a7a5db +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name U133_X3P' + diff --git a/recipes/bioconductor-pd.u133.x3p/post-link.sh b/recipes/bioconductor-pd.u133.x3p/post-link.sh new file mode 100644 index 0000000000000..c7e2a713a2220 --- /dev/null +++ b/recipes/bioconductor-pd.u133.x3p/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.u133.x3p_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.u133.x3p_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.u133.x3p_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.u133.x3p/bioconductor-pd.u133.x3p_3.12.0_src_all.tar.gz" +) +MD5="e3f343e32273667f851e26d7b8a7a5db" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.u133.x3p/pre-unlink.sh b/recipes/bioconductor-pd.u133.x3p/pre-unlink.sh new file mode 100644 index 0000000000000..3cc12106c6e17 --- /dev/null +++ b/recipes/bioconductor-pd.u133.x3p/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.u133.x3p diff --git a/recipes/bioconductor-pd.vitis.vinifera/meta.yaml b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml new file mode 100644 index 0000000000000..121fcd62ead73 --- /dev/null +++ b/recipes/bioconductor-pd.vitis.vinifera/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.vitis.vinifera" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 104a8ac33a9baa25a61f953679795696 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Vitis_Vinifera' + diff --git a/recipes/bioconductor-pd.vitis.vinifera/post-link.sh b/recipes/bioconductor-pd.vitis.vinifera/post-link.sh new file mode 100644 index 0000000000000..7bdc1562f6f75 --- /dev/null +++ b/recipes/bioconductor-pd.vitis.vinifera/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.vitis.vinifera_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.vitis.vinifera_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.vitis.vinifera_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.vitis.vinifera/bioconductor-pd.vitis.vinifera_3.12.0_src_all.tar.gz" +) +MD5="104a8ac33a9baa25a61f953679795696" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.vitis.vinifera/pre-unlink.sh b/recipes/bioconductor-pd.vitis.vinifera/pre-unlink.sh new file mode 100644 index 0000000000000..3eb70885d0dd2 --- /dev/null +++ b/recipes/bioconductor-pd.vitis.vinifera/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.vitis.vinifera diff --git a/recipes/bioconductor-pd.wheat/meta.yaml b/recipes/bioconductor-pd.wheat/meta.yaml new file mode 100644 index 0000000000000..2f50c4d627816 --- /dev/null +++ b/recipes/bioconductor-pd.wheat/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.wheat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 38a7183c8d3b874cf62391a9e9169bb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name wheat' + diff --git a/recipes/bioconductor-pd.wheat/post-link.sh b/recipes/bioconductor-pd.wheat/post-link.sh new file mode 100644 index 0000000000000..9d5b91253068d --- /dev/null +++ b/recipes/bioconductor-pd.wheat/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.wheat_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.wheat_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.wheat_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.wheat/bioconductor-pd.wheat_3.12.0_src_all.tar.gz" +) +MD5="38a7183c8d3b874cf62391a9e9169bb9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.wheat/pre-unlink.sh b/recipes/bioconductor-pd.wheat/pre-unlink.sh new file mode 100644 index 0000000000000..17108236df7cc --- /dev/null +++ b/recipes/bioconductor-pd.wheat/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.wheat diff --git a/recipes/bioconductor-pd.x.laevis.2/meta.yaml b/recipes/bioconductor-pd.x.laevis.2/meta.yaml new file mode 100644 index 0000000000000..8cd5317c6b0be --- /dev/null +++ b/recipes/bioconductor-pd.x.laevis.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.x.laevis.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 32416957e3cdc11ad4dbfcd9141ff113 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name X_laevis_2' + diff --git a/recipes/bioconductor-pd.x.laevis.2/post-link.sh b/recipes/bioconductor-pd.x.laevis.2/post-link.sh new file mode 100644 index 0000000000000..314748e1db2ff --- /dev/null +++ b/recipes/bioconductor-pd.x.laevis.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.x.laevis.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.x.laevis.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.x.laevis.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.x.laevis.2/bioconductor-pd.x.laevis.2_3.12.0_src_all.tar.gz" +) +MD5="32416957e3cdc11ad4dbfcd9141ff113" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.x.laevis.2/pre-unlink.sh b/recipes/bioconductor-pd.x.laevis.2/pre-unlink.sh new file mode 100644 index 0000000000000..5fec7ed0f7e70 --- /dev/null +++ b/recipes/bioconductor-pd.x.laevis.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.x.laevis.2 diff --git a/recipes/bioconductor-pd.x.tropicalis/meta.yaml b/recipes/bioconductor-pd.x.tropicalis/meta.yaml new file mode 100644 index 0000000000000..9a76ae659c39b --- /dev/null +++ b/recipes/bioconductor-pd.x.tropicalis/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.x.tropicalis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 79a4de91831e4b0153495e12b9c6e8d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name X_tropicalis' + diff --git a/recipes/bioconductor-pd.x.tropicalis/post-link.sh b/recipes/bioconductor-pd.x.tropicalis/post-link.sh new file mode 100644 index 0000000000000..033c2aba64140 --- /dev/null +++ b/recipes/bioconductor-pd.x.tropicalis/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.x.tropicalis_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.x.tropicalis_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.x.tropicalis_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.x.tropicalis/bioconductor-pd.x.tropicalis_3.12.0_src_all.tar.gz" +) +MD5="79a4de91831e4b0153495e12b9c6e8d3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.x.tropicalis/pre-unlink.sh b/recipes/bioconductor-pd.x.tropicalis/pre-unlink.sh new file mode 100644 index 0000000000000..434c9d68a3c8e --- /dev/null +++ b/recipes/bioconductor-pd.x.tropicalis/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.x.tropicalis diff --git a/recipes/bioconductor-pd.xenopus.laevis/meta.yaml b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml new file mode 100644 index 0000000000000..53654ca08bc0c --- /dev/null +++ b/recipes/bioconductor-pd.xenopus.laevis/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.xenopus.laevis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6d5c2c9e8e3891770b1c6e9dcd823c0d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Xenopus_laevis' + diff --git a/recipes/bioconductor-pd.xenopus.laevis/post-link.sh b/recipes/bioconductor-pd.xenopus.laevis/post-link.sh new file mode 100644 index 0000000000000..12e5b07b39af8 --- /dev/null +++ b/recipes/bioconductor-pd.xenopus.laevis/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.xenopus.laevis_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.xenopus.laevis_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.xenopus.laevis_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.xenopus.laevis/bioconductor-pd.xenopus.laevis_3.12.0_src_all.tar.gz" +) +MD5="6d5c2c9e8e3891770b1c6e9dcd823c0d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.xenopus.laevis/pre-unlink.sh b/recipes/bioconductor-pd.xenopus.laevis/pre-unlink.sh new file mode 100644 index 0000000000000..7fc8a689ad0fc --- /dev/null +++ b/recipes/bioconductor-pd.xenopus.laevis/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.xenopus.laevis diff --git a/recipes/bioconductor-pd.yeast.2/meta.yaml b/recipes/bioconductor-pd.yeast.2/meta.yaml new file mode 100644 index 0000000000000..e2fb06e7b8471 --- /dev/null +++ b/recipes/bioconductor-pd.yeast.2/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.yeast.2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 780f5139ee9cda46c9e38122538ce129 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Yeast_2' + diff --git a/recipes/bioconductor-pd.yeast.2/post-link.sh b/recipes/bioconductor-pd.yeast.2/post-link.sh new file mode 100644 index 0000000000000..ab7a742336b8b --- /dev/null +++ b/recipes/bioconductor-pd.yeast.2/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.yeast.2_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.yeast.2_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.yeast.2_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.yeast.2/bioconductor-pd.yeast.2_3.12.0_src_all.tar.gz" +) +MD5="780f5139ee9cda46c9e38122538ce129" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.yeast.2/pre-unlink.sh b/recipes/bioconductor-pd.yeast.2/pre-unlink.sh new file mode 100644 index 0000000000000..e263211fc5955 --- /dev/null +++ b/recipes/bioconductor-pd.yeast.2/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.yeast.2 diff --git a/recipes/bioconductor-pd.yg.s98/meta.yaml b/recipes/bioconductor-pd.yg.s98/meta.yaml new file mode 100644 index 0000000000000..ca4801af96ddc --- /dev/null +++ b/recipes/bioconductor-pd.yg.s98/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.yg.s98" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: caec3e8f29918f078b2dc7c76f4a74e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name YG_S98' + diff --git a/recipes/bioconductor-pd.yg.s98/post-link.sh b/recipes/bioconductor-pd.yg.s98/post-link.sh new file mode 100644 index 0000000000000..bbcce2c024fab --- /dev/null +++ b/recipes/bioconductor-pd.yg.s98/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.yg.s98_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.yg.s98_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.yg.s98_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.yg.s98/bioconductor-pd.yg.s98_3.12.0_src_all.tar.gz" +) +MD5="caec3e8f29918f078b2dc7c76f4a74e2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.yg.s98/pre-unlink.sh b/recipes/bioconductor-pd.yg.s98/pre-unlink.sh new file mode 100644 index 0000000000000..99dc46ef4d6aa --- /dev/null +++ b/recipes/bioconductor-pd.yg.s98/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.yg.s98 diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml new file mode 100644 index 0000000000000..177a43e329723 --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.0.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.zebgene.1.0.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 54fcf757b8069e95dd7e2f3ff74ae050 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix ZebGene-1_0-st' + diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh b/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh new file mode 100644 index 0000000000000..f217b96288308 --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.0.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.zebgene.1.0.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebgene.1.0.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.zebgene.1.0.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.0.st/bioconductor-pd.zebgene.1.0.st_3.12.0_src_all.tar.gz" +) +MD5="54fcf757b8069e95dd7e2f3ff74ae050" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.zebgene.1.0.st/pre-unlink.sh b/recipes/bioconductor-pd.zebgene.1.0.st/pre-unlink.sh new file mode 100644 index 0000000000000..ff70896e1f5cd --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.0.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.zebgene.1.0.st diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml new file mode 100644 index 0000000000000..6eb1b2cccf67b --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.1.st/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.zebgene.1.1.st" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d87028cd9024bc33be518635cf2f48fc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for Affymetrix ZebGene-1_1-st' + diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh b/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh new file mode 100644 index 0000000000000..c18a403206093 --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.1.st/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.zebgene.1.1.st_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebgene.1.1.st_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.zebgene.1.1.st_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebgene.1.1.st/bioconductor-pd.zebgene.1.1.st_3.12.0_src_all.tar.gz" +) +MD5="d87028cd9024bc33be518635cf2f48fc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.zebgene.1.1.st/pre-unlink.sh b/recipes/bioconductor-pd.zebgene.1.1.st/pre-unlink.sh new file mode 100644 index 0000000000000..3d3ce8f4bc803 --- /dev/null +++ b/recipes/bioconductor-pd.zebgene.1.1.st/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.zebgene.1.1.st diff --git a/recipes/bioconductor-pd.zebrafish/meta.yaml b/recipes/bioconductor-pd.zebrafish/meta.yaml new file mode 100644 index 0000000000000..3762d72509e1b --- /dev/null +++ b/recipes/bioconductor-pd.zebrafish/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "3.12.0" %} +{% set name = "pd.zebrafish" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 101f09a9d9304d1d8fbcc7f4812897b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-dbi >=0.3.1' + - 'r-rsqlite >=1.0.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Platform Design Info for The Manufacturer''s Name Zebrafish' + diff --git a/recipes/bioconductor-pd.zebrafish/post-link.sh b/recipes/bioconductor-pd.zebrafish/post-link.sh new file mode 100644 index 0000000000000..8c0d249d03995 --- /dev/null +++ b/recipes/bioconductor-pd.zebrafish/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pd.zebrafish_3.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pd.zebrafish_3.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/pd.zebrafish_3.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pd.zebrafish/bioconductor-pd.zebrafish_3.12.0_src_all.tar.gz" +) +MD5="101f09a9d9304d1d8fbcc7f4812897b1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pd.zebrafish/pre-unlink.sh b/recipes/bioconductor-pd.zebrafish/pre-unlink.sh new file mode 100644 index 0000000000000..fd63a7c292642 --- /dev/null +++ b/recipes/bioconductor-pd.zebrafish/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pd.zebrafish diff --git a/recipes/bioconductor-pdinfobuilder/build.sh b/recipes/bioconductor-pdinfobuilder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pdinfobuilder/build.sh +++ b/recipes/bioconductor-pdinfobuilder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml b/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-pdinfobuilder/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-pdinfobuilder/meta.yaml b/recipes/bioconductor-pdinfobuilder/meta.yaml index 70fbafad106fe..c6f8cd11105eb 100644 --- a/recipes/bioconductor-pdinfobuilder/meta.yaml +++ b/recipes/bioconductor-pdinfobuilder/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "pdInfoBuilder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 96f94b99e7db9a2a38dfa19cc518c87fddc465aeb654b5033933959914bcb172 + md5: 11f99f8aa61c41052f80979136449ca7 build: number: 0 rpaths: @@ -18,26 +18,26 @@ build: - lib/ requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-dbi >=0.3.1' - 'r-rsqlite >=1.0.0' @@ -48,10 +48,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Builds platform design information packages. These consist of a SQLite database containing feature-level data such as x, y position on chip and featureSet ID. The database also incorporates featureSet-level annotation data. The products of this packages are used by the oligo pkg.' extra: identifiers: - biotools:pdinfobuilder - doi:10.1093/bioinformatics/btq431 + parent_recipe: + name: bioconductor-pdinfobuilder + path: recipes/bioconductor-pdinfobuilder + version: 1.44.0 + diff --git a/recipes/bioconductor-peca/build.sh b/recipes/bioconductor-peca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-peca/build.sh +++ b/recipes/bioconductor-peca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-peca/conda_build_config.yaml b/recipes/bioconductor-peca/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-peca/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-peca/meta.yaml b/recipes/bioconductor-peca/meta.yaml index 094c365561e83..b3ed613696253 100644 --- a/recipes/bioconductor-peca/meta.yaml +++ b/recipes/bioconductor-peca/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "PECA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5b2e956f358d0c71ba825d877f4fa8c9085bdb6dc6ab750230535c5996bc42f + md5: 0403c0ac60f05fb12d20f3c186e0c140 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: SpikeIn requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rots >=1.8.0,<1.10.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rots >=1.10.0,<1.11.0' - r-aroma.affymetrix - r-aroma.core - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rots >=1.8.0,<1.10.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rots >=1.10.0,<1.11.0' - r-aroma.affymetrix - r-aroma.core - r-base @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Calculates Probe-level Expression Change Averages (PECA) to identify differential expression in Affymetrix gene expression microarray studies or in proteomic studies using peptide-level mesurements respectively.' extra: identifiers: - biotools:peca - doi:10.1007/978-1-4939-6518-2_11 + parent_recipe: + name: bioconductor-peca + path: recipes/bioconductor-peca + version: 1.16.0 + diff --git a/recipes/bioconductor-pedbarrayv10.db/meta.yaml b/recipes/bioconductor-pedbarrayv10.db/meta.yaml new file mode 100644 index 0000000000000..f6379720bc6de --- /dev/null +++ b/recipes/bioconductor-pedbarrayv10.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "pedbarrayv10.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 25acc3bfee229015ecca1c7d688e5168 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Nelson Lab pedbarrayv10 Annotation Data (pedbarrayv10) assembled using data from public repositories' + diff --git a/recipes/bioconductor-pedbarrayv10.db/post-link.sh b/recipes/bioconductor-pedbarrayv10.db/post-link.sh new file mode 100644 index 0000000000000..e1f720830c869 --- /dev/null +++ b/recipes/bioconductor-pedbarrayv10.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pedbarrayv10.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pedbarrayv10.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/pedbarrayv10.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv10.db/bioconductor-pedbarrayv10.db_3.2.3_src_all.tar.gz" +) +MD5="25acc3bfee229015ecca1c7d688e5168" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pedbarrayv10.db/pre-unlink.sh b/recipes/bioconductor-pedbarrayv10.db/pre-unlink.sh new file mode 100644 index 0000000000000..565a49a88e953 --- /dev/null +++ b/recipes/bioconductor-pedbarrayv10.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pedbarrayv10.db diff --git a/recipes/bioconductor-pedbarrayv9.db/meta.yaml b/recipes/bioconductor-pedbarrayv9.db/meta.yaml new file mode 100644 index 0000000000000..9ffa2202f5cf0 --- /dev/null +++ b/recipes/bioconductor-pedbarrayv9.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "pedbarrayv9.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: da4b2f9c0a672e0c9ee53f017bacaff7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'FHCRC Nelson Lab pedbarrayv9 Annotation Data (pedbarrayv9) assembled using data from public repositories' + diff --git a/recipes/bioconductor-pedbarrayv9.db/post-link.sh b/recipes/bioconductor-pedbarrayv9.db/post-link.sh new file mode 100644 index 0000000000000..1e9c2ffa4b060 --- /dev/null +++ b/recipes/bioconductor-pedbarrayv9.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pedbarrayv9.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pedbarrayv9.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/pedbarrayv9.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pedbarrayv9.db/bioconductor-pedbarrayv9.db_3.2.3_src_all.tar.gz" +) +MD5="da4b2f9c0a672e0c9ee53f017bacaff7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pedbarrayv9.db/pre-unlink.sh b/recipes/bioconductor-pedbarrayv9.db/pre-unlink.sh new file mode 100644 index 0000000000000..dd67a16fdeacc --- /dev/null +++ b/recipes/bioconductor-pedbarrayv9.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pedbarrayv9.db diff --git a/recipes/bioconductor-pepdat/meta.yaml b/recipes/bioconductor-pepdat/meta.yaml new file mode 100644 index 0000000000000..9e98dbf7bd463 --- /dev/null +++ b/recipes/bioconductor-pepdat/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2.0" %} +{% set name = "pepDat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6348dfe04bb83e78df150d7f67fb3e03 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides sample files and data for the vignettes of pepStat and Pviz as well as peptide collections for HIV and SIV.' + diff --git a/recipes/bioconductor-pepdat/post-link.sh b/recipes/bioconductor-pepdat/post-link.sh new file mode 100644 index 0000000000000..563fe1ea0e559 --- /dev/null +++ b/recipes/bioconductor-pepdat/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pepDat_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pepDat_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/pepDat_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pepdat/bioconductor-pepdat_1.2.0_src_all.tar.gz" +) +MD5="6348dfe04bb83e78df150d7f67fb3e03" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pepdat/pre-unlink.sh b/recipes/bioconductor-pepdat/pre-unlink.sh new file mode 100644 index 0000000000000..9be4906267754 --- /dev/null +++ b/recipes/bioconductor-pepdat/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pepDat diff --git a/recipes/bioconductor-pepsnmr/build.sh b/recipes/bioconductor-pepsnmr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pepsnmr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pepsnmr/meta.yaml b/recipes/bioconductor-pepsnmr/meta.yaml new file mode 100644 index 0000000000000..c95594739aa02 --- /dev/null +++ b/recipes/bioconductor-pepsnmr/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.1" %} +{% set name = "PepsNMR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7c24032f0d642d8d5965d0f60f9d1cf8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, markdown, rmarkdown, BiocStyle, PepsNMRData +requirements: + host: + - r-base + - r-ggplot2 + - r-gridextra + - r-matrix + - r-matrixstats + - r-ptw + - r-reshape2 + run: + - r-base + - r-ggplot2 + - r-gridextra + - r-matrix + - r-matrixstats + - r-ptw + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-2 | file LICENSE' + summary: 'This package provides R functions for common pre-procssing steps that are applied on 1H-NMR data. It also provides a function to read the FID signals directly in the Bruker format.' + diff --git a/recipes/bioconductor-pepsnmrdata/meta.yaml b/recipes/bioconductor-pepsnmrdata/meta.yaml new file mode 100644 index 0000000000000..f782f0ffbbff4 --- /dev/null +++ b/recipes/bioconductor-pepsnmrdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "PepsNMRData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ef7f2931dab1c82cb13f7b1af8bfd91f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, markdown, rmarkdown, BiocStyle +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL-2 | file LICENSE' + summary: 'This package contains all the datasets used in the PepsNMR package.' + diff --git a/recipes/bioconductor-pepsnmrdata/post-link.sh b/recipes/bioconductor-pepsnmrdata/post-link.sh new file mode 100644 index 0000000000000..cc029a12c3e5c --- /dev/null +++ b/recipes/bioconductor-pepsnmrdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PepsNMRData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PepsNMRData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/PepsNMRData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pepsnmrdata/bioconductor-pepsnmrdata_1.0.0_src_all.tar.gz" +) +MD5="ef7f2931dab1c82cb13f7b1af8bfd91f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pepsnmrdata/pre-unlink.sh b/recipes/bioconductor-pepsnmrdata/pre-unlink.sh new file mode 100644 index 0000000000000..b1831ff7e4b96 --- /dev/null +++ b/recipes/bioconductor-pepsnmrdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PepsNMRData diff --git a/recipes/bioconductor-pepstat/build.sh b/recipes/bioconductor-pepstat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pepstat/build.sh +++ b/recipes/bioconductor-pepstat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pepstat/meta.yaml b/recipes/bioconductor-pepstat/meta.yaml index 3606270eb4883..a0122ed4519ff 100644 --- a/recipes/bioconductor-pepstat/meta.yaml +++ b/recipes/bioconductor-pepstat/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pepStat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8e38350bee8eb0ebbaff0a1f3f7a1351a926593656b81dc64d6829d3523c3f4a + md5: c232a1a342e9683a99da75bc419d5f71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pepDat, Pviz, knitr, shiny requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-data.table - r-fields - r-ggplot2 - r-plyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-data.table - r-fields @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Statistical analysis of peptide microarrays' extra: identifiers: - biotools:pepstat - doi:10.1007/978-1-4939-3037-1_10 + parent_recipe: + name: bioconductor-pepstat + path: recipes/bioconductor-pepstat + version: 1.14.0 + diff --git a/recipes/bioconductor-pepxmltab/build.sh b/recipes/bioconductor-pepxmltab/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pepxmltab/build.sh +++ b/recipes/bioconductor-pepxmltab/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pepxmltab/meta.yaml b/recipes/bioconductor-pepxmltab/meta.yaml index efe4dfe2e16bc..72cb44cb66b2a 100644 --- a/recipes/bioconductor-pepxmltab/meta.yaml +++ b/recipes/bioconductor-pepxmltab/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pepXMLTab" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9e7613524c4d765c98dde2ba858e0727217f34427c76f6ee7213ac52bf157b24 + md5: a3075fd32320e746d5f22c265d7dc2d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Parsing pepXML files based one XML package. The package tries to handle pepXML files generated from different softwares. The output will be a peptide-spectrum-matching tabular file. The package also provide function to filter the PSMs based on FDR.' extra: identifiers: - biotools:pepxmltab - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pepxmltab + path: recipes/bioconductor-pepxmltab + version: 1.14.0 + diff --git a/recipes/bioconductor-perturbatr/build.sh b/recipes/bioconductor-perturbatr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-perturbatr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-perturbatr/meta.yaml b/recipes/bioconductor-perturbatr/meta.yaml new file mode 100644 index 0000000000000..3dc67dd2742dd --- /dev/null +++ b/recipes/bioconductor-perturbatr/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.2.0" %} +{% set name = "perturbatr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3efea2de3bac5c285a4b6a9979d06ddc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, lintr, knitr, rmarkdown, BiocStyle +requirements: + host: + - r-assertthat + - r-base + - r-diffusr + - r-doparallel + - r-dplyr + - r-foreach + - r-formula.tools + - r-ggplot2 + - r-igraph + - r-lazyeval + - r-lme4 + - r-magrittr + - r-rlang + - r-scales + - r-tibble + - r-tidyr + run: + - r-assertthat + - r-base + - r-diffusr + - r-doparallel + - r-dplyr + - r-foreach + - r-formula.tools + - r-ggplot2 + - r-igraph + - r-lazyeval + - r-lme4 + - r-magrittr + - r-rlang + - r-scales + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'perturbatr does stage-wise analysis of large-scale genetic perturbation screens for integrated data sets consisting of multiple screens. For multiple integrated perturbation screens a hierarchical model that considers the variance between different biological conditions is fitted. The resulting list of gene effects is then further extended using a network propagation algorithm to correct for false negatives.' + diff --git a/recipes/bioconductor-pfam.db/meta.yaml b/recipes/bioconductor-pfam.db/meta.yaml index 8d8fb59ddf021..22f829432db80 100644 --- a/recipes/bioconductor-pfam.db/meta.yaml +++ b/recipes/bioconductor-pfam.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "3.6.0" %} +{% set version = "3.7.0" %} {% set name = "PFAM.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3d020c7c6e0001bfc5b787d499bd6955d8916cc518c05d198082f219f4e599fe + md5: 4d7be786ff8dcff586998dc8fea9cf04 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: DBI requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'A set of protein ID mappings for PFAM assembled using data from public repositories' - +extra: + parent_recipe: + name: bioconductor-pfam.db + path: recipes/bioconductor-pfam.db + version: 3.6.0 diff --git a/recipes/bioconductor-pfam.db/post-link.sh b/recipes/bioconductor-pfam.db/post-link.sh index 7122705ed29e1..85bd62d0b2943 100644 --- a/recipes/bioconductor-pfam.db/post-link.sh +++ b/recipes/bioconductor-pfam.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="PFAM.db_3.6.0.tar.gz" +FN="PFAM.db_3.7.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/PFAM.db_3.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/PFAM.db_3.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PFAM.db_3.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/PFAM.db_3.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pfam.db/bioconductor-pfam.db_3.7.0_src_all.tar.gz" ) -MD5="84bf0f03fdf923d0be6d1c9eb18d54fb" +MD5="4d7be786ff8dcff586998dc8fea9cf04" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-pga/build.sh b/recipes/bioconductor-pga/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pga/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pga/meta.yaml b/recipes/bioconductor-pga/meta.yaml new file mode 100644 index 0000000000000..a0210cbab21ac --- /dev/null +++ b/recipes/bioconductor-pga/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.12.0" %} +{% set name = "PGA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f1a70d32276232c239cf7fe5ff102cb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RMariaDB, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocGenerics, BiocStyle, knitr, R.utils +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-customprodb >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-data.table + - r-ggplot2 + - r-nozzle.r1 + - r-pheatmap + - r-rcurl + - r-rsqlite + - r-stringr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-customprodb >=1.22.0,<1.23.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - r-data.table + - r-ggplot2 + - r-nozzle.r1 + - r-pheatmap + - r-rcurl + - r-rsqlite + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides functions for construction of customized protein databases based on RNA-Seq data with/without genome guided, database searching, post-processing and report generation. This kind of customized protein database includes both the reference database (such as Refseq or ENSEMBL) and the novel peptide sequences form RNA-Seq data.' + diff --git a/recipes/bioconductor-pgca/build.sh b/recipes/bioconductor-pgca/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pgca/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pgca/meta.yaml b/recipes/bioconductor-pgca/meta.yaml new file mode 100644 index 0000000000000..c9d68fa6a9150 --- /dev/null +++ b/recipes/bioconductor-pgca/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "pgca" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d900d4d7834d080450eb99f31843f122 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Protein Group Code Algorithm (PGCA) is a computationally inexpensive algorithm to merge protein summaries from multiple experimental quantitative proteomics data. The algorithm connects two or more groups with overlapping accession numbers. In some cases, pairwise groups are mutually exclusive but they may still be connected by another group (or set of groups) with overlapping accession numbers. Thus, groups created by PGCA from multiple experimental runs (i.e., global groups) are called "connected" groups. These identified global protein groups enable the analysis of quantitative data available for protein groups instead of unique protein identifiers.' + diff --git a/recipes/bioconductor-pgsea/build.sh b/recipes/bioconductor-pgsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pgsea/build.sh +++ b/recipes/bioconductor-pgsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pgsea/meta.yaml b/recipes/bioconductor-pgsea/meta.yaml index 6583101d6bbc9..bdb6bec05995a 100644 --- a/recipes/bioconductor-pgsea/meta.yaml +++ b/recipes/bioconductor-pgsea/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "PGSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a6ede559ce880fbf526dc09fa92252d00e5628eff1cae9605b1277ede196335b + md5: 59661093e4e69ad9cb79b2f1243da19e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GSEABase, GEOquery, org.Hs.eg.db, hgu95av2.db, limma requirements: host: - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base run: - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Parametric Analysis of Gene Set Enrichment' extra: identifiers: - biotools:pgsea - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pgsea + path: recipes/bioconductor-pgsea + version: 1.54.0 + diff --git a/recipes/bioconductor-phantasus/build.sh b/recipes/bioconductor-phantasus/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phantasus/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phantasus/meta.yaml b/recipes/bioconductor-phantasus/meta.yaml new file mode 100644 index 0000000000000..50be37d0706ce --- /dev/null +++ b/recipes/bioconductor-phantasus/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.2.0" %} +{% set name = "phantasus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f759d524b532e8ff5d11ea068193449 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, data.table +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-assertthat + - r-base + - r-ccapp + - r-ggplot2 + - r-gtable + - r-htmltools + - r-httpuv + - r-httr + - r-jsonlite + - r-matrix + - r-matrix.utils + - r-opencpu + - r-pheatmap + - r-protolite + - r-rook + - r-scales + - r-stringr + - r-svglite + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - r-assertthat + - r-base + - r-ccapp + - r-ggplot2 + - r-gtable + - r-htmltools + - r-httpuv + - r-httr + - r-jsonlite + - r-matrix + - r-matrix.utils + - r-opencpu + - r-pheatmap + - r-protolite + - r-rook + - r-scales + - r-stringr + - r-svglite +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Phantasus is a web-application for visual and interactive gene expression analysis. Phantasus is based on Morpheus – a web-based software for heatmap visualisation and analysis, which was integrated with an R environment via OpenCPU API. Aside from basic visualization and filtering methods, R-based methods such as k-means clustering, principal component analysis or differential expression analysis with limma package are supported.' + diff --git a/recipes/bioconductor-pharmacogx/build.sh b/recipes/bioconductor-pharmacogx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pharmacogx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pharmacogx/meta.yaml b/recipes/bioconductor-pharmacogx/meta.yaml new file mode 100644 index 0000000000000..59c68d93e5f9c --- /dev/null +++ b/recipes/bioconductor-pharmacogx/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.12.0" %} +{% set name = "PharmacoGx" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd3a5c92c8622f561b3c1cd6fe35e21b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xtable, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-piano >=1.22.0,<1.23.0' + - r-base + - r-catools + - r-downloader + - r-lsa + - r-magicaxis + - r-rcolorbrewer + - r-reshape2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-piano >=1.22.0,<1.23.0' + - r-base + - r-catools + - r-downloader + - r-lsa + - r-magicaxis + - r-rcolorbrewer + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains a set of functions to perform large-scale analysis of pharmacogenomic data.' + diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml index 2fd9f058d2491..c4124ff31ca39 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/meta.yaml @@ -1,43 +1,50 @@ {% set version = "3.7.2" %} {% set name = "phastCons100way.UCSC.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ca052a0f6e874bcc8079b29e3cc1a29cb6b852b32d5a7a45dea5cff7c924acca + md5: 65aa706a567f7e328dbba0095f995cf1 build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Store UCSC phastCons conservation scores for the human genome (hg19) calculated from multiple alignments with other 99 vertebrate species.' +extra: + parent_recipe: + name: bioconductor-phastcons100way.ucsc.hg19 + path: recipes/bioconductor-phastcons100way.ucsc.hg19 + version: 3.7.2 + diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh index e75d327f1937a..14b405c87ef61 100644 --- a/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh +++ b/recipes/bioconductor-phastcons100way.ucsc.hg19/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="phastCons100way.UCSC.hg19_3.7.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons100way.UCSC.hg19_3.7.2.tar.gz" "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg19_3.7.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg19/bioconductor-phastcons100way.ucsc.hg19_3.7.2_src_all.tar.gz" ) MD5="65aa706a567f7e328dbba0095f995cf1" diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml new file mode 100644 index 0000000000000..e98a973830ada --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.1" %} +{% set name = "phastCons100way.UCSC.hg38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 878c757f9270b3410d11e4e4a4213c8e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 99 vertebrate species.' + diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh b/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh new file mode 100644 index 0000000000000..1eaf5fc2742b9 --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="phastCons100way.UCSC.hg38_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons100way.UCSC.hg38_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/phastCons100way.UCSC.hg38_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons100way.ucsc.hg38/bioconductor-phastcons100way.ucsc.hg38_3.7.1_src_all.tar.gz" +) +MD5="878c757f9270b3410d11e4e4a4213c8e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-phastcons100way.ucsc.hg38/pre-unlink.sh b/recipes/bioconductor-phastcons100way.ucsc.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..7330e626fe190 --- /dev/null +++ b/recipes/bioconductor-phastcons100way.ucsc.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ phastCons100way.UCSC.hg38 diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml new file mode 100644 index 0000000000000..b2ffcbf010e7a --- /dev/null +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "3.7.1" %} +{% set name = "phastCons7way.UCSC.hg38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c2d87446b022c166c1c325ea2aef521d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Store UCSC phastCons conservation scores for the human genome (hg38) calculated from multiple alignments with other 6 vertebrate species.' + diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh b/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh new file mode 100644 index 0000000000000..1fcf36d1951f8 --- /dev/null +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="phastCons7way.UCSC.hg38_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/phastCons7way.UCSC.hg38_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/phastCons7way.UCSC.hg38_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-phastcons7way.ucsc.hg38/bioconductor-phastcons7way.ucsc.hg38_3.7.1_src_all.tar.gz" +) +MD5="c2d87446b022c166c1c325ea2aef521d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-phastcons7way.ucsc.hg38/pre-unlink.sh b/recipes/bioconductor-phastcons7way.ucsc.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..9013eaf30ef9c --- /dev/null +++ b/recipes/bioconductor-phastcons7way.ucsc.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ phastCons7way.UCSC.hg38 diff --git a/recipes/bioconductor-phenodist/conda_build_config.yaml b/recipes/bioconductor-phenodist/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-phenodist/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-phenopath/build.sh b/recipes/bioconductor-phenopath/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phenopath/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phenopath/meta.yaml b/recipes/bioconductor-phenopath/meta.yaml new file mode 100644 index 0000000000000..80f98a39da934 --- /dev/null +++ b/recipes/bioconductor-phenopath/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.6.0" %} +{% set name = "phenopath" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 212dfa7aecc32424ce587400cad72b1b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, forcats, testthat, BiocStyle, SingleCellExperiment +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-ggplot2 + - 'r-rcpp >=0.12.8' + - r-tibble + - r-tidyr + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-ggplot2 + - 'r-rcpp >=0.12.8' + - r-tibble + - r-tidyr + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (== 2.0)' + summary: 'PhenoPath infers genomic trajectories (pseudotimes) in the presence of heterogeneous genetic and environmental backgrounds and tests for interactions between them.' + diff --git a/recipes/bioconductor-phenotest/build.sh b/recipes/bioconductor-phenotest/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phenotest/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phenotest/meta.yaml b/recipes/bioconductor-phenotest/meta.yaml new file mode 100644 index 0000000000000..608f9b0ae5228 --- /dev/null +++ b/recipes/bioconductor-phenotest/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.30.0" %} +{% set name = "phenoTest" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 448ca78e9eca883a0f9801e31a0e4336 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GSEABase, KEGG.db, GO.db +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hopach >=2.42.0,<2.43.0' + - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - r-base + - r-bma + - r-ellipse + - r-ggplot2 + - r-gplots + - r-hmisc + - r-mgcv + - r-survival + - r-xtable + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-hgu133a.db >=3.2.0,<3.3.0' + - 'bioconductor-hopach >=2.42.0,<2.43.0' + - 'bioconductor-htsanalyzer >=2.34.0,<2.35.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-snpchip >=2.28.0,<2.29.0' + - r-base + - r-bma + - r-ellipse + - r-ggplot2 + - r-gplots + - r-hmisc + - r-mgcv + - r-survival + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Tools to test correlation between gene expression and phenotype in a way that is efficient, structured, fast and scalable. GSEA is also provided.' + diff --git a/recipes/bioconductor-phenstat/build.sh b/recipes/bioconductor-phenstat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-phenstat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phenstat/meta.yaml b/recipes/bioconductor-phenstat/meta.yaml new file mode 100644 index 0000000000000..6bc67e6fd8fdd --- /dev/null +++ b/recipes/bioconductor-phenstat/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "2.18.0" %} +{% set name = "PhenStat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fc479cbe4ee7b44cc984c3fbdc85b729 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-car + - r-corrplot + - r-ggplot2 + - r-knitr + - r-lme4 + - r-logistf + - r-mass + - r-msgps + - r-nlme + - r-nortest + - r-pingr + - r-reshape + - r-smoothwin + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-car + - r-corrplot + - r-ggplot2 + - r-knitr + - r-lme4 + - r-logistf + - r-mass + - r-msgps + - r-nlme + - r-nortest + - r-pingr + - r-reshape + - r-smoothwin +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Package contains methods for statistical analysis of phenotypic data.' + diff --git a/recipes/bioconductor-philr/build.sh b/recipes/bioconductor-philr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-philr/build.sh +++ b/recipes/bioconductor-philr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-philr/meta.yaml b/recipes/bioconductor-philr/meta.yaml index 0b7c58127b535..5ec0b9aa5c3ae 100644 --- a/recipes/bioconductor-philr/meta.yaml +++ b/recipes/bioconductor-philr/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "philr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 09f25c62ac4c8332a2066b932c141716ed7d0d0d2e00fecfb63a564e78c71d1e + md5: c0d3c03a1218b6f60c44667211f4ea63 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocStyle, phyloseq, glmnet, dplyr requirements: host: - - 'bioconductor-ggtree >=1.12.7,<1.14.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' - r-ape - r-base - r-ggplot2 - r-phangorn - r-tidyr run: - - 'bioconductor-ggtree >=1.12.7,<1.14.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' - r-ape - r-base - r-ggplot2 @@ -35,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.' + summary: 'PhILR is short for Phylogenetic Isometric Log-Ratio Transform. This package provides functions for the analysis of compositional data (e.g., data representing proportions of different variables/parts). Specifically this package allows analysis of compositional data where the parts can be related through a phylogenetic tree (as is common in microbiota survey data) and makes available the Isometric Log Ratio transform built from the phylogenetic tree and utilizing a weighted reference measure.' extra: identifiers: - biotools:philr + parent_recipe: + name: bioconductor-philr + path: recipes/bioconductor-philr + version: 1.6.0 + diff --git a/recipes/bioconductor-phosphonormalizer/build.sh b/recipes/bioconductor-phosphonormalizer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-phosphonormalizer/build.sh +++ b/recipes/bioconductor-phosphonormalizer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phosphonormalizer/meta.yaml b/recipes/bioconductor-phosphonormalizer/meta.yaml index c9103885ae6fc..9ce40608185b1 100644 --- a/recipes/bioconductor-phosphonormalizer/meta.yaml +++ b/recipes/bioconductor-phosphonormalizer/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "phosphonormalizer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9cde4fffab81f5523e754d8cb5f4e7a3e9d370863311f586bf78f42834ccb882 + md5: c2476b36059d282f900701bc4982e9fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat requirements: host: - r-base @@ -29,8 +31,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'It uses the overlap between enriched and non-enriched datasets to compensate for the bias introduced in global phosphorylation after applying median normalization.' - +extra: + parent_recipe: + name: bioconductor-phosphonormalizer + path: recipes/bioconductor-phosphonormalizer + version: 1.4.0 diff --git a/recipes/bioconductor-phyloseq/build.sh b/recipes/bioconductor-phyloseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-phyloseq/build.sh +++ b/recipes/bioconductor-phyloseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-phyloseq/meta.yaml b/recipes/bioconductor-phyloseq/meta.yaml index c65b83ab85d3e..83f0465c73fbd 100644 --- a/recipes/bioconductor-phyloseq/meta.yaml +++ b/recipes/bioconductor-phyloseq/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.24.2" %} +{% set version = "1.26.0" %} {% set name = "phyloseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1415d5b3ad475b46dc1e6d4ca962c45b544469e4adf403e783fa714fb4d6b11c + md5: f7030242a6dd0626c1006d0268c44b64 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle (>= 2.4), DESeq2 (>= 1.16.1), genefilter (>= 1.58), knitr (>= 1.16), metagenomeSeq (>= 1.14), rmarkdown (>= 1.6), testthat (>= 1.0.2) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomformat >=1.8.0,<1.10.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomformat >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base @@ -36,11 +38,11 @@ requirements: - 'r-scales >=0.4.0' - 'r-vegan >=2.5' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomformat >=1.8.0,<1.10.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomformat >=1.10.0,<1.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - 'r-ade4 >=1.7.4' - 'r-ape >=5.0' - r-base @@ -57,9 +59,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'phyloseq provides a set of classes and tools to facilitate the import, storage, analysis, and graphical display of microbiome census data.' extra: identifiers: - biotools:phyloseq + parent_recipe: + name: bioconductor-phyloseq + path: recipes/bioconductor-phyloseq + version: 1.24.2 + diff --git a/recipes/bioconductor-pi/build.sh b/recipes/bioconductor-pi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pi/meta.yaml b/recipes/bioconductor-pi/meta.yaml new file mode 100644 index 0000000000000..4a2559d3390a3 --- /dev/null +++ b/recipes/bioconductor-pi/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.10.0" %} +{% set name = "Pi" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2fc7306e9555e44f153cf1b2b48802e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: foreach, doParallel, BiocStyle, knitr, rmarkdown, png, GGally, gridExtra, ExpressionAtlas, ggforce, fgsea, pathview, tidyr +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-suprahex >=1.20.0,<1.21.0' + - r-base + - r-caret + - r-dnet + - r-ggplot2 + - r-ggrepel + - r-glmnet + - r-igraph + - r-lattice + - r-mass + - r-matrix + - r-plot3d + - r-randomforest + - r-rocr + - r-scales + - r-xgr + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-suprahex >=1.20.0,<1.21.0' + - r-base + - r-caret + - r-dnet + - r-ggplot2 + - r-ggrepel + - r-glmnet + - r-igraph + - r-lattice + - r-mass + - r-matrix + - r-plot3d + - r-randomforest + - r-rocr + - r-scales + - r-xgr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Priority index or Pi is developed as a genomic-led target prioritisation system, with the focus on leveraging human genetic data to prioritise potential drug targets at the gene, pathway and network level. The long term goal is to use such information to enhance early-stage target validation. Based on evidence of disease association from genome-wide association studies (GWAS), this prioritisation system is able to generate evidence to support identification of the specific modulated genes (seed genes) that are responsible for the genetic association signal by utilising knowledge of linkage disequilibrium (co-inherited genetic variants), distance of associated variants from the gene, evidence of independent genetic association with gene expression in disease-relevant tissues, cell types and states, and evidence of physical interactions between disease-associated genetic variants and gene promoters based on genome-wide capture HiC-generated promoter interactomes in primary blood cell types. Seed genes are scored in an integrative way, quantifying the genetic influence. Scored seed genes are subsequently used as baits to rank seed genes plus additional (non-seed) genes; this is achieved by iteratively exploring the global connectivity of a gene interaction network. Genes with the highest priority are further used to identify/prioritise pathways that are significantly enriched with highly prioritised genes. Prioritised genes are also used to identify a gene network interconnecting highly prioritised genes and a minimal number of less prioritised genes (which act as linkers bringing together highly prioritised genes).' + diff --git a/recipes/bioconductor-piano/build.sh b/recipes/bioconductor-piano/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-piano/build.sh +++ b/recipes/bioconductor-piano/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-piano/meta.yaml b/recipes/bioconductor-piano/meta.yaml index 3d074fcc5456e..1dc3f6533c707 100644 --- a/recipes/bioconductor-piano/meta.yaml +++ b/recipes/bioconductor-piano/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "piano" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11e0122d1189add38471fb1525f43b66a118512c687cb84acbfb55f4c797acdf + md5: ddf4cefb13b149cbac5ee9ecec0ffbc8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: yeast2.db, rsbml, plotrix, limma, affy, plier, affyPLM, gtools, biomaRt, snowfall, AnnotationDbi requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-gplots - r-igraph - r-relations run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-gplots - r-igraph @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Piano performs gene set analysis using various statistical methods, from different gene level statistics and a wide range of gene-set collections. Furthermore, the Piano package contains functions for combining the results of multiple runs of gene set analyses.' extra: identifiers: - biotools:piano + parent_recipe: + name: bioconductor-piano + path: recipes/bioconductor-piano + version: 1.20.1 + diff --git a/recipes/bioconductor-pickgene/build.sh b/recipes/bioconductor-pickgene/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pickgene/build.sh +++ b/recipes/bioconductor-pickgene/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pickgene/meta.yaml b/recipes/bioconductor-pickgene/meta.yaml index 2ceca0dd3bd93..9c5f8a8a4f301 100644 --- a/recipes/bioconductor-pickgene/meta.yaml +++ b/recipes/bioconductor-pickgene/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "pickgene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 30c46613430711840bd7453bd3c597e077258c1e2cc5e6d3169c4a138b232ddb + md5: 8c766281cb3b997e869fb2afe3ab0a03 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions to Analyze Microarray (Gene Expression) Data.' extra: identifiers: - biotools:pickgene - doi:10.1007/0-387-21679-0_13 + parent_recipe: + name: bioconductor-pickgene + path: recipes/bioconductor-pickgene + version: 1.52.0 + diff --git a/recipes/bioconductor-pics/build.sh b/recipes/bioconductor-pics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pics/build.sh +++ b/recipes/bioconductor-pics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pics/meta.yaml b/recipes/bioconductor-pics/meta.yaml index 820e7953e90fe..e6ea6fbcb2f9a 100644 --- a/recipes/bioconductor-pics/meta.yaml +++ b/recipes/bioconductor-pics/meta.yaml @@ -1,40 +1,40 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "PICS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 32c6d019d362f6baaad3a097cb437e6cc0d9e46204c4bfcf78211958c9ec892b + md5: 37aad6428e79e861d9e42d519aa133e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: ShortRead, rtracklayer, parallel +# SystemRequirements: GSL (GNU Scientific Library) requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - openblas run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - openblas build: - {{ compiler('c') }} - automake @@ -43,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' extra: identifiers: - biotools:pics + parent_recipe: + name: bioconductor-pics + path: recipes/bioconductor-pics + version: 2.24.0 + diff --git a/recipes/bioconductor-pig.db0/meta.yaml b/recipes/bioconductor-pig.db0/meta.yaml new file mode 100644 index 0000000000000..9d6619519106b --- /dev/null +++ b/recipes/bioconductor-pig.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "pig.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7c8a8945b98ad5bca03e2765046664f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for pig, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-pig.db0/post-link.sh b/recipes/bioconductor-pig.db0/post-link.sh new file mode 100644 index 0000000000000..2d252c3ee3a92 --- /dev/null +++ b/recipes/bioconductor-pig.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pig.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/pig.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/pig.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pig.db0/bioconductor-pig.db0_3.7.1_src_all.tar.gz" +) +MD5="7c8a8945b98ad5bca03e2765046664f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pig.db0/pre-unlink.sh b/recipes/bioconductor-pig.db0/pre-unlink.sh new file mode 100644 index 0000000000000..42df4ad75eb90 --- /dev/null +++ b/recipes/bioconductor-pig.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pig.db0 diff --git a/recipes/bioconductor-pigengene/build.sh b/recipes/bioconductor-pigengene/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pigengene/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pigengene/meta.yaml b/recipes/bioconductor-pigengene/meta.yaml new file mode 100644 index 0000000000000..4260d8358473a --- /dev/null +++ b/recipes/bioconductor-pigengene/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.8.0" %} +{% set name = "Pigengene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9a1b55edd6fa640512ed44c536f1ea18 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, org.Mm.eg.db, biomaRt (>= 2.30.0), knitr, BiocStyle, AnnotationDbi, energy +requirements: + host: + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-bnlearn + - 'r-c50 >=0.1.2' + - r-mass + - r-matrixstats + - r-partykit + - 'r-pheatmap >=1.0.8' + - r-wgcna + run: + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-bnlearn + - 'r-c50 >=0.1.2' + - r-mass + - r-matrixstats + - r-partykit + - 'r-pheatmap >=1.0.8' + - r-wgcna +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Pigengene package provides an efficient way to infer biological signatures from gene expression profiles. The signatures are independent from the underlying platform, e.g., the input can be microarray or RNA Seq data. It can even infer the signatures using data from one platform, and evaluate them on the other. Pigengene identifies the modules (clusters) of highly coexpressed genes using coexpression network analysis, summarizes the biological information of each module in an eigengene, learns a Bayesian network that models the probabilistic dependencies between modules, and builds a decision tree based on the expression of eigengenes.' + diff --git a/recipes/bioconductor-ping/build.sh b/recipes/bioconductor-ping/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ping/build.sh +++ b/recipes/bioconductor-ping/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ping/meta.yaml b/recipes/bioconductor-ping/meta.yaml index 615f8038e91af..a3df4b84c11d1 100644 --- a/recipes/bioconductor-ping/meta.yaml +++ b/recipes/bioconductor-ping/meta.yaml @@ -1,42 +1,43 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "PING" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b1a058aee9b313bbaf9855eaad021354d061f4097aa327c5ec5ba4c19344f827 + md5: d7d3a4467e3c8ea97ff0099a4e31285c build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, ShortRead, rtracklayer requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-pics >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pics >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-pics >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pics >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-fda build: @@ -47,9 +48,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Probabilistic inference of ChIP-Seq using an empirical Bayes mixture model approach.' extra: identifiers: - biotools:ping + parent_recipe: + name: bioconductor-ping + path: recipes/bioconductor-ping + version: 2.24.0 + diff --git a/recipes/bioconductor-pint/build.sh b/recipes/bioconductor-pint/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pint/build.sh +++ b/recipes/bioconductor-pint/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pint/meta.yaml b/recipes/bioconductor-pint/meta.yaml index 4bc1a9953e17a..c67ffbc547847 100644 --- a/recipes/bioconductor-pint/meta.yaml +++ b/recipes/bioconductor-pint/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "pint" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4d8805cff5d576139e6a7efd68fa3c88b1ecdae4f1248a8a0bdc2a7c88524cce + md5: 52094d95be76e9b7eb15f0c1f826f4fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -31,10 +32,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Pairwise data integration for functional genomics, including tools for DNA/RNA/miRNA dependency screens.' extra: identifiers: - biotools:pint - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pint + path: recipes/bioconductor-pint + version: 1.30.0 + diff --git a/recipes/bioconductor-pkgdeptools/build.sh b/recipes/bioconductor-pkgdeptools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pkgdeptools/build.sh +++ b/recipes/bioconductor-pkgdeptools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pkgdeptools/meta.yaml b/recipes/bioconductor-pkgdeptools/meta.yaml index b253ff6c69a00..2b60a54456583 100644 --- a/recipes/bioconductor-pkgdeptools/meta.yaml +++ b/recipes/bioconductor-pkgdeptools/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "pkgDepTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f7e5e3199cf227ab2267bfc6affdf94b4e9afec17d966e502e24967a42e13681 + md5: 9b7ac81bcf76d15218c6044b6620a931 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, Rgraphviz, RCurl, BiocManager requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides tools for computing and analyzing dependency relationships among R packages. It provides tools for building a graph-based representation of the dependencies among all packages in a list of CRAN-style package repositories. There are also utilities for computing installation order of a given package. If the RCurl package is available, an estimate of the download size required to install a given package and its dependencies can be obtained.' extra: identifiers: - biotools:pkgdeptools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pkgdeptools + path: recipes/bioconductor-pkgdeptools + version: 1.46.0 + diff --git a/recipes/bioconductor-plasfia/meta.yaml b/recipes/bioconductor-plasfia/meta.yaml new file mode 100644 index 0000000000000..47cde4a0e5f8c --- /dev/null +++ b/recipes/bioconductor-plasfia/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.10.0" %} +{% set name = "plasFIA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9eecc8e69adc6fae52eb4eac6d18de51 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-profia >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-profia >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Positive Ionization FIA-HRMS data of human plasma spiked with a pool of 40 compounds acquired in FIA-HRMS mode on an orbitrap fusion. plasFIA also include the result of the processing by the proFIA package with adapted parameters for an Orbitrap Fusion.' + diff --git a/recipes/bioconductor-plasfia/post-link.sh b/recipes/bioconductor-plasfia/post-link.sh new file mode 100644 index 0000000000000..5315a0ca02e4b --- /dev/null +++ b/recipes/bioconductor-plasfia/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="plasFIA_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/plasFIA_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/plasFIA_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasfia/bioconductor-plasfia_1.10.0_src_all.tar.gz" +) +MD5="9eecc8e69adc6fae52eb4eac6d18de51" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-plasfia/pre-unlink.sh b/recipes/bioconductor-plasfia/pre-unlink.sh new file mode 100644 index 0000000000000..95ca72ea7f511 --- /dev/null +++ b/recipes/bioconductor-plasfia/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ plasFIA diff --git a/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml new file mode 100644 index 0000000000000..f30d70b0bbb3d --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelescdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "plasmodiumanophelescdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 54c5c326977d6358c40cacf34cb2aca2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Plasmodium_Anopheles.cdf file.' + diff --git a/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh b/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh new file mode 100644 index 0000000000000..5d374f9983fe3 --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelescdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="plasmodiumanophelescdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/plasmodiumanophelescdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/plasmodiumanophelescdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelescdf/bioconductor-plasmodiumanophelescdf_2.18.0_src_all.tar.gz" +) +MD5="54c5c326977d6358c40cacf34cb2aca2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-plasmodiumanophelescdf/pre-unlink.sh b/recipes/bioconductor-plasmodiumanophelescdf/pre-unlink.sh new file mode 100644 index 0000000000000..0cd2630759201 --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelescdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ plasmodiumanophelescdf diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml new file mode 100644 index 0000000000000..dc0df3dd7bc18 --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelesprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "plasmodiumanophelesprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 281683dab923168c2eedb7b08c528935 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Plasmodium\_Anopheles\_probe\_tab.' + diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh b/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh new file mode 100644 index 0000000000000..0e09baf0a87b4 --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelesprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="plasmodiumanophelesprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/plasmodiumanophelesprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/plasmodiumanophelesprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-plasmodiumanophelesprobe/bioconductor-plasmodiumanophelesprobe_2.18.0_src_all.tar.gz" +) +MD5="281683dab923168c2eedb7b08c528935" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-plasmodiumanophelesprobe/pre-unlink.sh b/recipes/bioconductor-plasmodiumanophelesprobe/pre-unlink.sh new file mode 100644 index 0000000000000..d1391934b6732 --- /dev/null +++ b/recipes/bioconductor-plasmodiumanophelesprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ plasmodiumanophelesprobe diff --git a/recipes/bioconductor-platecore/build.sh b/recipes/bioconductor-platecore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-platecore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-platecore/meta.yaml b/recipes/bioconductor-platecore/meta.yaml new file mode 100644 index 0000000000000..cb19cc47fd2b2 --- /dev/null +++ b/recipes/bioconductor-platecore/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.40.0" %} +{% set name = "plateCore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: adfe7d777974de196346e991bae587f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gplots +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + - r-lattice + - r-latticeextra + - r-mass + - r-robustbase + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowstats >=3.40.0,<3.41.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - r-base + - r-lattice + - r-latticeextra + - r-mass + - r-robustbase +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides basic S4 data structures and routines for analyzing plate based flow cytometry data.' + diff --git a/recipes/bioconductor-plethy/build.sh b/recipes/bioconductor-plethy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-plethy/build.sh +++ b/recipes/bioconductor-plethy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plethy/meta.yaml b/recipes/bioconductor-plethy/meta.yaml index c4d6875195a4c..46b3fa0e8860c 100644 --- a/recipes/bioconductor-plethy/meta.yaml +++ b/recipes/bioconductor-plethy/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "plethy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e840e9572a14cc8cba3c8d6a4167175a64715c6d09456c893d51fe01c4085add + md5: cfaa49593a30cf99fe842236a8b34583 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-streamer >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-streamer >=1.28.0,<1.29.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 @@ -31,11 +33,11 @@ requirements: - r-reshape2 - 'r-rsqlite >=1.1' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-streamer >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-streamer >=1.28.0,<1.29.0' - r-base - 'r-dbi >=0.5-1' - r-ggplot2 @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides the infrastructure and tools to import, query and perform basic analysis of whole body plethysmography and metabolism data. Currently support is limited to data derived from Buxco respirometry instruments as exported by their FinePointe software.' extra: identifiers: - biotools:plethy - doi:10.1186/s12859-015-0547-7 + parent_recipe: + name: bioconductor-plethy + path: recipes/bioconductor-plethy + version: 1.18.0 + diff --git a/recipes/bioconductor-plgem/build.sh b/recipes/bioconductor-plgem/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-plgem/build.sh +++ b/recipes/bioconductor-plgem/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plgem/meta.yaml b/recipes/bioconductor-plgem/meta.yaml index 45ec52c62dddc..f90a1810ab15a 100644 --- a/recipes/bioconductor-plgem/meta.yaml +++ b/recipes/bioconductor-plgem/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "plgem" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 295cf196d66bbaa9acfcbde37a9bf77191a815299834f1eb1ddbfad5f006d389 + md5: c7ccf32696d765a7483845c47e770d1a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The Power Law Global Error Model (PLGEM) has been shown to faithfully model the variance-versus-mean dependence that exists in a variety of genome-wide datasets, including microarray and proteomics data. The use of PLGEM has been shown to improve the detection of differentially expressed genes or proteins in these datasets.' extra: identifiers: - biotools:plgem + parent_recipe: + name: bioconductor-plgem + path: recipes/bioconductor-plgem + version: 1.52.0 + diff --git a/recipes/bioconductor-plier/build.sh b/recipes/bioconductor-plier/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-plier/build.sh +++ b/recipes/bioconductor-plier/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plier/conda_build_config.yaml b/recipes/bioconductor-plier/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-plier/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-plier/meta.yaml b/recipes/bioconductor-plier/meta.yaml index b16f80743bed9..fe3c52b554480 100644 --- a/recipes/bioconductor-plier/meta.yaml +++ b/recipes/bioconductor-plier/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "plier" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c658643f7380b61dd09f213a9eef0bcb5d284c796dacd9520905d40723912e0e + md5: 878f9d104165863bb2779f78af70f559 build: number: 0 rpaths: @@ -18,12 +18,12 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -33,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The PLIER (Probe Logarithmic Error Intensity Estimate) method produces an improved signal by accounting for experimentally observed patterns in probe behavior and handling error at the appropriately at low and high signal values.' extra: identifiers: - biotools:plier - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-plier + path: recipes/bioconductor-plier + version: 1.50.0 + diff --git a/recipes/bioconductor-plotgrouper/build.sh b/recipes/bioconductor-plotgrouper/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plotgrouper/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plotgrouper/meta.yaml b/recipes/bioconductor-plotgrouper/meta.yaml new file mode 100644 index 0000000000000..a4b77f2a66e70 --- /dev/null +++ b/recipes/bioconductor-plotgrouper/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.0.0" %} +{% set name = "plotGrouper" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7c5172877655d6f81abae3cd5b58aa7d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, htmltools, BiocStyle, rmarkdown, testthat +requirements: + host: + - r-base + - 'r-colourpicker >=1.0' + - 'r-dplyr >=0.7.6' + - 'r-egg >=0.4.0' + - 'r-ggplot2 >=3.0.0' + - 'r-ggpubr >=0.1.8' + - 'r-gridextra >=2.3' + - 'r-gtable >=0.2.0' + - 'r-hmisc >=4.1.1' + - 'r-magrittr >=1.5' + - 'r-readr >=1.1.1' + - 'r-readxl >=1.1.0' + - 'r-rlang >=0.2.2' + - 'r-scales >=1.0.0' + - 'r-shiny >=1.1.0' + - 'r-shinythemes >=1.1.1' + - 'r-stringr >=1.3.1' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.2.0' + run: + - r-base + - 'r-colourpicker >=1.0' + - 'r-dplyr >=0.7.6' + - 'r-egg >=0.4.0' + - 'r-ggplot2 >=3.0.0' + - 'r-ggpubr >=0.1.8' + - 'r-gridextra >=2.3' + - 'r-gtable >=0.2.0' + - 'r-hmisc >=4.1.1' + - 'r-magrittr >=1.5' + - 'r-readr >=1.1.1' + - 'r-readxl >=1.1.0' + - 'r-rlang >=0.2.2' + - 'r-scales >=1.0.0' + - 'r-shiny >=1.1.0' + - 'r-shinythemes >=1.1.1' + - 'r-stringr >=1.3.1' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.2.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A shiny app-based GUI wrapper for ggplot with built-in statistical analysis. Import data from file and use dropdown menus and checkboxes to specify the plotting variables, graph type, and look of your plots. Once created, plots can be saved independently or stored in a report that can be saved as a pdf. If new data are added to the file, the report can be refreshed to include new data. Statistical tests can be selected and added to the graphs. Analysis of flow cytometry data is especially integrated with plotGrouper. Count data can be transformed to return the absolute number of cells in a sample (this feature requires inclusion of the number of beads per sample and information about any dilution performed).' + diff --git a/recipes/bioconductor-plpe/build.sh b/recipes/bioconductor-plpe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-plpe/build.sh +++ b/recipes/bioconductor-plpe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plpe/meta.yaml b/recipes/bioconductor-plpe/meta.yaml index 3d00be9e38cb1..465dd190b21a3 100644 --- a/recipes/bioconductor-plpe/meta.yaml +++ b/recipes/bioconductor-plpe/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "PLPE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b3f2099b79d052210e7fa2ebd1b42035ac4d7571fc345ae4cf37d1612b56053 + md5: e14a72c1493694cf9270d6b3f8c7888c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-lpe >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lpe >=1.56.0,<1.57.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-lpe >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-lpe >=1.56.0,<1.57.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package performs tests for paired high-throughput data.' extra: identifiers: - biotools:plpe - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-plpe + path: recipes/bioconductor-plpe + version: 1.40.0 + diff --git a/recipes/bioconductor-plrs/build.sh b/recipes/bioconductor-plrs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plrs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plrs/meta.yaml b/recipes/bioconductor-plrs/meta.yaml new file mode 100644 index 0000000000000..608e1acf494e2 --- /dev/null +++ b/recipes/bioconductor-plrs/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.22.0" %} +{% set name = "plrs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 41bf5ad9dc49a153c0fcb4ddfa4b5e44 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: mvtnorm, methods +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + - r-ic.infer + - r-quadprog + - r-rcsdp + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' + - r-base + - r-ic.infer + - r-quadprog + - r-rcsdp +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2.0)' + summary: 'The present package implements a flexible framework for modeling the relationship between DNA copy number and gene expression data using Piecewise Linear Regression Splines (PLRS).' + diff --git a/recipes/bioconductor-plw/build.sh b/recipes/bioconductor-plw/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-plw/build.sh +++ b/recipes/bioconductor-plw/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plw/conda_build_config.yaml b/recipes/bioconductor-plw/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-plw/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-plw/meta.yaml b/recipes/bioconductor-plw/meta.yaml index 34369e21fccd8..101e26a5073bd 100644 --- a/recipes/bioconductor-plw/meta.yaml +++ b/recipes/bioconductor-plw/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "plw" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b2efadc2037b501a9fc91a8b8e3658e3e8a2e937c58c150b05221ce9a034998b + md5: dc4109cd98ee3817f3ab6b5308f13680 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: limma requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base - r-mass run: - - 'bioconductor-affy >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' - r-base - r-mass build: @@ -32,9 +33,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Probe level Locally moderated Weighted median-t (PLW) and Locally Moderated Weighted-t (LMW).' extra: identifiers: - biotools:plw + parent_recipe: + name: bioconductor-plw + path: recipes/bioconductor-plw + version: 1.40.0 + diff --git a/recipes/bioconductor-plyranges/build.sh b/recipes/bioconductor-plyranges/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-plyranges/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-plyranges/meta.yaml b/recipes/bioconductor-plyranges/meta.yaml new file mode 100644 index 0000000000000..bb740cb6003ed --- /dev/null +++ b/recipes/bioconductor-plyranges/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.2.0" %} +{% set name = "plyranges" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7f6a2b20360203ca9fb94f75e10e0c17 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown, testthat, ggplot2, HelloRanges, HelloRangesData, BSgenome.Hsapiens.UCSC.hg19, pasillaBamSubset, covr +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-magrittr + - 'r-rlang >=0.2.0' + - r-tidyr + - r-tidyselect + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-dplyr + - r-magrittr + - 'r-rlang >=0.2.0' + - r-tidyr + - r-tidyselect +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A dplyr-like interface for interacting with the common Bioconductor classes Ranges and GenomicRanges. By providing a grammatical and consistent way of manipulating these classes their accessiblity for new Bioconductor users is hopefully increased.' + diff --git a/recipes/bioconductor-pmm/build.sh b/recipes/bioconductor-pmm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pmm/build.sh +++ b/recipes/bioconductor-pmm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pmm/meta.yaml b/recipes/bioconductor-pmm/meta.yaml index c8c94f6fa2971..caf671906ac4d 100644 --- a/recipes/bioconductor-pmm/meta.yaml +++ b/recipes/bioconductor-pmm/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pmm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bfb8b5126ab41da2b1947c39ca5d1f573e857283f93053b076c461a5bda103e1 + md5: 62c7a8f094a67345c7f968665c5da863 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The Parallel Mixed Model (PMM) approach is suitable for hit selection and cross-comparison of RNAi screens generated in experiments that are performed in parallel under several conditions. For example, we could think of the measurements or readouts from cells under RNAi knock-down, which are infected with several pathogens or which are grown from different cell lines.' extra: identifiers: - biotools:pmm - doi:10.3929/ethz-a-010607487 + parent_recipe: + name: bioconductor-pmm + path: recipes/bioconductor-pmm + version: 1.12.0 + diff --git a/recipes/bioconductor-pocrcannotation.db/meta.yaml b/recipes/bioconductor-pocrcannotation.db/meta.yaml new file mode 100644 index 0000000000000..35340caf36adb --- /dev/null +++ b/recipes/bioconductor-pocrcannotation.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "POCRCannotation.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: da1d4dacc5fffb9c5dfea55649974aa5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package containing metadata for POCRC arrays assembled using data from public repositories' + diff --git a/recipes/bioconductor-pocrcannotation.db/post-link.sh b/recipes/bioconductor-pocrcannotation.db/post-link.sh new file mode 100644 index 0000000000000..b4da8d9706211 --- /dev/null +++ b/recipes/bioconductor-pocrcannotation.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="POCRCannotation.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/POCRCannotation.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/POCRCannotation.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pocrcannotation.db/bioconductor-pocrcannotation.db_3.2.3_src_all.tar.gz" +) +MD5="da1d4dacc5fffb9c5dfea55649974aa5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pocrcannotation.db/pre-unlink.sh b/recipes/bioconductor-pocrcannotation.db/pre-unlink.sh new file mode 100644 index 0000000000000..1ad26424a2bf4 --- /dev/null +++ b/recipes/bioconductor-pocrcannotation.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ POCRCannotation.db diff --git a/recipes/bioconductor-podkat/build.sh b/recipes/bioconductor-podkat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-podkat/build.sh +++ b/recipes/bioconductor-podkat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-podkat/meta.yaml b/recipes/bioconductor-podkat/meta.yaml index fbaa531f561ef..ed7570fc93107 100644 --- a/recipes/bioconductor-podkat/meta.yaml +++ b/recipes/bioconductor-podkat/meta.yaml @@ -1,43 +1,44 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "podkat" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 631a2427117cf742bfb7e95d39525c4ce4813f4c37a86f4d5f359b53a77648a4 + md5: bf4f038d282695aaab44b9f08dd840ed build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg38.masked, TxDb.Hsapiens.UCSC.hg38.knownGene, BSgenome.Mmusculus.UCSC.mm10.masked, GWASTools (>= 1.13.24), VariantAnnotation, SummarizedExperiment, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-matrix - 'r-rcpp >=0.11.1' @@ -49,10 +50,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides an association test that is capable of dealing with very rare and even private variants. This is accomplished by a kernel-based approach that takes the positions of the variants into account. The test can be used for pre-processed matrix data, but also directly for variant data stored in VCF files. Association testing can be performed whole-genome, whole-exome, or restricted to pre-defined regions of interest. The test is complemented by tools for analyzing and visualizing the results.' extra: identifiers: - biotools:podkat - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-podkat + path: recipes/bioconductor-podkat + version: 1.12.0 + diff --git a/recipes/bioconductor-pogos/build.sh b/recipes/bioconductor-pogos/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-pogos/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pogos/meta.yaml b/recipes/bioconductor-pogos/meta.yaml new file mode 100644 index 0000000000000..be9a12180a8c5 --- /dev/null +++ b/recipes/bioconductor-pogos/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.2.0" %} +{% set name = "pogos" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7b05b4af8e7b91f52c22e25ba834ec4e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, DT, ontologyPlot, testthat +requirements: + host: + - 'bioconductor-ontoproc >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - 'r-httr >=1.3.1' + - 'r-rjson >=0.2.15' + - r-shiny + run: + - 'bioconductor-ontoproc >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-ggplot2 + - 'r-httr >=1.3.1' + - 'r-rjson >=0.2.15' + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provide simple utilities for querying bhklab PharmacoDB, modeling API outputs, and integrating to cell and compound ontologies.' + diff --git a/recipes/bioconductor-polyester/build.sh b/recipes/bioconductor-polyester/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-polyester/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-polyester/meta.yaml b/recipes/bioconductor-polyester/meta.yaml new file mode 100644 index 0000000000000..0850fca717bcd --- /dev/null +++ b/recipes/bioconductor-polyester/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.18.0" %} +{% set name = "polyester" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c7a2bb655890a4fa6f80eae248d10d94 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, ballgown +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-logspline + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + - r-logspline +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package can be used to simulate RNA-seq reads from differential expression experiments with replicates. The reads can then be aligned and used to perform comparisons of methods for differential expression.' + diff --git a/recipes/bioconductor-polyfit/build.sh b/recipes/bioconductor-polyfit/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-polyfit/build.sh +++ b/recipes/bioconductor-polyfit/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-polyfit/meta.yaml b/recipes/bioconductor-polyfit/meta.yaml index bf4d4342ae1dc..7cf93c0a1291f 100644 --- a/recipes/bioconductor-polyfit/meta.yaml +++ b/recipes/bioconductor-polyfit/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Polyfit" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e176aff4d0eeecce3c53fd16b74d66c6b531465498063853c6b42d5a9c5499bd + md5: 0e7b97a55b30181e9d40932891d40ea6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Polyfit is an add-on to the packages DESeq which ensures the p-value distribution is uniform over the interval [0, 1] for data satisfying the null hypothesis of no differential expression, and uses an adpated Storey-Tibshiran method to calculate q-values.' extra: identifiers: - biotools:polyfit - doi:10.7717/peerj.576 + parent_recipe: + name: bioconductor-polyfit + path: recipes/bioconductor-polyfit + version: 1.14.0 + diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml new file mode 100644 index 0000000000000..115229308ecf5 --- /dev/null +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.2" %} +{% set name = "PolyPhen.Hsapiens.dbSNP131" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 763e9cd4afd97b36f7e659f5454ef61f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Database of PolyPhen predictions for Homo sapiens dbSNP build 131' + diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh new file mode 100644 index 0000000000000..07c62534645ac --- /dev/null +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/PolyPhen.Hsapiens.dbSNP131_1.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-polyphen.hsapiens.dbsnp131/bioconductor-polyphen.hsapiens.dbsnp131_1.0.2_src_all.tar.gz" +) +MD5="763e9cd4afd97b36f7e659f5454ef61f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-polyphen.hsapiens.dbsnp131/pre-unlink.sh b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/pre-unlink.sh new file mode 100644 index 0000000000000..1138c73ff84f3 --- /dev/null +++ b/recipes/bioconductor-polyphen.hsapiens.dbsnp131/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PolyPhen.Hsapiens.dbSNP131 diff --git a/recipes/bioconductor-poplarcdf/meta.yaml b/recipes/bioconductor-poplarcdf/meta.yaml new file mode 100644 index 0000000000000..c89157967a51c --- /dev/null +++ b/recipes/bioconductor-poplarcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "poplarcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 556e7f8f6f76436552d8044ef29279cb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Poplar.cdf file.' + diff --git a/recipes/bioconductor-poplarcdf/post-link.sh b/recipes/bioconductor-poplarcdf/post-link.sh new file mode 100644 index 0000000000000..d91f5d7294c9d --- /dev/null +++ b/recipes/bioconductor-poplarcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="poplarcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/poplarcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/poplarcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-poplarcdf/bioconductor-poplarcdf_2.18.0_src_all.tar.gz" +) +MD5="556e7f8f6f76436552d8044ef29279cb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-poplarcdf/pre-unlink.sh b/recipes/bioconductor-poplarcdf/pre-unlink.sh new file mode 100644 index 0000000000000..afe3c70d3350f --- /dev/null +++ b/recipes/bioconductor-poplarcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ poplarcdf diff --git a/recipes/bioconductor-poplarprobe/meta.yaml b/recipes/bioconductor-poplarprobe/meta.yaml new file mode 100644 index 0000000000000..ae477aad7926c --- /dev/null +++ b/recipes/bioconductor-poplarprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "poplarprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 87a608cd86084a06973a88e9b51f799a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Poplar\_probe\_tab.' + diff --git a/recipes/bioconductor-poplarprobe/post-link.sh b/recipes/bioconductor-poplarprobe/post-link.sh new file mode 100644 index 0000000000000..930cd2a4b8708 --- /dev/null +++ b/recipes/bioconductor-poplarprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="poplarprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/poplarprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/poplarprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-poplarprobe/bioconductor-poplarprobe_2.18.0_src_all.tar.gz" +) +MD5="87a608cd86084a06973a88e9b51f799a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-poplarprobe/pre-unlink.sh b/recipes/bioconductor-poplarprobe/pre-unlink.sh new file mode 100644 index 0000000000000..74f2d7048ca86 --- /dev/null +++ b/recipes/bioconductor-poplarprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ poplarprobe diff --git a/recipes/bioconductor-porcine.db/meta.yaml b/recipes/bioconductor-porcine.db/meta.yaml new file mode 100644 index 0000000000000..4e909f8e254fa --- /dev/null +++ b/recipes/bioconductor-porcine.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "porcine.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a90a6ad39b7fda3f30c23ab315201317 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.ss.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.ss.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix porcine annotation data (chip porcine) assembled using data from public repositories' + diff --git a/recipes/bioconductor-porcine.db/post-link.sh b/recipes/bioconductor-porcine.db/post-link.sh new file mode 100644 index 0000000000000..25e305b0bb4ec --- /dev/null +++ b/recipes/bioconductor-porcine.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="porcine.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcine.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/porcine.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcine.db/bioconductor-porcine.db_3.2.3_src_all.tar.gz" +) +MD5="a90a6ad39b7fda3f30c23ab315201317" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-porcine.db/pre-unlink.sh b/recipes/bioconductor-porcine.db/pre-unlink.sh new file mode 100644 index 0000000000000..738f1b98ed68c --- /dev/null +++ b/recipes/bioconductor-porcine.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ porcine.db diff --git a/recipes/bioconductor-porcinecdf/meta.yaml b/recipes/bioconductor-porcinecdf/meta.yaml new file mode 100644 index 0000000000000..e96719cdc09a2 --- /dev/null +++ b/recipes/bioconductor-porcinecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "porcinecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 32a60b93829c06a935895fab0a469228 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Porcine.cdf file.' + diff --git a/recipes/bioconductor-porcinecdf/post-link.sh b/recipes/bioconductor-porcinecdf/post-link.sh new file mode 100644 index 0000000000000..a0eeb623c2d61 --- /dev/null +++ b/recipes/bioconductor-porcinecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="porcinecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcinecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/porcinecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcinecdf/bioconductor-porcinecdf_2.18.0_src_all.tar.gz" +) +MD5="32a60b93829c06a935895fab0a469228" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-porcinecdf/pre-unlink.sh b/recipes/bioconductor-porcinecdf/pre-unlink.sh new file mode 100644 index 0000000000000..4329679447db7 --- /dev/null +++ b/recipes/bioconductor-porcinecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ porcinecdf diff --git a/recipes/bioconductor-porcineprobe/meta.yaml b/recipes/bioconductor-porcineprobe/meta.yaml new file mode 100644 index 0000000000000..b63af99eba402 --- /dev/null +++ b/recipes/bioconductor-porcineprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "porcineprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5ac483b6329a012d4c9954e3dee8869e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Porcine\_probe\_tab.' + diff --git a/recipes/bioconductor-porcineprobe/post-link.sh b/recipes/bioconductor-porcineprobe/post-link.sh new file mode 100644 index 0000000000000..a36f598eadf82 --- /dev/null +++ b/recipes/bioconductor-porcineprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="porcineprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/porcineprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/porcineprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-porcineprobe/bioconductor-porcineprobe_2.18.0_src_all.tar.gz" +) +MD5="5ac483b6329a012d4c9954e3dee8869e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-porcineprobe/pre-unlink.sh b/recipes/bioconductor-porcineprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e1b7d8bee2674 --- /dev/null +++ b/recipes/bioconductor-porcineprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ porcineprobe diff --git a/recipes/bioconductor-post/build.sh b/recipes/bioconductor-post/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-post/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-post/meta.yaml b/recipes/bioconductor-post/meta.yaml new file mode 100644 index 0000000000000..bb09bd4b65c4c --- /dev/null +++ b/recipes/bioconductor-post/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.6.0" %} +{% set name = "POST" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 53dc1ab5813de6f37505e96d2dd29c5c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-compquadform + - r-matrix + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - r-base + - r-compquadform + - r-matrix + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Perform orthogonal projection of high dimensional data of a set, and statistical modeling of phenotye with projected vectors as predictor.' + diff --git a/recipes/bioconductor-powerexplorer/build.sh b/recipes/bioconductor-powerexplorer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-powerexplorer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-powerexplorer/meta.yaml b/recipes/bioconductor-powerexplorer/meta.yaml new file mode 100644 index 0000000000000..7418d7e56e737 --- /dev/null +++ b/recipes/bioconductor-powerexplorer/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.1" %} +{% set name = "PowerExplorer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 19fec1e9d12f12b48a970d1a97ab9aee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-rots >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gridextra + - r-mass + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-rots >=1.10.0,<1.11.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gridextra + - r-mass +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Estimate and predict power among groups and multiple sample sizes with simulated data, the simulations are operated based on distribution parameters estimated from the provided input dataset.' + diff --git a/recipes/bioconductor-powertcr/build.sh b/recipes/bioconductor-powertcr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-powertcr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-powertcr/meta.yaml b/recipes/bioconductor-powertcr/meta.yaml new file mode 100644 index 0000000000000..63bfbca2fee38 --- /dev/null +++ b/recipes/bioconductor-powertcr/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.2.0" %} +{% set name = "powerTCR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e355b3691f1b481999f271edce674a87 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics +requirements: + host: + - r-base + - r-cubature + - r-doparallel + - r-evmix + - r-foreach + - r-magrittr + - r-purrr + - r-tcr + - r-truncdist + - r-vegan + - r-vgam + run: + - r-base + - r-cubature + - r-doparallel + - r-evmix + - r-foreach + - r-magrittr + - r-purrr + - r-tcr + - r-truncdist + - r-vegan + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides a model for the clone size distribution of the TCR repertoire. Further, it permits comparative analysis of TCR repertoire libraries based on theoretical model fits.' + diff --git a/recipes/bioconductor-ppidata/meta.yaml b/recipes/bioconductor-ppidata/meta.yaml index 8fd1c09ffa508..69cf0836331fb 100644 --- a/recipes/bioconductor-ppidata/meta.yaml +++ b/recipes/bioconductor-ppidata/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "0.18.0" %} +{% set version = "0.20.0" %} {% set name = "ppiData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b13b804f9307b7f05356876bac395ade26b367c8642222d14c0dd04bc87c89ed + md5: eff4cead7fba4a8443cb3c3426391bb0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Sc.sgd.db, ppiStats requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package contains the directed graphs for protein interaction data as derived from Y2H and APMS as well as the code used to obtain the y2h data from IntAct Repository.' - +extra: + parent_recipe: + name: bioconductor-ppidata + path: recipes/bioconductor-ppidata + version: 0.18.0 diff --git a/recipes/bioconductor-ppidata/post-link.sh b/recipes/bioconductor-ppidata/post-link.sh index c21452f7a4827..40c1a1c281b3d 100644 --- a/recipes/bioconductor-ppidata/post-link.sh +++ b/recipes/bioconductor-ppidata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="ppiData_0.18.0.tar.gz" +FN="ppiData_0.20.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/ppiData_0.18.0.tar.gz" - "https://bioarchive.galaxyproject.org/ppiData_0.18.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.18.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ppiData_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ppiData_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ppidata/bioconductor-ppidata_0.20.0_src_all.tar.gz" ) -MD5="277d47ac92b8255e643f3b155d7a9d9d" +MD5="eff4cead7fba4a8443cb3c3426391bb0" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-ppinfer/build.sh b/recipes/bioconductor-ppinfer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ppinfer/build.sh +++ b/recipes/bioconductor-ppinfer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ppinfer/meta.yaml b/recipes/bioconductor-ppinfer/meta.yaml index afcbb546a4d53..e2eca61d16ec5 100644 --- a/recipes/bioconductor-ppinfer/meta.yaml +++ b/recipes/bioconductor-ppinfer/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "PPInfer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f0072e2f58d648aa5a1fe3a6cc24478109577e4c907fc462a72598d6d49acb96 + md5: 1bab262c551870668dd2624b346f3bd2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-stringdb >=1.20.0,<1.22.0' - - 'bioconductor-yeastexpdata >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-yeastexpdata >=0.28.0,<0.29.0' - r-base - r-ggplot2 - r-igraph - r-kernlab run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-fgsea >=1.6.0,<1.8.0' - - 'bioconductor-stringdb >=1.20.0,<1.22.0' - - 'bioconductor-yeastexpdata >=0.26.0,<0.28.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-fgsea >=1.8.0,<1.9.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - 'bioconductor-yeastexpdata >=0.28.0,<0.29.0' - r-base - r-ggplot2 - r-igraph @@ -39,8 +41,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Interactions between proteins occur in many, if not most, biological processes. Most proteins perform their functions in networks associated with other proteins and other biomolecules. This fact has motivated the development of a variety of experimental methods for the identification of protein interactions. This variety has in turn ushered in the development of numerous different computational approaches for modeling and predicting protein interactions. Sometimes an experiment is aimed at identifying proteins closely related to some interesting proteins. A network based statistical learning method is used to infer the putative functions of proteins from the known functions of its neighboring proteins on a PPI network. This package identifies such proteins often involved in the same or similar biological functions.' - +extra: + parent_recipe: + name: bioconductor-ppinfer + path: recipes/bioconductor-ppinfer + version: 1.6.0 diff --git a/recipes/bioconductor-ppistats/build.sh b/recipes/bioconductor-ppistats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ppistats/build.sh +++ b/recipes/bioconductor-ppistats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ppistats/meta.yaml b/recipes/bioconductor-ppistats/meta.yaml index d5f0f2063d0e4..e1e62c4eaeb10 100644 --- a/recipes/bioconductor-ppistats/meta.yaml +++ b/recipes/bioconductor-ppistats/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "ppiStats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ec0ee6d94961d3df686b8058d30d65fefd8606119fb8025766407c61c59ddc7f + md5: 143b0f3a760c921de1444f04cea91c98 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: yeastExpData, xtable requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-ppidata >=0.18.0,<0.20.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ppidata >=0.20.0,<0.21.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' - r-base - r-lattice - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-ppidata >=0.18.0,<0.20.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-ppidata >=0.20.0,<0.21.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' - r-base - r-lattice - r-rcolorbrewer @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools for the analysis of protein interaction data.' extra: identifiers: - biotools:ppistats - doi:10.1186/gb-2007-8-9-r186 + parent_recipe: + name: bioconductor-ppistats + path: recipes/bioconductor-ppistats + version: 1.46.0 + diff --git a/recipes/bioconductor-pqsfinder/build.sh b/recipes/bioconductor-pqsfinder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pqsfinder/build.sh +++ b/recipes/bioconductor-pqsfinder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pqsfinder/meta.yaml b/recipes/bioconductor-pqsfinder/meta.yaml index f008790489891..0bc788735e7f8 100644 --- a/recipes/bioconductor-pqsfinder/meta.yaml +++ b/recipes/bioconductor-pqsfinder/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "pqsfinder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f6e003939f0fcc580f9e9479a42743a79f9edbddbf6e4a5686000268481e8f21 + md5: ad81bbb70003e7a96e2eb916b19e81d3 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, Gviz, rtracklayer, ggplot2, BSgenome.Hsapiens.UCSC.hg38, testthat, stringr +# SystemRequirements: GNU make, C++11 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - 'r-bh >=1.62.0' + - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.3' run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - - 'r-bh >=1.62.0' + - 'r-bh >=1.66.0' - 'r-rcpp >=0.12.3' build: - {{ compiler('c') }} @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'The main functionality of this package is to detect DNA sequence patterns that are likely to fold into an intramolecular G-quadruplex (G4). Unlike many other approaches, this package is able to detect sequences responsible for G4s folded from imperfect G-runs containing bulges or mismatches and as such is more sensitive than competing algorithms.' extra: identifiers: - biotools:pqsfinder - doi:10.1093/bioinformatics/btv272 + parent_recipe: + name: bioconductor-pqsfinder + path: recipes/bioconductor-pqsfinder + version: 1.8.0 + diff --git a/recipes/bioconductor-prada/build.sh b/recipes/bioconductor-prada/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-prada/build.sh +++ b/recipes/bioconductor-prada/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prada/meta.yaml b/recipes/bioconductor-prada/meta.yaml index aecd722717036..239c7c0292af8 100644 --- a/recipes/bioconductor-prada/meta.yaml +++ b/recipes/bioconductor-prada/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "prada" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 601a09c83d87dcdef2ae5e6dde37812c7c66178b2cf4a38279321b5845bb8d43 + md5: 2d259c19a5364bdd155445a8e2430c2c build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: cellHTS2, tcltk requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - r-rcolorbrewer - r-rrcov run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-mass - r-rcolorbrewer @@ -38,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Tools for analysing and navigating data from high-throughput phenotyping experiments based on cellular assays and fluorescent detection (flow cytometry (FACS), high-content screening microscopy).' extra: identifiers: - biotools:prada - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-prada + path: recipes/bioconductor-prada + version: 1.56.0 + diff --git a/recipes/bioconductor-prebs/build.sh b/recipes/bioconductor-prebs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-prebs/build.sh +++ b/recipes/bioconductor-prebs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prebs/conda_build_config.yaml b/recipes/bioconductor-prebs/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-prebs/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-prebs/meta.yaml b/recipes/bioconductor-prebs/meta.yaml index 68f061c9a6106..2f5ffc805d019 100644 --- a/recipes/bioconductor-prebs/meta.yaml +++ b/recipes/bioconductor-prebs/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "prebs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 00a0f2d25b0214d735e21ee53345c36ede45c2b747aae92f67bc635bf7c6ee5c + md5: 339b874803bc26c3d5f72c75174bf155 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: prebsdata, hgu133plus2cdf, hgu133plus2probe requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rpa >=1.36.0,<1.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rpa >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rpa >=1.36.0,<1.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rpa >=1.38.0,<1.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The prebs package aims at making RNA-sequencing (RNA-seq) data more comparable to microarray data. The comparability is achieved by summarizing sequencing-based expressions of probe regions using a modified version of RMA algorithm. The pipeline takes mapped reads in BAM format as an input and produces either gene expressions or original microarray probe set expressions as an output.' extra: identifiers: - biotools:prebs + parent_recipe: + name: bioconductor-prebs + path: recipes/bioconductor-prebs + version: 1.20.0 + diff --git a/recipes/bioconductor-prebsdata/meta.yaml b/recipes/bioconductor-prebsdata/meta.yaml new file mode 100644 index 0000000000000..d135499c74a77 --- /dev/null +++ b/recipes/bioconductor-prebsdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "prebsdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ddb000d474c089466ab15aa67b44cdfa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains data required to run examples in ''prebs'' package. The data files include: 1) Small sample bam files for demonstration purposes 2) Probe sequence mappings for Custom CDF (taken from http://brainarray.mbni.med.umich.edu/brainarray/Database/CustomCDF/genomic_curated_CDF.asp) 3) Probe sequence mappings for manufacturer''s CDF (manually created using bowtie)' + diff --git a/recipes/bioconductor-prebsdata/post-link.sh b/recipes/bioconductor-prebsdata/post-link.sh new file mode 100644 index 0000000000000..2973fed125299 --- /dev/null +++ b/recipes/bioconductor-prebsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prebsdata_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prebsdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/prebsdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prebsdata/bioconductor-prebsdata_1.18.0_src_all.tar.gz" +) +MD5="ddb000d474c089466ab15aa67b44cdfa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prebsdata/pre-unlink.sh b/recipes/bioconductor-prebsdata/pre-unlink.sh new file mode 100644 index 0000000000000..37d61f92e5aaf --- /dev/null +++ b/recipes/bioconductor-prebsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prebsdata diff --git a/recipes/bioconductor-preda/build.sh b/recipes/bioconductor-preda/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-preda/build.sh +++ b/recipes/bioconductor-preda/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-preda/meta.yaml b/recipes/bioconductor-preda/meta.yaml index 5a712a5c21bfc..b757008f8cad4 100644 --- a/recipes/bioconductor-preda/meta.yaml +++ b/recipes/bioconductor-preda/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.0" %} {% set name = "PREDA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1a1ac227170f62fee5a8de030f96b60a76ffb0a55c1fdc7b891b7c4a75bd28ff + md5: 4bb593ea42c1bf03653cadffd9202aa4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: quantsmooth, qvalue, limma, caTools, affy, PREDAsampledata requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - 'r-lokern >=1.0.9' run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - 'r-lokern >=1.0.9' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Package for the position related analysis of quantitative functional genomics data.' extra: identifiers: - biotools:preda - doi:10.1093/bioinformatics/btr404 + parent_recipe: + name: bioconductor-preda + path: recipes/bioconductor-preda + version: 1.26.1 + diff --git a/recipes/bioconductor-predasampledata/meta.yaml b/recipes/bioconductor-predasampledata/meta.yaml new file mode 100644 index 0000000000000..243b4635db246 --- /dev/null +++ b/recipes/bioconductor-predasampledata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "0.22.0" %} +{% set name = "PREDAsampledata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f8850b39d6ecfc64fe4cc26f6e305751 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: hgu133plus2.db, hgu133plus2cdf +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preda >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preda >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Sample data for PREDA package. (annotations objects synchronized with GeneAnnot custom CDFs version 2.2.0)' + diff --git a/recipes/bioconductor-predasampledata/post-link.sh b/recipes/bioconductor-predasampledata/post-link.sh new file mode 100644 index 0000000000000..1b8569971c49c --- /dev/null +++ b/recipes/bioconductor-predasampledata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PREDAsampledata_0.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PREDAsampledata_0.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/PREDAsampledata_0.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-predasampledata/bioconductor-predasampledata_0.22.0_src_all.tar.gz" +) +MD5="f8850b39d6ecfc64fe4cc26f6e305751" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-predasampledata/pre-unlink.sh b/recipes/bioconductor-predasampledata/pre-unlink.sh new file mode 100644 index 0000000000000..e9efc9b16bd7f --- /dev/null +++ b/recipes/bioconductor-predasampledata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PREDAsampledata diff --git a/recipes/bioconductor-predictionet/build.sh b/recipes/bioconductor-predictionet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-predictionet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-predictionet/meta.yaml b/recipes/bioconductor-predictionet/meta.yaml new file mode 100644 index 0000000000000..156b2258d45a0 --- /dev/null +++ b/recipes/bioconductor-predictionet/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.28.0" %} +{% set name = "predictionet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d95f178dcf079e1c8c9d0a2462fba591 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: network, minet, knitr +requirements: + host: + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-catnet + - r-igraph + - r-mass + - r-penalized + run: + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-catnet + - r-igraph + - r-mass + - r-penalized + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains a set of functions related to network inference combining genomic data and prior information extracted from biomedical literature and structured biological databases. The main function is able to generate networks using Bayesian or regression-based inference methods; while the former is limited to < 100 of variables, the latter may infer networks with hundreds of variables. Several statistics at the edge and node levels have been implemented (edge stability, predictive ability of each node, ...) in order to help the user to focus on high quality subnetworks. Ultimately, this package is used in the ''Predictive Networks'' web application developed by the Dana-Farber Cancer Institute in collaboration with Entagen.' + diff --git a/recipes/bioconductor-preprocesscore/build.sh b/recipes/bioconductor-preprocesscore/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-preprocesscore/build.sh +++ b/recipes/bioconductor-preprocesscore/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-preprocesscore/meta.yaml b/recipes/bioconductor-preprocesscore/meta.yaml index 53bd4b5b7ca2c..c307a09dc9013 100644 --- a/recipes/bioconductor-preprocesscore/meta.yaml +++ b/recipes/bioconductor-preprocesscore/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "preprocessCore" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7371a739d3481544c2e95e956d873fcc03e8f03e4761fd573d3b95747ec8caa9 + md5: 973ffdd342f2443573ca0fe558fb0cdc build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A library of core preprocessing routines.' extra: identifiers: - biotools:preprocesscore - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-preprocesscore + path: recipes/bioconductor-preprocesscore + version: 1.42.0 + diff --git a/recipes/bioconductor-primeviewcdf/meta.yaml b/recipes/bioconductor-primeviewcdf/meta.yaml new file mode 100644 index 0000000000000..c7bd21a48e60a --- /dev/null +++ b/recipes/bioconductor-primeviewcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "primeviewcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 71e39a59a5907e9b8a8dba58d36eee50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the PrimeView.cdf file.' + diff --git a/recipes/bioconductor-primeviewcdf/post-link.sh b/recipes/bioconductor-primeviewcdf/post-link.sh new file mode 100644 index 0000000000000..4d88dbacba130 --- /dev/null +++ b/recipes/bioconductor-primeviewcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="primeviewcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/primeviewcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/primeviewcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-primeviewcdf/bioconductor-primeviewcdf_2.18.0_src_all.tar.gz" +) +MD5="71e39a59a5907e9b8a8dba58d36eee50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-primeviewcdf/pre-unlink.sh b/recipes/bioconductor-primeviewcdf/pre-unlink.sh new file mode 100644 index 0000000000000..ba88cc17e2132 --- /dev/null +++ b/recipes/bioconductor-primeviewcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ primeviewcdf diff --git a/recipes/bioconductor-primeviewprobe/meta.yaml b/recipes/bioconductor-primeviewprobe/meta.yaml new file mode 100644 index 0000000000000..fb57e540993f6 --- /dev/null +++ b/recipes/bioconductor-primeviewprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "primeviewprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 87cc56a8da4fb742ab1558ce1d3d26cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was PrimeView\_probe\_tab.' + diff --git a/recipes/bioconductor-primeviewprobe/post-link.sh b/recipes/bioconductor-primeviewprobe/post-link.sh new file mode 100644 index 0000000000000..1d63723c36a4e --- /dev/null +++ b/recipes/bioconductor-primeviewprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="primeviewprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/primeviewprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/primeviewprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-primeviewprobe/bioconductor-primeviewprobe_2.18.0_src_all.tar.gz" +) +MD5="87cc56a8da4fb742ab1558ce1d3d26cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-primeviewprobe/pre-unlink.sh b/recipes/bioconductor-primeviewprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3489b3de75df2 --- /dev/null +++ b/recipes/bioconductor-primeviewprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ primeviewprobe diff --git a/recipes/bioconductor-primirtss/build.sh b/recipes/bioconductor-primirtss/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-primirtss/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-primirtss/meta.yaml b/recipes/bioconductor-primirtss/meta.yaml new file mode 100644 index 0000000000000..d2975b8adf89d --- /dev/null +++ b/recipes/bioconductor-primirtss/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.0" %} +{% set name = "primirTSS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6a05d403ab67452b78150d0c5020508d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' + - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-purrr >=0.2.5' + - 'r-r.utils >=2.6.0' + - 'r-shiny >=1.0.5' + - 'r-stringr >=1.3.1' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.8.1' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-jaspar2018 >=1.1.0,<1.2.0' + - 'bioconductor-phastcons100way.ucsc.hg38 >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-tfbstools >=1.20.0,<1.21.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-purrr >=0.2.5' + - 'r-r.utils >=2.6.0' + - 'r-shiny >=1.0.5' + - 'r-stringr >=1.3.1' + - 'r-tibble >=1.4.2' + - 'r-tidyr >=0.8.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A fast, convenient tool to identify the TSSs of miRNAs by integrating the data of H3K4me3 and Pol II as well as combining the conservation level and sequence feature, provided within both command-line and graphical interfaces, which achieves a better performance than the previous non-cell-specific methods on miRNA TSSs.' + diff --git a/recipes/bioconductor-prize/build.sh b/recipes/bioconductor-prize/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-prize/build.sh +++ b/recipes/bioconductor-prize/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prize/meta.yaml b/recipes/bioconductor-prize/meta.yaml index b638938b99eea..6c32fed419ef8 100644 --- a/recipes/bioconductor-prize/meta.yaml +++ b/recipes/bioconductor-prize/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "Prize" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cc5f5a907f8ad8bc5b331db6c08e0ede4c259ff7d5b92f0e0f3ab316c737d706 + md5: 2dec7aaf8421d2f2d1ed23559af587e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The high throughput studies often produce large amounts of numerous genes and proteins of interest. While it is difficult to study and validate all of them. Analytic Hierarchy Process (AHP) offers a novel approach to narrowing down long lists of candidates by prioritizing them based on how well they meet the research goal. AHP is a mathematical technique for organizing and analyzing complex decisions where multiple criteria are involved. The technique structures problems into a hierarchy of elements, and helps to specify numerical weights representing the relative importance of each element. Numerical weight or priority derived from each element allows users to find alternatives that best suit their goal and their understanding of the problem.' extra: identifiers: - biotools:prize - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-prize + path: recipes/bioconductor-prize + version: 1.10.0 + diff --git a/recipes/bioconductor-probamr/build.sh b/recipes/bioconductor-probamr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-probamr/build.sh +++ b/recipes/bioconductor-probamr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-probamr/meta.yaml b/recipes/bioconductor-probamr/meta.yaml index 35b46d4ad264f..59852d0bb5991 100644 --- a/recipes/bioconductor-probamr/meta.yaml +++ b/recipes/bioconductor-probamr/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "proBAMr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c88e11f33b601d1df49e994a72c08afe59aad6cc9a12d2ece659cb826f8aca8e + md5: cb59e471a54b77323e3d8aa981f253b4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Mapping PSMs back to genome. The package builds SAM file from shotgun proteomics data The package also provides function to prepare annotation from GTF file.' extra: identifiers: - biotools:probamr - doi:10.1074/mcp.M115.052860 + parent_recipe: + name: bioconductor-probamr + path: recipes/bioconductor-probamr + version: 1.14.0 + diff --git a/recipes/bioconductor-process/build.sh b/recipes/bioconductor-process/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-process/build.sh +++ b/recipes/bioconductor-process/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-process/meta.yaml b/recipes/bioconductor-process/meta.yaml index 7224eeba730bc..3da4bfbef17a3 100644 --- a/recipes/bioconductor-process/meta.yaml +++ b/recipes/bioconductor-process/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "PROcess" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ec635ccc30b4e347a7f85b60a02dba2bdc0ba2b5b11622d40a9671a71d18a24 + md5: e0b3f4defaace7d76c7b0c95792dfa53 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-icens >=1.52.0,<1.54.0' + - 'bioconductor-icens >=1.54.0,<1.55.0' - r-base run: - - 'bioconductor-icens >=1.52.0,<1.54.0' + - 'bioconductor-icens >=1.54.0,<1.55.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A package for processing protein mass spectrometry data.' extra: identifiers: - biotools:process - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-process + path: recipes/bioconductor-process + version: 1.56.0 + diff --git a/recipes/bioconductor-procoil/build.sh b/recipes/bioconductor-procoil/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-procoil/build.sh +++ b/recipes/bioconductor-procoil/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-procoil/meta.yaml b/recipes/bioconductor-procoil/meta.yaml index a2d6d0adcc37b..f7fae1f341037 100644 --- a/recipes/bioconductor-procoil/meta.yaml +++ b/recipes/bioconductor-procoil/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "procoil" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b92f0583661c74b66a741973e9bc019a509440d25eeb1d02e81e111ef104f004 + md5: 270f49603fd44f3062e45a3af865959a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-kebabs >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-kebabs >=1.14.0,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-kebabs >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package allows for predicting whether a coiled coil sequence (amino acid sequence plus heptad register) is more likely to form a dimer or more likely to form a trimer. Additionally to the prediction itself, a prediction profile is computed which allows for determining the strengths to which the individual residues are indicative for either class. Prediction profiles can also be visualized as curves or heatmaps.' extra: identifiers: - biotools:procoil + parent_recipe: + name: bioconductor-procoil + path: recipes/bioconductor-procoil + version: 2.8.0 + diff --git a/recipes/bioconductor-prodata/meta.yaml b/recipes/bioconductor-prodata/meta.yaml new file mode 100644 index 0000000000000..cca6ef858e145 --- /dev/null +++ b/recipes/bioconductor-prodata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "ProData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c3b90d81fe5c686b86ea33d8d4c15e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'A data package of SELDI-TOF protein mass spectrometry data of 167 breast cancer and normal samples.' + diff --git a/recipes/bioconductor-prodata/post-link.sh b/recipes/bioconductor-prodata/post-link.sh new file mode 100644 index 0000000000000..36f2d7e580d73 --- /dev/null +++ b/recipes/bioconductor-prodata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ProData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/ProData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/ProData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prodata/bioconductor-prodata_1.20.0_src_all.tar.gz" +) +MD5="3c3b90d81fe5c686b86ea33d8d4c15e8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prodata/pre-unlink.sh b/recipes/bioconductor-prodata/pre-unlink.sh new file mode 100644 index 0000000000000..6851be8c76064 --- /dev/null +++ b/recipes/bioconductor-prodata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ProData diff --git a/recipes/bioconductor-profia/build.sh b/recipes/bioconductor-profia/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-profia/build.sh +++ b/recipes/bioconductor-profia/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-profia/meta.yaml b/recipes/bioconductor-profia/meta.yaml index dcd3ae3fa33bc..8ef463b015211 100644 --- a/recipes/bioconductor-profia/meta.yaml +++ b/recipes/bioconductor-profia/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "proFIA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c1be762b9e1028d3f538f8e7a01e2e6f5a036f6de07be26bdf7ba1a75d6cddc + md5: 73a7a422c8cf6bacae5608e341cda743 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocGenerics, plasFIA, knitr, requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-ropls >=1.12.0,<1.14.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-minpack.lm - r-missforest - r-pracma run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-ropls >=1.12.0,<1.14.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - r-minpack.lm - r-missforest @@ -42,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Flow Injection Analysis coupled to High-Resolution Mass Spectrometry is a promising approach for high-throughput metabolomics. FIA- HRMS data, however, cannot be pre-processed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Here we present the proFIA package, which implements a new methodology to pre-process FIA-HRMS raw data (netCDF, mzData, mzXML, and mzML) including noise modelling and injection peak reconstruction, and generate the peak table. The workflow includes noise modelling, band detection and filtering then signal matching and missing value imputation. The peak table can then be exported as a .tsv file for further analysis. Visualisations to assess the quality of the data and of the signal made are easely produced.' extra: identifiers: - biotools:profia - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-profia + path: recipes/bioconductor-profia + version: 1.6.0 + diff --git a/recipes/bioconductor-profilescoredist/build.sh b/recipes/bioconductor-profilescoredist/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-profilescoredist/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-profilescoredist/meta.yaml b/recipes/bioconductor-profilescoredist/meta.yaml new file mode 100644 index 0000000000000..bd7dadf5fae7f --- /dev/null +++ b/recipes/bioconductor-profilescoredist/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.10.0" %} +{% set name = "profileScoreDist" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c1043816d33dad80676d2e4b4b675a82 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, MotifDb +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-rcpp + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Regularization and score distributions for position count matrices.' + diff --git a/recipes/bioconductor-progeny/build.sh b/recipes/bioconductor-progeny/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-progeny/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-progeny/meta.yaml b/recipes/bioconductor-progeny/meta.yaml new file mode 100644 index 0000000000000..66792ab1b0fd9 --- /dev/null +++ b/recipes/bioconductor-progeny/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "progeny" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d76e2c4ffa77a0a3f6b6feca21d09d75 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: airway, biomaRt, BiocFileCache, broom, DESeq2, dplyr, knitr, readr, readxl +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License (== 2.0) | file LICENSE' + summary: 'This package provides a function to infer pathway activity from gene expression using PROGENy. It contains the linear model we inferred in the publication "Perturbation-response genes reveal signaling footprints in cancer gene expression".' + diff --git a/recipes/bioconductor-proloc/build.sh b/recipes/bioconductor-proloc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-proloc/build.sh +++ b/recipes/bioconductor-proloc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proloc/conda_build_config.yaml b/recipes/bioconductor-proloc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-proloc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-proloc/meta.yaml b/recipes/bioconductor-proloc/meta.yaml index cf69eb5ce1243..02e101bee4078 100644 --- a/recipes/bioconductor-proloc/meta.yaml +++ b/recipes/bioconductor-proloc/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.20.2" %} +{% set version = "1.22.0" %} {% set name = "pRoloc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8772783ee6bd4df8f733ab1874c73f3c3bfd6fe82e7b5cd7d0033536732eff4e + md5: 2c1d6b48b0b30ff176fff8cffdb62f9b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, rmarkdown, pRolocdata (>= 1.9.4), roxygen2, synapter, xtable, rgl, BiocStyle (>= 2.5.19), hpar (>= 1.15.3), dplyr, GO.db, AnnotationDbi, Rtsne (>= 0.13), nipals requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-mlinterfaces >=1.60.1,<1.62.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' - r-base - r-caret - r-class + - r-coda - r-dendextend - r-e1071 - r-fnn @@ -35,9 +37,11 @@ requirements: - r-hexbin - r-kernlab - r-knitr + - r-laplacesdemon - r-lattice - r-mass - 'r-mclust >=4.3' + - r-mixtools - r-mvtnorm - r-nnet - r-plyr @@ -49,15 +53,16 @@ requirements: - r-sampling - r-scales run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-mlinterfaces >=1.60.1,<1.62.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' - r-base - r-caret - r-class + - r-coda - r-dendextend - r-e1071 - r-fnn @@ -66,9 +71,11 @@ requirements: - r-hexbin - r-kernlab - r-knitr + - r-laplacesdemon - r-lattice - r-mass - 'r-mclust >=4.3' + - r-mixtools - r-mvtnorm - r-nnet - r-plyr @@ -87,9 +94,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The pRoloc package implements machine learning and visualisation methods for the analysis and interogation of quantitiative mass spectrometry data to reliably infer protein sub-cellular localisation.' extra: identifiers: - biotools:proloc + parent_recipe: + name: bioconductor-proloc + path: recipes/bioconductor-proloc + version: 1.20.2 + diff --git a/recipes/bioconductor-prolocdata/meta.yaml b/recipes/bioconductor-prolocdata/meta.yaml new file mode 100644 index 0000000000000..4637e9a6f0c9d --- /dev/null +++ b/recipes/bioconductor-prolocdata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.20.0" %} +{% set name = "pRolocdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a251f615e1307eb3129875b823c2ed22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: pRoloc (>= 1.13.8), testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Mass-spectrometry based spatial proteomics data sets and protein complex separation data. Also contains the time course expression experiment from Mulvey et al. 2015.' + diff --git a/recipes/bioconductor-prolocdata/post-link.sh b/recipes/bioconductor-prolocdata/post-link.sh new file mode 100644 index 0000000000000..3bbb38c4fa3aa --- /dev/null +++ b/recipes/bioconductor-prolocdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pRolocdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pRolocdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/pRolocdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prolocdata/bioconductor-prolocdata_1.20.0_src_all.tar.gz" +) +MD5="a251f615e1307eb3129875b823c2ed22" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prolocdata/pre-unlink.sh b/recipes/bioconductor-prolocdata/pre-unlink.sh new file mode 100644 index 0000000000000..3f0b49e7679a7 --- /dev/null +++ b/recipes/bioconductor-prolocdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pRolocdata diff --git a/recipes/bioconductor-prolocgui/build.sh b/recipes/bioconductor-prolocgui/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-prolocgui/build.sh +++ b/recipes/bioconductor-prolocgui/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prolocgui/conda_build_config.yaml b/recipes/bioconductor-prolocgui/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-prolocgui/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-prolocgui/meta.yaml b/recipes/bioconductor-prolocgui/meta.yaml index a1203549e527a..7e9b93437bb5f 100644 --- a/recipes/bioconductor-prolocgui/meta.yaml +++ b/recipes/bioconductor-prolocgui/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "pRolocGUI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b254d49ec1c977e0904e8336cdc8ceaf4e4fff180770ced2b44ba0cfb53de4b1 + md5: 00b70d7e6c984f287bfbff80c165e87f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pRolocdata, knitr, BiocStyle (>= 2.5.19), rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-proloc >=1.20.2,<1.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-proloc >=1.22.0,<1.23.0' - r-base - r-dplyr - 'r-dt >=0.1.40' @@ -28,9 +30,9 @@ requirements: - r-scales - 'r-shiny >=0.9.1' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-proloc >=1.20.2,<1.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-proloc >=1.22.0,<1.23.0' - r-base - r-dplyr - 'r-dt >=0.1.40' @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package pRolocGUI comprises functions to interactively visualise organelle (spatial) proteomics data on the basis of pRoloc, pRolocdata and shiny.' extra: identifiers: - biotools:prolocgui - doi:10.1038/ncomms9992 + parent_recipe: + name: bioconductor-prolocgui + path: recipes/bioconductor-prolocgui + version: 1.14.0 + diff --git a/recipes/bioconductor-promise/build.sh b/recipes/bioconductor-promise/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-promise/build.sh +++ b/recipes/bioconductor-promise/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-promise/meta.yaml b/recipes/bioconductor-promise/meta.yaml index 9847b164acf0c..9b3780be4d262 100644 --- a/recipes/bioconductor-promise/meta.yaml +++ b/recipes/bioconductor-promise/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "PROMISE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 24127027591044e485d0cb293de277037cdf3a506f91f4dbe533462cde45afed + md5: 1551860b6a6c1cb1e2e1c2eca0188269 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A general tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables as described in Pounds et. al. (2009) Bioinformatics 25: 2013-2019' extra: identifiers: - biotools:promise - doi:10.1093/bioinformatics/btp357 + parent_recipe: + name: bioconductor-promise + path: recipes/bioconductor-promise + version: 1.32.0 + diff --git a/recipes/bioconductor-proper/build.sh b/recipes/bioconductor-proper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-proper/build.sh +++ b/recipes/bioconductor-proper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proper/meta.yaml b/recipes/bioconductor-proper/meta.yaml index 875b57ecbd18d..1ed3163dc0a9c 100644 --- a/recipes/bioconductor-proper/meta.yaml +++ b/recipes/bioconductor-proper/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "PROPER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4ea98b7824e7bec9f69ae1cf43d8be86ef7c7b0041928b46625bf697b6159ee8 + md5: ed2a4d37d9731accfe2288be221e93de build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle,DESeq,DSS,knitr requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base run: - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'This package provide simulation based methods for evaluating the statistical power in differential expression analysis from RNA-seq data.' extra: identifiers: - biotools:proper + parent_recipe: + name: bioconductor-proper + path: recipes/bioconductor-proper + version: 1.12.0 + diff --git a/recipes/bioconductor-props/build.sh b/recipes/bioconductor-props/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-props/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-props/meta.yaml b/recipes/bioconductor-props/meta.yaml new file mode 100644 index 0000000000000..9840ef878d91d --- /dev/null +++ b/recipes/bioconductor-props/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.4.0" %} +{% set name = "PROPS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e52f805ee22719f72202aa8768657455 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-bnlearn + - r-reshape2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-base + - r-bnlearn + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package calculates probabilistic pathway scores using gene expression data. Gene expression values are aggregated into pathway-based scores using Bayesian network representations of biological pathways.' + diff --git a/recipes/bioconductor-prostar/build.sh b/recipes/bioconductor-prostar/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-prostar/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prostar/meta.yaml b/recipes/bioconductor-prostar/meta.yaml new file mode 100644 index 0000000000000..f71cde70909ab --- /dev/null +++ b/recipes/bioconductor-prostar/meta.yaml @@ -0,0 +1,83 @@ +{% set version = "1.14.7" %} +{% set name = "Prostar" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c02426ae8669501c780f1ca321630701 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat +requirements: + host: + - 'bioconductor-dapar >=1.14.0,<1.15.0' + - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - r-base + - r-biocmanager + - r-colourpicker + - r-data.table + - r-dt + - r-future + - r-highcharter + - r-htmlwidgets + - r-later + - r-promises + - r-r.utils + - r-rclipboard + - r-rhandsontable + - r-shiny + - r-shinyace + - r-shinybs + - r-shinycssloaders + - r-shinyjqui + - r-shinyjs + - r-shinythemes + - r-shinytree + - r-shinywidgets + - r-webshot + - r-xml + run: + - 'bioconductor-dapar >=1.14.0,<1.15.0' + - 'bioconductor-dapardata >=1.12.0,<1.13.0' + - r-base + - r-biocmanager + - r-colourpicker + - r-data.table + - r-dt + - r-future + - r-highcharter + - r-htmlwidgets + - r-later + - r-promises + - r-r.utils + - r-rclipboard + - r-rhandsontable + - r-shiny + - r-shinyace + - r-shinybs + - r-shinycssloaders + - r-shinyjqui + - r-shinyjs + - r-shinythemes + - r-shinytree + - r-shinywidgets + - r-webshot + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides a GUI interface for DAPAR.' + diff --git a/recipes/bioconductor-prostatecancercamcap/meta.yaml b/recipes/bioconductor-prostatecancercamcap/meta.yaml new file mode 100644 index 0000000000000..d122cb979e28d --- /dev/null +++ b/recipes/bioconductor-prostatecancercamcap/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "prostateCancerCamcap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd8f6f0d10eaeebeb45ec56d911ee8d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Bioconductor data package for the Ross-Adams (2015) Prostate Cancer dataset.' + diff --git a/recipes/bioconductor-prostatecancercamcap/post-link.sh b/recipes/bioconductor-prostatecancercamcap/post-link.sh new file mode 100644 index 0000000000000..573236d860378 --- /dev/null +++ b/recipes/bioconductor-prostatecancercamcap/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prostateCancerCamcap_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerCamcap_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerCamcap_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancercamcap/bioconductor-prostatecancercamcap_1.10.0_src_all.tar.gz" +) +MD5="bd8f6f0d10eaeebeb45ec56d911ee8d3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prostatecancercamcap/pre-unlink.sh b/recipes/bioconductor-prostatecancercamcap/pre-unlink.sh new file mode 100644 index 0000000000000..4f0b4cdb27b1e --- /dev/null +++ b/recipes/bioconductor-prostatecancercamcap/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prostateCancerCamcap diff --git a/recipes/bioconductor-prostatecancergrasso/meta.yaml b/recipes/bioconductor-prostatecancergrasso/meta.yaml new file mode 100644 index 0000000000000..4abf92a20e8a0 --- /dev/null +++ b/recipes/bioconductor-prostatecancergrasso/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "prostateCancerGrasso" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 91b4dadaaa9d775625c625dc7763b6bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Bioconductor data package for the Grasso (2012) Prostate Cancer dataset.' + diff --git a/recipes/bioconductor-prostatecancergrasso/post-link.sh b/recipes/bioconductor-prostatecancergrasso/post-link.sh new file mode 100644 index 0000000000000..cfe865f958b94 --- /dev/null +++ b/recipes/bioconductor-prostatecancergrasso/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prostateCancerGrasso_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerGrasso_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerGrasso_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancergrasso/bioconductor-prostatecancergrasso_1.10.0_src_all.tar.gz" +) +MD5="91b4dadaaa9d775625c625dc7763b6bd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prostatecancergrasso/pre-unlink.sh b/recipes/bioconductor-prostatecancergrasso/pre-unlink.sh new file mode 100644 index 0000000000000..5b3cef9edc989 --- /dev/null +++ b/recipes/bioconductor-prostatecancergrasso/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prostateCancerGrasso diff --git a/recipes/bioconductor-prostatecancerstockholm/meta.yaml b/recipes/bioconductor-prostatecancerstockholm/meta.yaml new file mode 100644 index 0000000000000..1752a84d6b842 --- /dev/null +++ b/recipes/bioconductor-prostatecancerstockholm/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "prostateCancerStockholm" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e76e4cf258025b14950fa035662b7be5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Bioconductor data package for the Stockholm dataset' + diff --git a/recipes/bioconductor-prostatecancerstockholm/post-link.sh b/recipes/bioconductor-prostatecancerstockholm/post-link.sh new file mode 100644 index 0000000000000..3c3a8b66c9b77 --- /dev/null +++ b/recipes/bioconductor-prostatecancerstockholm/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prostateCancerStockholm_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerStockholm_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerStockholm_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancerstockholm/bioconductor-prostatecancerstockholm_1.10.0_src_all.tar.gz" +) +MD5="e76e4cf258025b14950fa035662b7be5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prostatecancerstockholm/pre-unlink.sh b/recipes/bioconductor-prostatecancerstockholm/pre-unlink.sh new file mode 100644 index 0000000000000..549bd2e891a77 --- /dev/null +++ b/recipes/bioconductor-prostatecancerstockholm/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prostateCancerStockholm diff --git a/recipes/bioconductor-prostatecancertaylor/meta.yaml b/recipes/bioconductor-prostatecancertaylor/meta.yaml new file mode 100644 index 0000000000000..85b27b10bfc09 --- /dev/null +++ b/recipes/bioconductor-prostatecancertaylor/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "prostateCancerTaylor" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 17217ff2d4cfaa8ff50b4fb5b1da2bf1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery, org.Hs.eg.db +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Bioconductor data package for the Taylor et al (2010) dataset.' + diff --git a/recipes/bioconductor-prostatecancertaylor/post-link.sh b/recipes/bioconductor-prostatecancertaylor/post-link.sh new file mode 100644 index 0000000000000..bfe5ae9d02094 --- /dev/null +++ b/recipes/bioconductor-prostatecancertaylor/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prostateCancerTaylor_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerTaylor_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerTaylor_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancertaylor/bioconductor-prostatecancertaylor_1.10.0_src_all.tar.gz" +) +MD5="17217ff2d4cfaa8ff50b4fb5b1da2bf1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prostatecancertaylor/pre-unlink.sh b/recipes/bioconductor-prostatecancertaylor/pre-unlink.sh new file mode 100644 index 0000000000000..972673f520258 --- /dev/null +++ b/recipes/bioconductor-prostatecancertaylor/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prostateCancerTaylor diff --git a/recipes/bioconductor-prostatecancervarambally/meta.yaml b/recipes/bioconductor-prostatecancervarambally/meta.yaml new file mode 100644 index 0000000000000..4bed5a0299dda --- /dev/null +++ b/recipes/bioconductor-prostatecancervarambally/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "prostateCancerVarambally" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c35f1f99121183a4332dbbc56a3de36b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A Bioconductor data package for the Varambally dataset' + diff --git a/recipes/bioconductor-prostatecancervarambally/post-link.sh b/recipes/bioconductor-prostatecancervarambally/post-link.sh new file mode 100644 index 0000000000000..b1fd0d87f9f75 --- /dev/null +++ b/recipes/bioconductor-prostatecancervarambally/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="prostateCancerVarambally_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/prostateCancerVarambally_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/prostateCancerVarambally_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-prostatecancervarambally/bioconductor-prostatecancervarambally_1.10.0_src_all.tar.gz" +) +MD5="c35f1f99121183a4332dbbc56a3de36b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-prostatecancervarambally/pre-unlink.sh b/recipes/bioconductor-prostatecancervarambally/pre-unlink.sh new file mode 100644 index 0000000000000..efc9ebb1c0b31 --- /dev/null +++ b/recipes/bioconductor-prostatecancervarambally/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ prostateCancerVarambally diff --git a/recipes/bioconductor-prot2d/build.sh b/recipes/bioconductor-prot2d/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-prot2d/build.sh +++ b/recipes/bioconductor-prot2d/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-prot2d/meta.yaml b/recipes/bioconductor-prot2d/meta.yaml index 35d6ce626d26e..82e045f3231ea 100644 --- a/recipes/bioconductor-prot2d/meta.yaml +++ b/recipes/bioconductor-prot2d/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "prot2D" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b9fa1a7e5d6c16bbff19671330ef02eb9dc6e92daba1eb15ce3106a564d914b + md5: 886c3086c4e35f8966e19c0c22facbfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: made4,affy requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-mulcom >=1.30.0,<1.32.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mulcom >=1.32.0,<1.33.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-fdrtool - r-mass - r-samr - r-st run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-mulcom >=1.30.0,<1.32.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mulcom >=1.32.0,<1.33.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-fdrtool - r-mass @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The purpose of this package is to analyze (i.e. Normalize and select significant spots) data issued from 2D GEl experiments' extra: identifiers: - biotools:prot2d + parent_recipe: + name: bioconductor-prot2d + path: recipes/bioconductor-prot2d + version: 1.18.0 + diff --git a/recipes/bioconductor-proteinprofiles/build.sh b/recipes/bioconductor-proteinprofiles/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-proteinprofiles/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proteinprofiles/meta.yaml b/recipes/bioconductor-proteinprofiles/meta.yaml new file mode 100644 index 0000000000000..c47bcd74b0a2c --- /dev/null +++ b/recipes/bioconductor-proteinprofiles/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.22.0" %} +{% set name = "proteinProfiles" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b6351027c4dfef576a396a03a053c864 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Significance assessment for distance measures of time-course protein profiles' + diff --git a/recipes/bioconductor-proteomicsannotationhubdata/build.sh b/recipes/bioconductor-proteomicsannotationhubdata/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-proteomicsannotationhubdata/build.sh +++ b/recipes/bioconductor-proteomicsannotationhubdata/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml b/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-proteomicsannotationhubdata/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml index 3cf6ee386b48e..602b4f127ea9f 100644 --- a/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml +++ b/recipes/bioconductor-proteomicsannotationhubdata/meta.yaml @@ -1,52 +1,59 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "ProteomicsAnnotationHubData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d9581b7a047cad2489ddc313dbeace66a42194ac454651271f3d03db3e96bda0 + md5: afbe09761bee9c27606041a3bef95f08 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-annotationhubdata >=1.10.2,<1.12.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base + - r-biocmanager - r-rcurl run: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-annotationhubdata >=1.10.2,<1.12.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotationhubdata >=1.12.0,<1.13.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base + - r-biocmanager - r-rcurl test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'These recipes convert a variety and a growing number of public proteomics data sets into easily-used standard Bioconductor data structures.' extra: identifiers: - biotools:proteomicsannotationhubdata - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-proteomicsannotationhubdata + path: recipes/bioconductor-proteomicsannotationhubdata + version: 1.10.0 + diff --git a/recipes/bioconductor-proteomm/build.sh b/recipes/bioconductor-proteomm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-proteomm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proteomm/meta.yaml b/recipes/bioconductor-proteomm/meta.yaml new file mode 100644 index 0000000000000..7f6d364c7ac29 --- /dev/null +++ b/recipes/bioconductor-proteomm/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.0.0" %} +{% set name = "ProteoMM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0fbe0a6120951bd31424c327b5448c0e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-gdata + - r-ggplot2 + - r-ggrepel + - r-gtools + - r-matrixstats + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - r-base + - r-gdata + - r-ggplot2 + - r-ggrepel + - r-gtools + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: MIT + summary: 'ProteoMM is a statistical method to perform model-based peptide-level differential expression analysis of single or multiple datasets. For multiple datasets ProteoMM produces a single fold change and p-value for each protein across multiple datasets. ProteoMM provides functionality for normalization, missing value imputation and differential expression. Model-based peptide-level imputation and differential expression analysis component of package follows the analysis described in “A statistical framework for protein quantitation in bottom-up MS based proteomics" (Karpievitch et al. Bioinformatics 2009). EigenMS normalisation is implemented as described in "Normalization of peak intensities in bottom-up MS-based proteomics using singular value decomposition." (Karpievitch et al. Bioinformatics 2009).' + diff --git a/recipes/bioconductor-proteoqc/build.sh b/recipes/bioconductor-proteoqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-proteoqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-proteoqc/meta.yaml b/recipes/bioconductor-proteoqc/meta.yaml new file mode 100644 index 0000000000000..03824d09b95fc --- /dev/null +++ b/recipes/bioconductor-proteoqc/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.18.0" %} +{% set name = "proteoQC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c733881810b96aa22096e2c290c5799d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RforProteomics, knitr, BiocStyle, R.utils, RUnit,BiocGenerics +requirements: + host: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-rpx >=1.18.0,<1.19.0' + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-nozzle.r1 + - r-plotly + - r-plyr + - r-reshape2 + - r-rmarkdown + - r-seqinr + - r-tidyr + - r-venndiagram + - r-xml + run: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-rpx >=1.18.0,<1.19.0' + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-nozzle.r1 + - r-plotly + - r-plyr + - r-reshape2 + - r-rmarkdown + - r-seqinr + - r-tidyr + - r-venndiagram + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-2 + summary: 'This package creates an HTML format QC report for MS/MS-based proteomics data. The report is intended to allow the user to quickly assess the quality of proteomics data.' + diff --git a/recipes/bioconductor-protgenerics/build.sh b/recipes/bioconductor-protgenerics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-protgenerics/build.sh +++ b/recipes/bioconductor-protgenerics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-protgenerics/meta.yaml b/recipes/bioconductor-protgenerics/meta.yaml index 2043f25c87948..4884d7bd6b99e 100644 --- a/recipes/bioconductor-protgenerics/meta.yaml +++ b/recipes/bioconductor-protgenerics/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ProtGenerics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 96b1140b0baeb7799e0abe11cc84a7905766c0eb12a828e2469e472578534b16 + md5: 837d899bc08e3518bf11a892f6b95e50 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'S4 generic functions needed by Bioconductor proteomics packages.' extra: identifiers: - biotools:protgenerics - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-protgenerics + path: recipes/bioconductor-protgenerics + version: 1.12.0 + diff --git a/recipes/bioconductor-psea/build.sh b/recipes/bioconductor-psea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-psea/build.sh +++ b/recipes/bioconductor-psea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-psea/meta.yaml b/recipes/bioconductor-psea/meta.yaml index bf07e36e1c8de..c37d1b687676b 100644 --- a/recipes/bioconductor-psea/meta.yaml +++ b/recipes/bioconductor-psea/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "PSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0d0c0cd836d52f1464f1e3faced8703b52e969719ad30692849de680c85419af + md5: 70a53aecf51323ffa3ed319f0983e175 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Deconvolution of gene expression data by Population-Specific Expression Analysis (PSEA).' extra: identifiers: - biotools:psea - doi:10.1038/scibx.2011.1159 + parent_recipe: + name: bioconductor-psea + path: recipes/bioconductor-psea + version: 1.14.0 + diff --git a/recipes/bioconductor-psichomics/build.sh b/recipes/bioconductor-psichomics/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-psichomics/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-psichomics/meta.yaml b/recipes/bioconductor-psichomics/meta.yaml new file mode 100644 index 0000000000000..2f5f21e9f0dd0 --- /dev/null +++ b/recipes/bioconductor-psichomics/meta.yaml @@ -0,0 +1,98 @@ +{% set version = "1.8.1" %} +{% set name = "psichomics" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 348aac50fd1626722ed857f8d1d7b679 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat, knitr, parallel, devtools, rmarkdown, gplots, covr, car, rstudioapi +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-recount >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-colourpicker + - r-data.table + - r-digest + - r-dplyr + - 'r-dt >=0.2' + - r-fastica + - r-fastmatch + - r-ggplot2 + - r-ggrepel + - 'r-highcharter >=0.5.0' + - r-htmltools + - r-httr + - r-jsonlite + - r-misctools + - r-pairsd3 + - r-plyr + - r-r.utils + - 'r-rcpp >=0.12.14' + - 'r-shiny >=1.0.3' + - r-shinybs + - r-shinyjs + - r-stringr + - r-survival + - r-xml + - r-xtable + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-recount >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-colourpicker + - r-data.table + - r-digest + - r-dplyr + - 'r-dt >=0.2' + - r-fastica + - r-fastmatch + - r-ggplot2 + - r-ggrepel + - 'r-highcharter >=0.5.0' + - r-htmltools + - r-httr + - r-jsonlite + - r-misctools + - r-pairsd3 + - r-plyr + - r-r.utils + - 'r-rcpp >=0.12.14' + - 'r-shiny >=1.0.3' + - r-shinybs + - r-shinyjs + - r-stringr + - r-survival + - r-xml + - r-xtable + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Interactive R package with an intuitive Shiny-based graphical interface for alternative splicing quantification and integrative analyses of alternative splicing and gene expression based on The Cancer Genome Atlas (TCGA), the Genotype-Tissue Expression project (GTEx), Sequence Read Archive (SRA) and user-provided data. The tool interactively performs survival, dimensionality reduction and median- and variance-based differential splicing and gene expression analyses that benefit from the incorporation of clinical and molecular sample-associated features (such as tumour stage or survival). Interactive visual access to genomic mapping and functional annotation of selected alternative splicing events is also included.' + diff --git a/recipes/bioconductor-psicquic/build.sh b/recipes/bioconductor-psicquic/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-psicquic/build.sh +++ b/recipes/bioconductor-psicquic/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-psicquic/meta.yaml b/recipes/bioconductor-psicquic/meta.yaml index 3c86c686ae559..0ecf3327f78b8 100644 --- a/recipes/bioconductor-psicquic/meta.yaml +++ b/recipes/bioconductor-psicquic/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.18.1" %} +{% set version = "1.20.0" %} {% set name = "PSICQUIC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d9b363a9a8057baffee92e7c3c9d270d7ed22976180030d566ae14049f0933e2 + md5: 019a4417247c16e5ebcdf22ffac1c77b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Hs.eg.db requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-httr - r-plyr - r-rcurl run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-httr - r-plyr @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'PSICQUIC is a project within the HUPO Proteomics Standard Initiative (HUPO-PSI). It standardises programmatic access to molecular interaction databases.' extra: identifiers: - biotools:psicquic - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-psicquic + path: recipes/bioconductor-psicquic + version: 1.18.1 + diff --git a/recipes/bioconductor-psygenet2r/build.sh b/recipes/bioconductor-psygenet2r/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-psygenet2r/build.sh +++ b/recipes/bioconductor-psygenet2r/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-psygenet2r/conda_build_config.yaml b/recipes/bioconductor-psygenet2r/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-psygenet2r/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-psygenet2r/meta.yaml b/recipes/bioconductor-psygenet2r/meta.yaml index f31151eb62bbb..98582e70fb369 100644 --- a/recipes/bioconductor-psygenet2r/meta.yaml +++ b/recipes/bioconductor-psygenet2r/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "psygenet2r" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c5edc497c9016d1ea4e61467c2ca3537f3d2b2d4304f5cfe24ebe9370ec75b66 + md5: ad685186daa974d0b5e6b91e0cc7d0b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr requirements: host: - - 'bioconductor-bgeedb >=2.6.2,<2.8.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-bgeedb >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base + - r-biocmanager - r-ggplot2 - r-igraph - r-labeling @@ -32,13 +34,13 @@ requirements: - r-reshape2 - r-stringr run: - - 'bioconductor-bgeedb >=2.6.2,<2.8.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-bgeedb >=2.8.0,<2.9.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base + - r-biocmanager - r-ggplot2 - r-igraph - r-labeling @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Package to retrieve data from PsyGeNET database (www.psygenet.org) and to perform comorbidity studies with PsyGeNET''s and user''s data.' extra: identifiers: - biotools:psygenet2r - doi:10.1093/bioinformatics/btv301 + parent_recipe: + name: bioconductor-psygenet2r + path: recipes/bioconductor-psygenet2r + version: 1.12.0 + diff --git a/recipes/bioconductor-pth2o2lipids/meta.yaml b/recipes/bioconductor-pth2o2lipids/meta.yaml new file mode 100644 index 0000000000000..72ffc249c294c --- /dev/null +++ b/recipes/bioconductor-pth2o2lipids/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.8.0" %} +{% set name = "PtH2O2lipids" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4e581e8fef911bd546261ddc9c4f7cb7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: gplots, RColorBrewer, cluster, vegan, clustsig +requirements: + host: + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-lobstahs >=1.8.0,<1.9.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' + - r-base + run: + - 'bioconductor-camera >=1.38.0,<1.39.0' + - 'bioconductor-lobstahs >=1.8.0,<1.9.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Annotated HPLC-ESI-MS lipid data in positive ionization mode from an experiment in which cultures of the marine diatom Phaeodactylum tricornutum were treated with various concentrations of hydrogen peroxide (H2O2) to induce oxidative stress. The experiment is described in Graff van Creveld, et al., 2015, "Early perturbation in mitochondria redox homeostasis in response to environmental stress predicts cell fate in diatoms," ISME Journal 9:385-395. PtH2O2lipids consists of two objects: A CAMERA xsAnnotate object (ptH2O2lipids$xsAnnotate) and LOBSTAHS LOBSet object (ptH2O2lipids$xsAnnotate$LOBSet). The LOBSet includes putative compound assignments from the default LOBSTAHS database. Isomer annotation is recorded in three other LOBSet slots.' + diff --git a/recipes/bioconductor-pth2o2lipids/post-link.sh b/recipes/bioconductor-pth2o2lipids/post-link.sh new file mode 100644 index 0000000000000..b55eb240d54d0 --- /dev/null +++ b/recipes/bioconductor-pth2o2lipids/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PtH2O2lipids_1.8.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PtH2O2lipids_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/PtH2O2lipids_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pth2o2lipids/bioconductor-pth2o2lipids_1.8.0_src_all.tar.gz" +) +MD5="4e581e8fef911bd546261ddc9c4f7cb7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pth2o2lipids/pre-unlink.sh b/recipes/bioconductor-pth2o2lipids/pre-unlink.sh new file mode 100644 index 0000000000000..997d143d254f7 --- /dev/null +++ b/recipes/bioconductor-pth2o2lipids/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PtH2O2lipids diff --git a/recipes/bioconductor-puma/build.sh b/recipes/bioconductor-puma/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-puma/build.sh +++ b/recipes/bioconductor-puma/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-puma/conda_build_config.yaml b/recipes/bioconductor-puma/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-puma/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-puma/meta.yaml b/recipes/bioconductor-puma/meta.yaml index 8cd1f47d2c82c..a239dc9825488 100644 --- a/recipes/bioconductor-puma/meta.yaml +++ b/recipes/bioconductor-puma/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "3.22.0" %} +{% set version = "3.24.0" %} {% set name = "puma" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: dd39ad777211a794773dc196541631162ae999b8426ef8de5863b2f83e788032 + md5: c27be11118a5db7432f6b9cde9f06d5b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: pumadata, affydata, snow, limma, ROCR,annotate requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - r-base - r-mclust run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' - r-base - r-mclust build: @@ -40,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Most analyses of Affymetrix GeneChip data (including tranditional 3'' arrays and exon arrays and Human Transcriptome Array 2.0) are based on point estimates of expression levels and ignore the uncertainty of such estimates. By propagating uncertainty to downstream analyses we can improve results from microarray analyses. For the first time, the puma package makes a suite of uncertainty propagation methods available to a general audience. In additon to calculte gene expression from Affymetrix 3'' arrays, puma also provides methods to process exon arrays and produces gene and isoform expression for alternative splicing study. puma also offers improvements in terms of scope and speed of execution over previously available uncertainty propagation methods. Included are summarisation, differential expression detection, clustering and PCA methods, together with useful plotting functions.' extra: identifiers: - biotools:puma + parent_recipe: + name: bioconductor-puma + path: recipes/bioconductor-puma + version: 3.22.0 + diff --git a/recipes/bioconductor-pumadata/meta.yaml b/recipes/bioconductor-pumadata/meta.yaml new file mode 100644 index 0000000000000..c6afdbfa36c04 --- /dev/null +++ b/recipes/bioconductor-pumadata/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.18.0" %} +{% set name = "pumadata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ec6c6ebbaa066139f26af9e175936484 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-puma >=3.24.0,<3.25.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-puma >=3.24.0,<3.25.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This is a simple data package including various data sets derived from the estrogen data for use with the puma (Propagating Uncertainty in Microarray Analysis) package.' + diff --git a/recipes/bioconductor-pumadata/post-link.sh b/recipes/bioconductor-pumadata/post-link.sh new file mode 100644 index 0000000000000..2f80f84f248c9 --- /dev/null +++ b/recipes/bioconductor-pumadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="pumadata_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/pumadata_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/pumadata_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pumadata/bioconductor-pumadata_2.18.0_src_all.tar.gz" +) +MD5="ec6c6ebbaa066139f26af9e175936484" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pumadata/pre-unlink.sh b/recipes/bioconductor-pumadata/pre-unlink.sh new file mode 100644 index 0000000000000..85650433cb089 --- /dev/null +++ b/recipes/bioconductor-pumadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ pumadata diff --git a/recipes/bioconductor-purecn/build.sh b/recipes/bioconductor-purecn/build.sh index 6324723bbdebd..c1d13421f5f1e 100644 --- a/recipes/bioconductor-purecn/build.sh +++ b/recipes/bioconductor-purecn/build.sh @@ -1,16 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . - -extdata=$PREFIX/lib/R/library/PureCN/extdata -mkdir -p $PREFIX/bin - -for S in Coverage.R Dx.R FilterCallableLoci.R IntervalFile.R NormalDB.R -do - perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' $extdata/$S - ln -s $extdata/$S $PREFIX/bin/PureCN_${S} -done - -perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' $extdata/PureCN.R -ln -s $extdata/PureCN.R $PREFIX/bin/PureCN.R +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-purecn/meta.yaml b/recipes/bioconductor-purecn/meta.yaml index e41c001e6f894..6eeba1eacb465 100644 --- a/recipes/bioconductor-purecn/meta.yaml +++ b/recipes/bioconductor-purecn/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "1.13.1" %} +{% set version = "1.12.1" %} {% set name = "PureCN" %} {% set bioc = "3.8" %} @@ -6,75 +6,75 @@ package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/lima1/PureCN/archive/de563d2.tar.gz - #url: https://depot.galaxyproject.org/software/bioconductor-purecn/bioconductor-purecn_{{ version }}_src_all.tar.gz - sha256: fd38af3a8b7e62e3280d5178040ece0ad4deb5e385ea9ff3126b088b95770308 + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9f30c118ba5234d2854f0b782a111e88 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: PSCBS, BiocStyle, BiocParallel, knitr, optparse, TxDb.Hsapiens.UCSC.hg19.knownGene, org.Hs.eg.db, covr, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-copynumber>=1.20.0,<1.22.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-edger >=3.22.0,<3.24.0' - - 'bioconductor-limma >=3.36.0,<3.38.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - - r-deconstructsigs - r-futile.logger - - r-gridextra - r-ggplot2 - - r-optparse + - r-gridextra + - r-matrix - r-rcolorbrewer - r-vgam run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-copynumber>=1.20.0,<1.22.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-edger >=3.22.0,<3.24.0' - - 'bioconductor-limma >=3.36.0,<3.38.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - - r-deconstructsigs - r-futile.logger - - r-gridextra - r-ggplot2 - - r-optparse + - r-gridextra + - r-matrix - r-rcolorbrewer - r-vgam test: commands: - '$R -e "library(''{{ name }}'')"' - - PureCN.R -h about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with standard somatic variant detection and copy number pipelines, and has support for tumor samples without matching normal samples.' extra: identifiers: - biotools:purecn + parent_recipe: + name: bioconductor-purecn + path: recipes/bioconductor-purecn + version: 1.13.1 + diff --git a/recipes/bioconductor-pvac/build.sh b/recipes/bioconductor-pvac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pvac/build.sh +++ b/recipes/bioconductor-pvac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pvac/conda_build_config.yaml b/recipes/bioconductor-pvac/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-pvac/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-pvac/meta.yaml b/recipes/bioconductor-pvac/meta.yaml index 4c86922d0bf74..610677add7809 100644 --- a/recipes/bioconductor-pvac/meta.yaml +++ b/recipes/bioconductor-pvac/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "pvac" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: afc020ec92f2d744d3d54c042c0592410ce46ea0f7f5028693a16a64a7176233 + md5: 2d1c05d44125333ae877c99001bcfa6b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pbapply, affydata, ALLMLL, genefilter requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'The package contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC).' extra: identifiers: - biotools:pvac - doi:10.1093/nar/gkr241 + parent_recipe: + name: bioconductor-pvac + path: recipes/bioconductor-pvac + version: 1.28.0 + diff --git a/recipes/bioconductor-pvca/build.sh b/recipes/bioconductor-pvca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pvca/build.sh +++ b/recipes/bioconductor-pvca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pvca/conda_build_config.yaml b/recipes/bioconductor-pvca/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-pvca/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-pvca/meta.yaml b/recipes/bioconductor-pvca/meta.yaml index d9421a513d469..b713169bcee03 100644 --- a/recipes/bioconductor-pvca/meta.yaml +++ b/recipes/bioconductor-pvca/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "pvca" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2ff90cebdd80f32c30a1af3c2c417af37ee89ec88581ced8d8f2504962ef9a37 + md5: d138f4edb7fa0c055c6f0abad5dac160 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: golubEsets requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-lme4 - r-matrix run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-lme4 - r-matrix @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2.0)' summary: 'This package contains the function to assess the batch sourcs by fitting all "sources" as random effects including two-way interaction terms in the Mixed Model(depends on lme4 package) to selected principal components, which were obtained from the original data correlation matrix. This package accompanies the book "Batch Effects and Noise in Microarray Experiements, chapter 12.' extra: identifiers: - biotools:pvca - doi:10.1002/9780470685983.ch12 + parent_recipe: + name: bioconductor-pvca + path: recipes/bioconductor-pvca + version: 1.20.0 + diff --git a/recipes/bioconductor-pviz/build.sh b/recipes/bioconductor-pviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pviz/build.sh +++ b/recipes/bioconductor-pviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pviz/meta.yaml b/recipes/bioconductor-pviz/meta.yaml index 7cd0031cc53e2..12f24e101dacb 100644 --- a/recipes/bioconductor-pviz/meta.yaml +++ b/recipes/bioconductor-pviz/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Pviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 722b05d01d1e26c4feeaae73c9c053b606d1babab0b921720c5c0aa60a1fbcfb + md5: f5bd670dee87e666b06e6e506d39c2e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, pepDat requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-data.table run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-data.table test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Pviz adapts the Gviz package for protein sequences and data.' extra: identifiers: - biotools:pviz - doi:10.1007/978-1-4939-3037-1_10 + parent_recipe: + name: bioconductor-pviz + path: recipes/bioconductor-pviz + version: 1.14.0 + diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml new file mode 100644 index 0000000000000..8c8e652a981ea --- /dev/null +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "4.16.0" %} +{% set name = "PWMEnrich.Dmelanogaster.background" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 265967f539c3da744389a1fb5a3f112a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + run: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'PWMEnrich pre-compiled background objects for Drosophila melanogaster and MotifDb D. melanogaster motifs.' + diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh new file mode 100644 index 0000000000000..2f8178363bd35 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Dmelanogaster.background_4.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.dmelanogaster.background/bioconductor-pwmenrich.dmelanogaster.background_4.16.0_src_all.tar.gz" +) +MD5="265967f539c3da744389a1fb5a3f112a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pwmenrich.dmelanogaster.background/pre-unlink.sh b/recipes/bioconductor-pwmenrich.dmelanogaster.background/pre-unlink.sh new file mode 100644 index 0000000000000..60fe3d861bb46 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.dmelanogaster.background/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PWMEnrich.Dmelanogaster.background diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml new file mode 100644 index 0000000000000..58464b99c0078 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "4.16.0" %} +{% set name = "PWMEnrich.Hsapiens.background" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bffb6a95c2c744fe3a430bbb758dc8e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + run: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'PWMEnrich pre-compiled background objects for H. sapiens (human) and MotifDb H. sapiens motifs.' + diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh new file mode 100644 index 0000000000000..08025fc168909 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PWMEnrich.Hsapiens.background_4.16.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Hsapiens.background_4.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Hsapiens.background_4.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.hsapiens.background/bioconductor-pwmenrich.hsapiens.background_4.16.0_src_all.tar.gz" +) +MD5="bffb6a95c2c744fe3a430bbb758dc8e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pwmenrich.hsapiens.background/pre-unlink.sh b/recipes/bioconductor-pwmenrich.hsapiens.background/pre-unlink.sh new file mode 100644 index 0000000000000..98a64ba3d316c --- /dev/null +++ b/recipes/bioconductor-pwmenrich.hsapiens.background/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PWMEnrich.Hsapiens.background diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml new file mode 100644 index 0000000000000..457ff00ef6d28 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "4.16.0" %} +{% set name = "PWMEnrich.Mmusculus.background" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a26cdb4eb465daba22b3e13e4db1a86b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + run: + - 'bioconductor-pwmenrich >=4.18.0,<4.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'PWMEnrich pre-compiled background objects for M.musculus (mouse) and MotifDb M. musculus motifs.' + diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh new file mode 100644 index 0000000000000..9509089e3f0b7 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="PWMEnrich.Mmusculus.background_4.16.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/PWMEnrich.Mmusculus.background_4.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/PWMEnrich.Mmusculus.background_4.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-pwmenrich.mmusculus.background/bioconductor-pwmenrich.mmusculus.background_4.16.0_src_all.tar.gz" +) +MD5="a26cdb4eb465daba22b3e13e4db1a86b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-pwmenrich.mmusculus.background/pre-unlink.sh b/recipes/bioconductor-pwmenrich.mmusculus.background/pre-unlink.sh new file mode 100644 index 0000000000000..8f35899efbf96 --- /dev/null +++ b/recipes/bioconductor-pwmenrich.mmusculus.background/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ PWMEnrich.Mmusculus.background diff --git a/recipes/bioconductor-pwmenrich/build.sh b/recipes/bioconductor-pwmenrich/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pwmenrich/build.sh +++ b/recipes/bioconductor-pwmenrich/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pwmenrich/meta.yaml b/recipes/bioconductor-pwmenrich/meta.yaml index 1a80d3537efb0..9cfc62d587ff7 100644 --- a/recipes/bioconductor-pwmenrich/meta.yaml +++ b/recipes/bioconductor-pwmenrich/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "4.16.0" %} +{% set version = "4.18.0" %} {% set name = "PWMEnrich" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fd648dda7ed9f4d6e570a76b0ee4b4992469b2910d1c75e803c80df6d72fe838 + md5: b04f4faa148db904e60269da8b987bd6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MotifDb, BSgenome.Dmelanogaster.UCSC.dm3, PWMEnrich.Dmelanogaster.background, testthat, gtools, parallel, PWMEnrich.Hsapiens.background, PWMEnrich.Mmusculus.background, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base - r-evd - r-gdata run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base - r-evd - r-gdata @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.' extra: identifiers: - biotools:pwmenrich - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-pwmenrich + path: recipes/bioconductor-pwmenrich + version: 4.16.0 + diff --git a/recipes/bioconductor-pwomics/build.sh b/recipes/bioconductor-pwomics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-pwomics/build.sh +++ b/recipes/bioconductor-pwomics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-pwomics/conda_build_config.yaml b/recipes/bioconductor-pwomics/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-pwomics/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-pwomics/meta.yaml b/recipes/bioconductor-pwomics/meta.yaml index 3eb315f0d8892..80b8d66154b57 100644 --- a/recipes/bioconductor-pwomics/meta.yaml +++ b/recipes/bioconductor-pwomics/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "pwOmics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7288ed9d0e6102383e884ecedc23c64cd81ff881e29f30542ed2962747ecfe33 + md5: e762db025a30377ad4908bb3191d20e8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ebdbNet, longitudinal, Mfuzz requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' - - 'bioconductor-stringdb >=1.20.0,<1.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' - r-base - r-data.table - r-gplots - r-igraph run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbiopaxparser >=2.20.0,<2.22.0' - - 'bioconductor-stringdb >=1.20.0,<1.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbiopaxparser >=2.22.0,<2.23.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' - r-base - r-data.table - r-gplots @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'pwOmics performs pathway-based level-specific data comparison of matching omics data sets based on pre-analysed user-specified lists of differential genes/transcripts and phosphoproteins. A separate downstream analysis of phosphoproteomic data including pathway identification, transcription factor identification and target gene identification is opposed to the upstream analysis starting with gene or transcript information as basis for identification of upstream transcription factors and potential proteomic regulators. The cross-platform comparative analysis allows for comprehensive analysis of single time point experiments and time-series experiments by providing static and dynamic analysis tools for data integration. In addition, it provides functions to identify individual signaling axes based on data integration.' extra: identifiers: - biotools:pwomics - doi:10.1093/bioinformatics/btv323 + parent_recipe: + name: bioconductor-pwomics + path: recipes/bioconductor-pwomics + version: 1.12.0 + diff --git a/recipes/bioconductor-qcmetrics/build.sh b/recipes/bioconductor-qcmetrics/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qcmetrics/build.sh +++ b/recipes/bioconductor-qcmetrics/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qcmetrics/meta.yaml b/recipes/bioconductor-qcmetrics/meta.yaml index d9c46c67b0da8..3ed0de082eef0 100644 --- a/recipes/bioconductor-qcmetrics/meta.yaml +++ b/recipes/bioconductor-qcmetrics/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "qcmetrics" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e85a7a296adcda4ee012ab1a1621290c3261ce2b799fb3b4817467654e108042 + md5: 386d96a1c06106d5e802b1cec772420c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affy, MSnbase, ggplot2, lattice, yaqcaffy, MAQCsubsetAFX, RforProteomics, AnnotationDbi, mzR, hgu133plus2cdf, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-knitr - r-nozzle.r1 - r-pander - r-xtable run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-knitr - r-nozzle.r1 @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package provides a framework for generic quality control of data. It permits to create, manage and visualise individual or sets of quality control metrics and generate quality control reports in various formats.' extra: identifiers: - biotools:qcmetrics - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-qcmetrics + path: recipes/bioconductor-qcmetrics + version: 1.18.0 + diff --git a/recipes/bioconductor-qdnaseq.hg19/meta.yaml b/recipes/bioconductor-qdnaseq.hg19/meta.yaml new file mode 100644 index 0000000000000..b111bab278242 --- /dev/null +++ b/recipes/bioconductor-qdnaseq.hg19/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.12.0" %} +{% set name = "QDNAseq.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5644d966c2331d01df686107f85f0899 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - r-base + run: + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'This package provides QDNAseq bin annotations for the human genome build hg19.' + diff --git a/recipes/bioconductor-qdnaseq.hg19/post-link.sh b/recipes/bioconductor-qdnaseq.hg19/post-link.sh new file mode 100644 index 0000000000000..6d5f3827ae74d --- /dev/null +++ b/recipes/bioconductor-qdnaseq.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="QDNAseq.hg19_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QDNAseq.hg19_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/QDNAseq.hg19_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.hg19/bioconductor-qdnaseq.hg19_1.12.0_src_all.tar.gz" +) +MD5="5644d966c2331d01df686107f85f0899" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-qdnaseq.hg19/pre-unlink.sh b/recipes/bioconductor-qdnaseq.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..7b9deeef93e80 --- /dev/null +++ b/recipes/bioconductor-qdnaseq.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ QDNAseq.hg19 diff --git a/recipes/bioconductor-qdnaseq.mm10/meta.yaml b/recipes/bioconductor-qdnaseq.mm10/meta.yaml index 25a4029e65847..05b00c08fd035 100644 --- a/recipes/bioconductor-qdnaseq.mm10/meta.yaml +++ b/recipes/bioconductor-qdnaseq.mm10/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "QDNAseq.mm10" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a8fc7be0a41bf03d12d1184413aa9d0eea562156b62ca06f23f8a6beb801d048 + md5: 3557bc3a5f5820eb17d7a643730ed314 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-qdnaseq >=1.16.0,<1.18.0' + - 'bioconductor-qdnaseq >=1.18.0,<1.19.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL summary: 'This package provides QDNAseq bin annotations for the mouse genome build mm10.' - +extra: + parent_recipe: + name: bioconductor-qdnaseq.mm10 + path: recipes/bioconductor-qdnaseq.mm10 + version: 1.10.0 diff --git a/recipes/bioconductor-qdnaseq.mm10/post-link.sh b/recipes/bioconductor-qdnaseq.mm10/post-link.sh index 62206bcda0485..991ac13319d90 100644 --- a/recipes/bioconductor-qdnaseq.mm10/post-link.sh +++ b/recipes/bioconductor-qdnaseq.mm10/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="QDNAseq.mm10_1.10.0.tar.gz" +FN="QDNAseq.mm10_1.12.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/QDNAseq.mm10_1.10.0.tar.gz" - "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.10.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.10.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QDNAseq.mm10_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/QDNAseq.mm10_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qdnaseq.mm10/bioconductor-qdnaseq.mm10_1.12.0_src_all.tar.gz" ) -MD5="89069a71fa4182e83c6029345d3aefdf" +MD5="3557bc3a5f5820eb17d7a643730ed314" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-qdnaseq/build.sh b/recipes/bioconductor-qdnaseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qdnaseq/build.sh +++ b/recipes/bioconductor-qdnaseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qdnaseq/meta.yaml b/recipes/bioconductor-qdnaseq/meta.yaml index 85b2c8d2708bb..4a13346463ffb 100644 --- a/recipes/bioconductor-qdnaseq/meta.yaml +++ b/recipes/bioconductor-qdnaseq/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "QDNAseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8d73b6224d1c82a2e8c540ec3c7c29ac6993704f9a4e024f03cdf1ee5d4d46de + md5: d25872be8df20f65786d1df51d79181b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle (>= 1.8.0), BSgenome (>= 1.38.0), digest (>= 0.6.8), GenomeInfoDb (>= 1.6.0), future (>= 0.14.0), R.cache (>= 0.12.0) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-cghcall >=2.42.0,<2.44.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-cghcall >=2.44.0,<2.45.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - 'r-matrixstats >=0.50.2' - 'r-r.utils >=2.3.0' @@ -45,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Quantitative DNA sequencing for chromosomal aberrations. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.' extra: identifiers: - biotools:qdnaseq + parent_recipe: + name: bioconductor-qdnaseq + path: recipes/bioconductor-qdnaseq + version: 1.16.0 + diff --git a/recipes/bioconductor-qpcrnorm/build.sh b/recipes/bioconductor-qpcrnorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qpcrnorm/build.sh +++ b/recipes/bioconductor-qpcrnorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qpcrnorm/conda_build_config.yaml b/recipes/bioconductor-qpcrnorm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-qpcrnorm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-qpcrnorm/meta.yaml b/recipes/bioconductor-qpcrnorm/meta.yaml index ea4b24554d2b5..9d34ef69b31a8 100644 --- a/recipes/bioconductor-qpcrnorm/meta.yaml +++ b/recipes/bioconductor-qpcrnorm/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "qpcrNorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 707f345dc26c1930c5c1429e45990ba50a3cfe378f51ce7cfc7357eefbd317ce + md5: 16a79fad66a1af84d66805d099ba0c58 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'The package contains functions to perform normalization of high-throughput qPCR data. Basic functions for processing raw Ct data plus functions to generate diagnostic plots are also available.' extra: identifiers: - biotools:qpcrnorm - doi:10.1186/1471-2105-10-110 + parent_recipe: + name: bioconductor-qpcrnorm + path: recipes/bioconductor-qpcrnorm + version: 1.38.0 + diff --git a/recipes/bioconductor-qpgraph/build.sh b/recipes/bioconductor-qpgraph/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qpgraph/build.sh +++ b/recipes/bioconductor-qpgraph/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qpgraph/meta.yaml b/recipes/bioconductor-qpgraph/meta.yaml index 79bee7542d58f..45a12101a0629 100644 --- a/recipes/bioconductor-qpgraph/meta.yaml +++ b/recipes/bioconductor-qpgraph/meta.yaml @@ -1,50 +1,51 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "qpgraph" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8ece88886836fcb2693e43cee82a18c277b53548e40a716b3abc49d78fb3827e + md5: c31410ede77ec4bde909a2755488d2af build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, BiocStyle, genefilter, org.EcK12.eg.db, rlecuyer, snow, Category, GOstats requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm - r-qtl run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-matrix >=1.0' - r-mvtnorm @@ -57,9 +58,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Estimate gene and eQTL networks from high-throughput expression and genotyping assays.' extra: identifiers: - biotools:qpgraph + parent_recipe: + name: bioconductor-qpgraph + path: recipes/bioconductor-qpgraph + version: 2.14.0 + diff --git a/recipes/bioconductor-qplexanalyzer/build.sh b/recipes/bioconductor-qplexanalyzer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qplexanalyzer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qplexanalyzer/meta.yaml b/recipes/bioconductor-qplexanalyzer/meta.yaml new file mode 100644 index 0000000000000..b6940e3b0f2c2 --- /dev/null +++ b/recipes/bioconductor-qplexanalyzer/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.0.2" %} +{% set name = "qPLEXanalyzer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c9017d6450f890e437194a79ba39be13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: UniProt.ws, knitr, qPLEXdata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-magrittr + - r-purrr + - r-rcolorbrewer + - r-statmod + - r-stringr + - r-tibble + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - r-assertthat + - r-base + - r-dplyr + - r-ggdendro + - r-ggplot2 + - r-magrittr + - r-purrr + - r-rcolorbrewer + - r-statmod + - r-stringr + - r-tibble + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Tools for quantitative proteomics data analysis generated from qPLEX-RIME method.' + diff --git a/recipes/bioconductor-qplexdata/meta.yaml b/recipes/bioconductor-qplexdata/meta.yaml new file mode 100644 index 0000000000000..6ae164b62a7fd --- /dev/null +++ b/recipes/bioconductor-qplexdata/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.1" %} +{% set name = "qPLEXdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 27c05de065b8225c34d8a99ac7ce1992 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qplexanalyzer >=1.0.0,<1.1.0' + - r-base + - r-dplyr + - r-knitr + run: + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-qplexanalyzer >=1.0.0,<1.1.0' + - r-base + - r-dplyr + - r-knitr + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'qPLEX-RIME and Full proteome TMT mass spectrometry datasets.' + diff --git a/recipes/bioconductor-qplexdata/post-link.sh b/recipes/bioconductor-qplexdata/post-link.sh new file mode 100644 index 0000000000000..80d46e1644008 --- /dev/null +++ b/recipes/bioconductor-qplexdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="qPLEXdata_1.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/qPLEXdata_1.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/qPLEXdata_1.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qplexdata/bioconductor-qplexdata_1.0.1_src_all.tar.gz" +) +MD5="27c05de065b8225c34d8a99ac7ce1992" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-qplexdata/pre-unlink.sh b/recipes/bioconductor-qplexdata/pre-unlink.sh new file mode 100644 index 0000000000000..f40113f7936c9 --- /dev/null +++ b/recipes/bioconductor-qplexdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ qPLEXdata diff --git a/recipes/bioconductor-qrqc/build.sh b/recipes/bioconductor-qrqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qrqc/build.sh +++ b/recipes/bioconductor-qrqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qrqc/meta.yaml b/recipes/bioconductor-qrqc/meta.yaml index 06c312d43fdb1..548aca1ecd18e 100644 --- a/recipes/bioconductor-qrqc/meta.yaml +++ b/recipes/bioconductor-qrqc/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "qrqc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5c0acfd1c4e980b045411cd1c1de94f8de89c272e0e82edbe753ca6e82ee36bd + md5: f6cafce11da089f3c97ce564659f07a4 build: number: 0 rpaths: @@ -18,9 +18,9 @@ build: - lib/ requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-brew - r-ggplot2 @@ -29,9 +29,9 @@ requirements: - r-testthat - r-xtable run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-biovizbase >=1.28.2,<1.30.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-brew - r-ggplot2 @@ -46,10 +46,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Quickly scans reads and gathers statistics on base and quality frequencies, read length, k-mers by position, and frequent sequences. Produces graphical output of statistics for use in quality control pipelines, and an optional HTML quality report. S4 SequenceSummary objects allow specific tests and functionality to be written around the data collected.' extra: identifiers: - biotools:qrqc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-qrqc + path: recipes/bioconductor-qrqc + version: 1.34.0 + diff --git a/recipes/bioconductor-qsea/build.sh b/recipes/bioconductor-qsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qsea/build.sh +++ b/recipes/bioconductor-qsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qsea/conda_build_config.yaml b/recipes/bioconductor-qsea/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-qsea/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-qsea/meta.yaml b/recipes/bioconductor-qsea/meta.yaml index 2da57e9688fea..9eaad569bac3f 100644 --- a/recipes/bioconductor-qsea/meta.yaml +++ b/recipes/bioconductor-qsea/meta.yaml @@ -1,49 +1,50 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "qsea" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8c06249fd05d91fd116e21f8261a83a2687d8895fa922c4c903477d42d0489df + md5: c2a094a5f1c9135228c41eef8ac4f639 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg19, MEDIPSData, testthat, BiocStyle, knitr, rmarkdown, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-hmmcopy >=1.22.0,<1.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hmmcopy >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-gtools - r-zoo run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-hmmcopy >=1.22.0,<1.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hmmcopy >=1.24.0,<1.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-gtools - r-zoo @@ -54,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'qsea (quantitative sequencing enrichment analysis) was developed as the successor of the MEDIPS package for analyzing data derived from methylated DNA immunoprecipitation (MeDIP) experiments followed by sequencing (MeDIP-seq). However, qsea provides several functionalities for the analysis of other kinds of quantitative sequencing data (e.g. ChIP-seq, MBD-seq, CMS-seq and others) including calculation of differential enrichment between groups of samples.' extra: identifiers: - biotools:qsea + parent_recipe: + name: bioconductor-qsea + path: recipes/bioconductor-qsea + version: 1.6.0 + diff --git a/recipes/bioconductor-qsutils/build.sh b/recipes/bioconductor-qsutils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qsutils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qsutils/meta.yaml b/recipes/bioconductor-qsutils/meta.yaml new file mode 100644 index 0000000000000..bf2bc397fe697 --- /dev/null +++ b/recipes/bioconductor-qsutils/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "QSutils" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1dcee86cb9a096cdc552fb279ce8f094 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, ggplot2 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-ape + - r-base + - r-psych + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-ape + - r-base + - r-psych +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Set of utility functions for viral quasispecies analysis with NGS data. Most functions are equally useful for metagenomic studies. There are three main types: (1) data manipulation and exploration—functions useful for converting reads to haplotypes and frequencies, repairing reads, intersecting strand haplotypes, and visualizing haplotype alignments. (2) diversity indices—functions to compute diversity and entropy, in which incidence, abundance, and functional indices are considered. (3) data simulation—functions useful for generating random viral quasispecies data.' + diff --git a/recipes/bioconductor-qualifier/build.sh b/recipes/bioconductor-qualifier/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qualifier/build.sh +++ b/recipes/bioconductor-qualifier/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qualifier/meta.yaml b/recipes/bioconductor-qualifier/meta.yaml index eebb168125928..3f3c36c7d2537 100644 --- a/recipes/bioconductor-qualifier/meta.yaml +++ b/recipes/bioconductor-qualifier/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.24.1" %} +{% set version = "1.26.0" %} {% set name = "QUALIFIER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: aa7e37c1e5749e42dbccf9b3cac7eb6a63c160ca4621a0870a847a031366e1eb + md5: 30ff0cb2ff2920f6141547a9546c5cf1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RSVGTipsDevice, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - r-base - r-data.table - r-hwriter @@ -32,11 +34,11 @@ requirements: - r-reshape - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-flowcore >=1.46.2,<1.48.0' - - 'bioconductor-flowviz >=1.44.0,<1.46.0' - - 'bioconductor-flowworkspace >=3.28.2,<3.30.0' - - 'bioconductor-ncdfflow >=2.26.0,<2.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - 'bioconductor-flowviz >=1.46.0,<1.47.0' + - 'bioconductor-flowworkspace >=3.30.0,<3.31.0' + - 'bioconductor-ncdfflow >=2.28.0,<2.29.0' - r-base - r-data.table - r-hwriter @@ -49,10 +51,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides quality control and quality assessment tools for gated flow cytometry data.' extra: identifiers: - biotools:qualifier - doi:10.1186/1471-2105-13-252 + parent_recipe: + name: bioconductor-qualifier + path: recipes/bioconductor-qualifier + version: 1.24.1 + diff --git a/recipes/bioconductor-quantro/build.sh b/recipes/bioconductor-quantro/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-quantro/build.sh +++ b/recipes/bioconductor-quantro/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quantro/meta.yaml b/recipes/bioconductor-quantro/meta.yaml index ffccab5112639..399df2ae3dfa3 100644 --- a/recipes/bioconductor-quantro/meta.yaml +++ b/recipes/bioconductor-quantro/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "quantro" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 27733c7023986edb3465639e1fa799bf20c29756d0229ec083deaac18e2e5255 + md5: f7d79a596f7a2e9c965a1e341aeca26c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - r-doparallel - r-foreach @@ -27,8 +29,8 @@ requirements: - r-iterators - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - r-doparallel - r-foreach @@ -39,9 +41,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'A data-driven test for the assumptions of quantile normalization using raw data such as objects that inherit eSets (e.g. ExpressionSet, MethylSet). Group level information about each sample (such as Tumor / Normal status) must also be provided because the test assesses if there are global differences in the distributions between the user-defined groups.' extra: identifiers: - biotools:quantro + parent_recipe: + name: bioconductor-quantro + path: recipes/bioconductor-quantro + version: 1.14.0 + diff --git a/recipes/bioconductor-quantsmooth/build.sh b/recipes/bioconductor-quantsmooth/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-quantsmooth/build.sh +++ b/recipes/bioconductor-quantsmooth/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quantsmooth/meta.yaml b/recipes/bioconductor-quantsmooth/meta.yaml index bfb6143e85e21..c09b5df117174 100644 --- a/recipes/bioconductor-quantsmooth/meta.yaml +++ b/recipes/bioconductor-quantsmooth/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "quantsmooth" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d9375e834dcfec05b0e139382c44326b3e2b7917ba22785f45af15d0e6b98d2b + md5: 6617f7e9ad5b4d7f66a5eb214d6b7cee build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Implements quantile smoothing as introduced in: Quantile smoothing of array CGH data; Eilers PH, de Menezes RX; Bioinformatics. 2005 Apr 1;21(7):1146-53.' extra: identifiers: - biotools:quantsmooth - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-quantsmooth + path: recipes/bioconductor-quantsmooth + version: 1.46.0 + diff --git a/recipes/bioconductor-quartpac/build.sh b/recipes/bioconductor-quartpac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-quartpac/build.sh +++ b/recipes/bioconductor-quartpac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quartpac/meta.yaml b/recipes/bioconductor-quartpac/meta.yaml index 2a08a3cd37d26..ce935fe15b18a 100644 --- a/recipes/bioconductor-quartpac/meta.yaml +++ b/recipes/bioconductor-quartpac/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "QuartPAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b8b85da86c4c8778060744baf5dd7e342e85a62376d5ef8f7b7bda81881c210 + md5: f423fa2cb29443befb977c06700a8dcf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-graphpac >=1.22.1,<1.24.0' - - 'bioconductor-ipac >=1.24.2,<1.26.0' - - 'bioconductor-spacepac >=1.18.3,<1.20.0' + - 'bioconductor-graphpac >=1.24.0,<1.25.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-spacepac >=1.20.0,<1.21.0' - r-base - r-data.table run: - - 'bioconductor-graphpac >=1.22.1,<1.24.0' - - 'bioconductor-ipac >=1.24.2,<1.26.0' - - 'bioconductor-spacepac >=1.18.3,<1.20.0' + - 'bioconductor-graphpac >=1.24.0,<1.25.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' + - 'bioconductor-spacepac >=1.20.0,<1.21.0' - r-base - r-data.table test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies clustering of somatic mutations in proteins over the entire quaternary structure.' extra: identifiers: - biotools:quartpac - doi:10.1186/s12859-016-0963-3 + parent_recipe: + name: bioconductor-quartpac + path: recipes/bioconductor-quartpac + version: 1.12.1 + diff --git a/recipes/bioconductor-quasr/build.sh b/recipes/bioconductor-quasr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-quasr/build.sh +++ b/recipes/bioconductor-quasr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quasr/conda_build_config.yaml b/recipes/bioconductor-quasr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-quasr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-quasr/meta.yaml b/recipes/bioconductor-quasr/meta.yaml index 8dd862752ddbd..01d83a41d6f73 100644 --- a/recipes/bioconductor-quasr/meta.yaml +++ b/recipes/bioconductor-quasr/meta.yaml @@ -1,62 +1,63 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "QuasR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 837ba80f1ca3408aa6511e2c7bf0d24683f2ae5cc854b2ab66f318a55369969e + md5: 4add73c5e114233621711ace6c8d1e35 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Gviz, RUnit, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbowtie >=1.20.0,<1.22.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbowtie >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-biocmanager run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicfiles >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbowtie >=1.20.0,<1.22.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbowtie >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-biocmanager build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -65,9 +66,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a framework for the quantification and analysis of Short Reads. It covers a complete workflow starting from raw sequence reads, over creation of alignments and quality control plots, to the quantification of genomic regions of interest.' extra: identifiers: - biotools:quasr + parent_recipe: + name: bioconductor-quasr + path: recipes/bioconductor-quasr + version: 1.20.0 + diff --git a/recipes/bioconductor-quaternaryprod/build.sh b/recipes/bioconductor-quaternaryprod/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-quaternaryprod/build.sh +++ b/recipes/bioconductor-quaternaryprod/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-quaternaryprod/meta.yaml b/recipes/bioconductor-quaternaryprod/meta.yaml index cb81ab31166a4..8c5b82ddbc372 100644 --- a/recipes/bioconductor-quaternaryprod/meta.yaml +++ b/recipes/bioconductor-quaternaryprod/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "QuaternaryProd" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 80062acdc4ac821389fe86388bb7d3a3ee5ec2f6154dd261a9cf43154a56598f + md5: 47be657148eb3d8caa9db8d007f65c25 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr requirements: host: - r-base @@ -35,9 +36,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'QuaternaryProd is an R package that performs causal reasoning on biological networks, including publicly available networks such as STRINGdb. QuaternaryProd is an open-source alternative to commercial products such as Inginuity Pathway Analysis. For a given a set of differentially expressed genes, QuaternaryProd computes the significance of upstream regulators in the network by performing causal reasoning using the Quaternary Dot Product Scoring Statistic (Quaternary Statistic), Ternary Dot product Scoring Statistic (Ternary Statistic) and Fisher''s exact test (Enrichment test). The Quaternary Statistic handles signed, unsigned and ambiguous edges in the network. Ambiguity arises when the direction of causality is unknown, or when the source node (e.g., a protein) has edges with conflicting signs for the same target gene. On the other hand, the Ternary Statistic provides causal reasoning using the signed and unambiguous edges only. The Vignette provides more details on the Quaternary Statistic and illustrates an example of how to perform causal reasoning using STRINGdb.' extra: identifiers: - biotools:quaternaryprod + parent_recipe: + name: bioconductor-quaternaryprod + path: recipes/bioconductor-quaternaryprod + version: 1.14.0 + diff --git a/recipes/bioconductor-qubic/build.sh b/recipes/bioconductor-qubic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-qubic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qubic/meta.yaml b/recipes/bioconductor-qubic/meta.yaml new file mode 100644 index 0000000000000..dbe0a6f4ab588 --- /dev/null +++ b/recipes/bioconductor-qubic/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.10.0" %} +{% set name = "QUBIC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ab39857fee893ea726e3d3d1392ee190 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: QUBICdata, qgraph, fields, knitr, rmarkdown +# SystemRequirements: C++11, Rtools (>= 3.1) +requirements: + host: + - r-base + - r-biclust + - r-matrix + - 'r-rcpp >=0.11.0' + - r-rcpparmadillo + run: + - r-base + - r-biclust + - r-matrix + - 'r-rcpp >=0.11.0' + - r-rcpparmadillo + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'CC BY-NC-ND 4.0 + file LICENSE' + summary: 'The core function of this R package is to provide the implementation of the well-cited and well-reviewed QUBIC algorithm, aiming to deliver an effective and efficient biclustering capability. This package also includes the following related functions: (i) a qualitative representation of the input gene expression data, through a well-designed discretization way considering the underlying data property, which can be directly used in other biclustering programs; (ii) visualization of identified biclusters using heatmap in support of overall expression pattern analysis; (iii) bicluster-based co-expression network elucidation and visualization, where different correlation coefficient scores between a pair of genes are provided; and (iv) a generalize output format of biclusters and corresponding network can be freely downloaded so that a user can easily do following comprehensive functional enrichment analysis (e.g. DAVID) and advanced network visualization (e.g. Cytoscape).' + diff --git a/recipes/bioconductor-qubicdata/meta.yaml b/recipes/bioconductor-qubicdata/meta.yaml new file mode 100644 index 0000000000000..8dac9db9e950d --- /dev/null +++ b/recipes/bioconductor-qubicdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "QUBICdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 66ed9092477ac1c0ddf2b367d55682e1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'Unlimited | file LICENSE' + summary: 'The data employed in the vignette of the QUBIC package. These data belong to Many Microbe Microarrays Database and STRING v10.' + diff --git a/recipes/bioconductor-qubicdata/post-link.sh b/recipes/bioconductor-qubicdata/post-link.sh new file mode 100644 index 0000000000000..6802402680e15 --- /dev/null +++ b/recipes/bioconductor-qubicdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="QUBICdata_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/QUBICdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/QUBICdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-qubicdata/bioconductor-qubicdata_1.10.0_src_all.tar.gz" +) +MD5="66ed9092477ac1c0ddf2b367d55682e1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-qubicdata/pre-unlink.sh b/recipes/bioconductor-qubicdata/pre-unlink.sh new file mode 100644 index 0000000000000..2e38f0aa77ede --- /dev/null +++ b/recipes/bioconductor-qubicdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ QUBICdata diff --git a/recipes/bioconductor-qusage/build.sh b/recipes/bioconductor-qusage/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qusage/build.sh +++ b/recipes/bioconductor-qusage/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qusage/meta.yaml b/recipes/bioconductor-qusage/meta.yaml index 68330e57b18f0..825a5238c8396 100644 --- a/recipes/bioconductor-qusage/meta.yaml +++ b/recipes/bioconductor-qusage/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "qusage" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 649cbeefa4e3b56d6a9728035007febfc36c5b361312cfb920e19a6fc6204500 + md5: c5cf3b109d420f357734c27ee166124b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-lsmeans - r-nlme run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-lsmeans - r-nlme @@ -33,9 +34,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package is an implementation the Quantitative Set Analysis for Gene Expression (QuSAGE) method described in (Yaari G. et al, Nucl Acids Res, 2013). This is a novel Gene Set Enrichment-type test, which is designed to provide a faster, more accurate, and easier to understand test for gene expression studies. qusage accounts for inter-gene correlations using the Variance Inflation Factor technique proposed by Wu et al. (Nucleic Acids Res, 2012). In addition, rather than simply evaluating the deviation from a null hypothesis with a single number (a P value), qusage quantifies gene set activity with a complete probability density function (PDF). From this PDF, P values and confidence intervals can be easily extracted. Preserving the PDF also allows for post-hoc analysis (e.g., pair-wise comparisons of gene set activity) while maintaining statistical traceability. Finally, while qusage is compatible with individual gene statistics from existing methods (e.g., LIMMA), a Welch-based method is implemented that is shown to improve specificity. For questions, contact Chris Bolen (cbolen1@gmail.com) or Steven Kleinstein (steven.kleinstein@yale.edu)' extra: identifiers: - biotools:qusage + parent_recipe: + name: bioconductor-qusage + path: recipes/bioconductor-qusage + version: 2.14.0 + diff --git a/recipes/bioconductor-qvalue/build.sh b/recipes/bioconductor-qvalue/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-qvalue/build.sh +++ b/recipes/bioconductor-qvalue/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-qvalue/meta.yaml b/recipes/bioconductor-qvalue/meta.yaml index ddd4746a076c1..1b776d413f88c 100644 --- a/recipes/bioconductor-qvalue/meta.yaml +++ b/recipes/bioconductor-qvalue/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.12.0" %} +{% set version = "2.14.0" %} {% set name = "qvalue" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 485bf1c3086e4f1ee46dab4f24d9aaae1e8dfb7460074c3da7641f08819cbcd9 + md5: 7cae0cf8fe37a8d025f9f93150fa464a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -29,8 +31,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package takes a list of p-values resulting from the simultaneous testing of many hypotheses and estimates their q-values and local FDR values. The q-value of a test measures the proportion of false positives incurred (called the false discovery rate) when that particular test is called significant. The local FDR measures the posterior probability the null hypothesis is true given the test''s p-value. Various plots are automatically generated, allowing one to make sensible significance cut-offs. Several mathematical results have recently been shown on the conservative accuracy of the estimated q-values from this software. The software can be applied to problems in genomics, brain imaging, astrophysics, and data mining.' - +extra: + parent_recipe: + name: bioconductor-qvalue + path: recipes/bioconductor-qvalue + version: 2.12.0 diff --git a/recipes/bioconductor-r10kcod.db/meta.yaml b/recipes/bioconductor-r10kcod.db/meta.yaml new file mode 100644 index 0000000000000..b4561e63b7fd8 --- /dev/null +++ b/recipes/bioconductor-r10kcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "r10kcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4a7a25fee64294cfb5adccaa6cf28772 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink UniSet Rat I Bioarray (~10 000 rat gene targets) annotation data (chip r10kcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-r10kcod.db/post-link.sh b/recipes/bioconductor-r10kcod.db/post-link.sh new file mode 100644 index 0000000000000..986774e50c771 --- /dev/null +++ b/recipes/bioconductor-r10kcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="r10kcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/r10kcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/r10kcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-r10kcod.db/bioconductor-r10kcod.db_3.4.0_src_all.tar.gz" +) +MD5="4a7a25fee64294cfb5adccaa6cf28772" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-r10kcod.db/pre-unlink.sh b/recipes/bioconductor-r10kcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..1b92254df186e --- /dev/null +++ b/recipes/bioconductor-r10kcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ r10kcod.db diff --git a/recipes/bioconductor-r3cpet/build.sh b/recipes/bioconductor-r3cpet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-r3cpet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-r3cpet/meta.yaml b/recipes/bioconductor-r3cpet/meta.yaml new file mode 100644 index 0000000000000..7d7109198bcc5 --- /dev/null +++ b/recipes/bioconductor-r3cpet/meta.yaml @@ -0,0 +1,68 @@ +{% set version = "1.14.0" %} +{% set name = "R3CPET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de75b6f33919464203ed7042c9fc5f6e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, biovizBase, biomaRt, AnnotationDbi, org.Hs.eg.db, shiny, ChIPpeakAnno +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-clues + - r-clvalid + - r-data.table + - r-ggplot2 + - r-hmisc + - r-igraph + - r-pheatmap + - 'r-rcpp >=0.10.4' + - r-rcurl + - r-reshape2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-clues + - r-clvalid + - r-data.table + - r-ggplot2 + - r-hmisc + - r-igraph + - r-pheatmap + - 'r-rcpp >=0.10.4' + - r-rcurl + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'The package provides a method to infer the set of proteins that are more probably to work together to maintain chormatin interaction given a ChIA-PET experiment results.' + diff --git a/recipes/bioconductor-r3cseq/build.sh b/recipes/bioconductor-r3cseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-r3cseq/build.sh +++ b/recipes/bioconductor-r3cseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-r3cseq/meta.yaml b/recipes/bioconductor-r3cseq/meta.yaml index 728785e88eee4..70ebd66a1ecd6 100644 --- a/recipes/bioconductor-r3cseq/meta.yaml +++ b/recipes/bioconductor-r3cseq/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "r3Cseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4f098382523baaec799ca476a4a4b9b37d074e2287d54bddd8698cb722344b0b + md5: e900fcaf098fd698650694cf4f2b3dad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Mmusculus.UCSC.mm9.masked, BSgenome.Mmusculus.UCSC.mm10.masked, BSgenome.Hsapiens.UCSC.hg18.masked, BSgenome.Hsapiens.UCSC.hg19.masked, BSgenome.Rnorvegicus.UCSC.rn5.masked requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-data.table - r-rcolorbrewer - r-sqldf - r-vgam run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-data.table - r-rcolorbrewer @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is an implementation of data analysis for the long-range interactions from 3C-seq assay.' extra: identifiers: - biotools:r3cseq - doi:10.1093/nar/gkt373 + parent_recipe: + name: bioconductor-r3cseq + path: recipes/bioconductor-r3cseq + version: 1.26.0 + diff --git a/recipes/bioconductor-r453plus1toolbox/build.sh b/recipes/bioconductor-r453plus1toolbox/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-r453plus1toolbox/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-r453plus1toolbox/meta.yaml b/recipes/bioconductor-r453plus1toolbox/meta.yaml new file mode 100644 index 0000000000000..39c2da66fa4d3 --- /dev/null +++ b/recipes/bioconductor-r453plus1toolbox/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.32.0" %} +{% set name = "R453Plus1Toolbox" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4a5bb4fe4d331ca8c30ca120a0d8ea17 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: rtracklayer, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Scerevisiae.UCSC.sacCer2 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + - r-r2html + - r-teachingdemos + - r-xtable + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + - r-r2html + - r-teachingdemos + - r-xtable + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'The R453Plus1 Toolbox comprises useful functions for the analysis of data generated by Roche''s 454 sequencing platform. It adds functions for quality assurance as well as for annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. Further, a pipeline for the detection of structural variants is provided.' + diff --git a/recipes/bioconductor-r4rna/build.sh b/recipes/bioconductor-r4rna/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-r4rna/build.sh +++ b/recipes/bioconductor-r4rna/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-r4rna/meta.yaml b/recipes/bioconductor-r4rna/meta.yaml index eab2552fe3740..b8a5ee2deb5a4 100644 --- a/recipes/bioconductor-r4rna/meta.yaml +++ b/recipes/bioconductor-r4rna/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "R4RNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f142ff234c09f125799cb71ccd50cf7db6ac4a32856069b1015b07caa9ef02b8 + md5: e6c4cca4a785471fb80fbf9f3d66358e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A package for RNA basepair analysis, including the visualization of basepairs as arc diagrams for easy comparison and annotation of sequence and structure. Arc diagrams can additionally be projected onto multiple sequence alignments to assess basepair conservation and covariation, with numerical methods for computing statistics for each.' extra: identifiers: - biotools:r4rna + parent_recipe: + name: bioconductor-r4rna + path: recipes/bioconductor-r4rna + version: 1.8.0 + diff --git a/recipes/bioconductor-rae230a.db/meta.yaml b/recipes/bioconductor-rae230a.db/meta.yaml new file mode 100644 index 0000000000000..1d989be598dd4 --- /dev/null +++ b/recipes/bioconductor-rae230a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rae230a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fb9d6a02ce85cc521c0477a1a6f861f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Expression Set 230 annotation data (chip rae230a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rae230a.db/post-link.sh b/recipes/bioconductor-rae230a.db/post-link.sh new file mode 100644 index 0000000000000..35a1153957d93 --- /dev/null +++ b/recipes/bioconductor-rae230a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rae230a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230a.db/bioconductor-rae230a.db_3.2.3_src_all.tar.gz" +) +MD5="fb9d6a02ce85cc521c0477a1a6f861f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230a.db/pre-unlink.sh b/recipes/bioconductor-rae230a.db/pre-unlink.sh new file mode 100644 index 0000000000000..808f790f5e768 --- /dev/null +++ b/recipes/bioconductor-rae230a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230a.db diff --git a/recipes/bioconductor-rae230acdf/meta.yaml b/recipes/bioconductor-rae230acdf/meta.yaml new file mode 100644 index 0000000000000..dfe646d312dd5 --- /dev/null +++ b/recipes/bioconductor-rae230acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rae230acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f2281124e1be164d5fd599e84f6adbc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RAE230A.CDF file.' + diff --git a/recipes/bioconductor-rae230acdf/post-link.sh b/recipes/bioconductor-rae230acdf/post-link.sh new file mode 100644 index 0000000000000..f23870faecc85 --- /dev/null +++ b/recipes/bioconductor-rae230acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rae230acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230acdf/bioconductor-rae230acdf_2.18.0_src_all.tar.gz" +) +MD5="6f2281124e1be164d5fd599e84f6adbc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230acdf/pre-unlink.sh b/recipes/bioconductor-rae230acdf/pre-unlink.sh new file mode 100644 index 0000000000000..e0cfe25e5fbf1 --- /dev/null +++ b/recipes/bioconductor-rae230acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230acdf diff --git a/recipes/bioconductor-rae230aprobe/meta.yaml b/recipes/bioconductor-rae230aprobe/meta.yaml new file mode 100644 index 0000000000000..1a846af66b330 --- /dev/null +++ b/recipes/bioconductor-rae230aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rae230aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f2d77e1d9c1e3afb96ef78b3202bb0b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230A\_probe\_tab.' + diff --git a/recipes/bioconductor-rae230aprobe/post-link.sh b/recipes/bioconductor-rae230aprobe/post-link.sh new file mode 100644 index 0000000000000..d826c1810d3d2 --- /dev/null +++ b/recipes/bioconductor-rae230aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rae230aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230aprobe/bioconductor-rae230aprobe_2.18.0_src_all.tar.gz" +) +MD5="6f2d77e1d9c1e3afb96ef78b3202bb0b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230aprobe/pre-unlink.sh b/recipes/bioconductor-rae230aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..03b92e9a8b2e7 --- /dev/null +++ b/recipes/bioconductor-rae230aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230aprobe diff --git a/recipes/bioconductor-rae230b.db/meta.yaml b/recipes/bioconductor-rae230b.db/meta.yaml new file mode 100644 index 0000000000000..e4f4984c0ca55 --- /dev/null +++ b/recipes/bioconductor-rae230b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rae230b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 23fb8fd2cf3f178020db9b7f5692a28d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Expression Set 230 annotation data (chip rae230b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rae230b.db/post-link.sh b/recipes/bioconductor-rae230b.db/post-link.sh new file mode 100644 index 0000000000000..a6ad41c26083d --- /dev/null +++ b/recipes/bioconductor-rae230b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rae230b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230b.db/bioconductor-rae230b.db_3.2.3_src_all.tar.gz" +) +MD5="23fb8fd2cf3f178020db9b7f5692a28d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230b.db/pre-unlink.sh b/recipes/bioconductor-rae230b.db/pre-unlink.sh new file mode 100644 index 0000000000000..79393070dfb0d --- /dev/null +++ b/recipes/bioconductor-rae230b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230b.db diff --git a/recipes/bioconductor-rae230bcdf/meta.yaml b/recipes/bioconductor-rae230bcdf/meta.yaml new file mode 100644 index 0000000000000..2014fe4270303 --- /dev/null +++ b/recipes/bioconductor-rae230bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rae230bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bd61c17402e9c04be1000c16e0356618 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RAE230B.CDF file.' + diff --git a/recipes/bioconductor-rae230bcdf/post-link.sh b/recipes/bioconductor-rae230bcdf/post-link.sh new file mode 100644 index 0000000000000..5bb434c6827ad --- /dev/null +++ b/recipes/bioconductor-rae230bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rae230bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230bcdf/bioconductor-rae230bcdf_2.18.0_src_all.tar.gz" +) +MD5="bd61c17402e9c04be1000c16e0356618" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230bcdf/pre-unlink.sh b/recipes/bioconductor-rae230bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..fa0691c0815c3 --- /dev/null +++ b/recipes/bioconductor-rae230bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230bcdf diff --git a/recipes/bioconductor-rae230bprobe/meta.yaml b/recipes/bioconductor-rae230bprobe/meta.yaml new file mode 100644 index 0000000000000..0ad9b2e9fc2c6 --- /dev/null +++ b/recipes/bioconductor-rae230bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rae230bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7bdb3a07e1f00de8ff510a69bdac4c53 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RAE230B\_probe\_tab.' + diff --git a/recipes/bioconductor-rae230bprobe/post-link.sh b/recipes/bioconductor-rae230bprobe/post-link.sh new file mode 100644 index 0000000000000..e280c29f60741 --- /dev/null +++ b/recipes/bioconductor-rae230bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rae230bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rae230bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rae230bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rae230bprobe/bioconductor-rae230bprobe_2.18.0_src_all.tar.gz" +) +MD5="7bdb3a07e1f00de8ff510a69bdac4c53" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rae230bprobe/pre-unlink.sh b/recipes/bioconductor-rae230bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..6045510a7fce3 --- /dev/null +++ b/recipes/bioconductor-rae230bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rae230bprobe diff --git a/recipes/bioconductor-raex10stprobeset.db/meta.yaml b/recipes/bioconductor-raex10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..83854f12a3323 --- /dev/null +++ b/recipes/bioconductor-raex10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "raex10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9cdc6abb3cf39eb7363fe74a0963c5b7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix raex10 annotation data (chip raex10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-raex10stprobeset.db/post-link.sh b/recipes/bioconductor-raex10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..a1b0e1a717bec --- /dev/null +++ b/recipes/bioconductor-raex10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="raex10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/raex10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/raex10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raex10stprobeset.db/bioconductor-raex10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="9cdc6abb3cf39eb7363fe74a0963c5b7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-raex10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-raex10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..bba24408b3466 --- /dev/null +++ b/recipes/bioconductor-raex10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ raex10stprobeset.db diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..b3972b4473d94 --- /dev/null +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "raex10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3eb2d97bfffb595e6b23550f4a27a8c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix raex10 annotation data (chip raex10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..c69196a44ab5e --- /dev/null +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="raex10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/raex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/raex10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raex10sttranscriptcluster.db/bioconductor-raex10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="3eb2d97bfffb595e6b23550f4a27a8c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-raex10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-raex10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..c60e677d956ba --- /dev/null +++ b/recipes/bioconductor-raex10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ raex10sttranscriptcluster.db diff --git a/recipes/bioconductor-raexexonprobesetlocation/meta.yaml b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml new file mode 100644 index 0000000000000..8e55e2f5145d5 --- /dev/null +++ b/recipes/bioconductor-raexexonprobesetlocation/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.15.0" %} +{% set name = "RaExExonProbesetLocation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d547bcd30685495283b32f0f86ecc79b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.7.17. The exon-level probeset genome location was retrieved from Netaffx using AffyCompatible.' + diff --git a/recipes/bioconductor-raexexonprobesetlocation/post-link.sh b/recipes/bioconductor-raexexonprobesetlocation/post-link.sh new file mode 100644 index 0000000000000..e42205b196dde --- /dev/null +++ b/recipes/bioconductor-raexexonprobesetlocation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RaExExonProbesetLocation_1.15.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RaExExonProbesetLocation_1.15.0.tar.gz" + "https://bioarchive.galaxyproject.org/RaExExonProbesetLocation_1.15.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-raexexonprobesetlocation/bioconductor-raexexonprobesetlocation_1.15.0_src_all.tar.gz" +) +MD5="d547bcd30685495283b32f0f86ecc79b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-raexexonprobesetlocation/pre-unlink.sh b/recipes/bioconductor-raexexonprobesetlocation/pre-unlink.sh new file mode 100644 index 0000000000000..5f93f7fefdc3b --- /dev/null +++ b/recipes/bioconductor-raexexonprobesetlocation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RaExExonProbesetLocation diff --git a/recipes/bioconductor-ragene10stprobeset.db/meta.yaml b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..36986607d49b1 --- /dev/null +++ b/recipes/bioconductor-ragene10stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene10stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7338948d43b2200ca255aeb87cf99f3e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene10 annotation data (chip ragene10stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene10stprobeset.db/post-link.sh b/recipes/bioconductor-ragene10stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..7db691a1a7092 --- /dev/null +++ b/recipes/bioconductor-ragene10stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene10stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene10stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stprobeset.db/bioconductor-ragene10stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="7338948d43b2200ca255aeb87cf99f3e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene10stprobeset.db/pre-unlink.sh b/recipes/bioconductor-ragene10stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..9b4aebbf07722 --- /dev/null +++ b/recipes/bioconductor-ragene10stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene10stprobeset.db diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..5c26abfef3dac --- /dev/null +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene10sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2523540bab5f12e6e5c1e140c1663832 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene10 annotation data (chip ragene10sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..1f4d5e95e09c2 --- /dev/null +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene10sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene10sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10sttranscriptcluster.db/bioconductor-ragene10sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="2523540bab5f12e6e5c1e140c1663832" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene10sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-ragene10sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..94c0ed34d14f8 --- /dev/null +++ b/recipes/bioconductor-ragene10sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene10sttranscriptcluster.db diff --git a/recipes/bioconductor-ragene10stv1cdf/meta.yaml b/recipes/bioconductor-ragene10stv1cdf/meta.yaml new file mode 100644 index 0000000000000..532fc2b40020a --- /dev/null +++ b/recipes/bioconductor-ragene10stv1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ragene10stv1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: df696e9dbf5b3f2761b6a0a5914be058 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RaGene-1_0-st-v1.cdf file.' + diff --git a/recipes/bioconductor-ragene10stv1cdf/post-link.sh b/recipes/bioconductor-ragene10stv1cdf/post-link.sh new file mode 100644 index 0000000000000..6c394ecfd9d4e --- /dev/null +++ b/recipes/bioconductor-ragene10stv1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene10stv1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stv1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene10stv1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1cdf/bioconductor-ragene10stv1cdf_2.18.0_src_all.tar.gz" +) +MD5="df696e9dbf5b3f2761b6a0a5914be058" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene10stv1cdf/pre-unlink.sh b/recipes/bioconductor-ragene10stv1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..bab75815f4cf7 --- /dev/null +++ b/recipes/bioconductor-ragene10stv1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene10stv1cdf diff --git a/recipes/bioconductor-ragene10stv1probe/meta.yaml b/recipes/bioconductor-ragene10stv1probe/meta.yaml new file mode 100644 index 0000000000000..1c86c67966c58 --- /dev/null +++ b/recipes/bioconductor-ragene10stv1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ragene10stv1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 94978b6efb075aacf31ccdc8000e40fa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RaGene-1\_0-st-v1\_probe\_tab.' + diff --git a/recipes/bioconductor-ragene10stv1probe/post-link.sh b/recipes/bioconductor-ragene10stv1probe/post-link.sh new file mode 100644 index 0000000000000..959d40221fcdc --- /dev/null +++ b/recipes/bioconductor-ragene10stv1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene10stv1probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene10stv1probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene10stv1probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene10stv1probe/bioconductor-ragene10stv1probe_2.18.0_src_all.tar.gz" +) +MD5="94978b6efb075aacf31ccdc8000e40fa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene10stv1probe/pre-unlink.sh b/recipes/bioconductor-ragene10stv1probe/pre-unlink.sh new file mode 100644 index 0000000000000..994c458d1cce7 --- /dev/null +++ b/recipes/bioconductor-ragene10stv1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene10stv1probe diff --git a/recipes/bioconductor-ragene11stprobeset.db/meta.yaml b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..2efc31a7a2fc2 --- /dev/null +++ b/recipes/bioconductor-ragene11stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene11stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5ce8dfb793afc7307106f3d4872dfeb1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene11 annotation data (chip ragene11stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene11stprobeset.db/post-link.sh b/recipes/bioconductor-ragene11stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..ad9d2e606e770 --- /dev/null +++ b/recipes/bioconductor-ragene11stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene11stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene11stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene11stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene11stprobeset.db/bioconductor-ragene11stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="5ce8dfb793afc7307106f3d4872dfeb1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene11stprobeset.db/pre-unlink.sh b/recipes/bioconductor-ragene11stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..99436e57649f1 --- /dev/null +++ b/recipes/bioconductor-ragene11stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene11stprobeset.db diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..9a81c54faeb70 --- /dev/null +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene11sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 81a645c32105ffb4bfb45eb8bcf13855 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene11 annotation data (chip ragene11sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..afcd3d90b18f2 --- /dev/null +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene11sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene11sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene11sttranscriptcluster.db/bioconductor-ragene11sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="81a645c32105ffb4bfb45eb8bcf13855" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene11sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-ragene11sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..4e9242748a21f --- /dev/null +++ b/recipes/bioconductor-ragene11sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene11sttranscriptcluster.db diff --git a/recipes/bioconductor-ragene20stprobeset.db/meta.yaml b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..163aeb1174cdd --- /dev/null +++ b/recipes/bioconductor-ragene20stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene20stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dd4e8701fd716e8564da2581d52ce1db +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene20 annotation data (chip ragene20stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene20stprobeset.db/post-link.sh b/recipes/bioconductor-ragene20stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..dd8a7cd3e42da --- /dev/null +++ b/recipes/bioconductor-ragene20stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene20stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene20stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene20stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene20stprobeset.db/bioconductor-ragene20stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="dd4e8701fd716e8564da2581d52ce1db" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene20stprobeset.db/pre-unlink.sh b/recipes/bioconductor-ragene20stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..bf2c4b48675f2 --- /dev/null +++ b/recipes/bioconductor-ragene20stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene20stprobeset.db diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..c748c9b50d549 --- /dev/null +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene20sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 79693b35c3837f9e5fe7337ac3e86e1f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene20 annotation data (chip ragene20sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..221463d0b2328 --- /dev/null +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene20sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene20sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene20sttranscriptcluster.db/bioconductor-ragene20sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="79693b35c3837f9e5fe7337ac3e86e1f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene20sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-ragene20sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..8662bf1d57bb8 --- /dev/null +++ b/recipes/bioconductor-ragene20sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene20sttranscriptcluster.db diff --git a/recipes/bioconductor-ragene21stprobeset.db/meta.yaml b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml new file mode 100644 index 0000000000000..55679f655ce19 --- /dev/null +++ b/recipes/bioconductor-ragene21stprobeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene21stprobeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9a2e1eb46277622a673eb3e11ca14aee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene21 annotation data (chip ragene21stprobeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene21stprobeset.db/post-link.sh b/recipes/bioconductor-ragene21stprobeset.db/post-link.sh new file mode 100644 index 0000000000000..4c592d8b1e55c --- /dev/null +++ b/recipes/bioconductor-ragene21stprobeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene21stprobeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene21stprobeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene21stprobeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene21stprobeset.db/bioconductor-ragene21stprobeset.db_8.7.0_src_all.tar.gz" +) +MD5="9a2e1eb46277622a673eb3e11ca14aee" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene21stprobeset.db/pre-unlink.sh b/recipes/bioconductor-ragene21stprobeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..ac30e9600d8da --- /dev/null +++ b/recipes/bioconductor-ragene21stprobeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene21stprobeset.db diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..5f575d48bf059 --- /dev/null +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "ragene21sttranscriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 45a0cfb35fc78ec28705024a8d091163 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix ragene21 annotation data (chip ragene21sttranscriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh b/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..c0aeade5e8a98 --- /dev/null +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ragene21sttranscriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ragene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/ragene21sttranscriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ragene21sttranscriptcluster.db/bioconductor-ragene21sttranscriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="45a0cfb35fc78ec28705024a8d091163" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ragene21sttranscriptcluster.db/pre-unlink.sh b/recipes/bioconductor-ragene21sttranscriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..10d5cd20eaaee --- /dev/null +++ b/recipes/bioconductor-ragene21sttranscriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ragene21sttranscriptcluster.db diff --git a/recipes/bioconductor-raggedexperiment/build.sh b/recipes/bioconductor-raggedexperiment/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-raggedexperiment/build.sh +++ b/recipes/bioconductor-raggedexperiment/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-raggedexperiment/meta.yaml b/recipes/bioconductor-raggedexperiment/meta.yaml index b9e781c65eeb7..2a62441ece65f 100644 --- a/recipes/bioconductor-raggedexperiment/meta.yaml +++ b/recipes/bioconductor-raggedexperiment/meta.yaml @@ -1,42 +1,50 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "RaggedExperiment" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 98d8ac3444bf3a507e751a7d6c43d649cc490281f4a6a7e6d8e7f56e5f4379dc + md5: a07596ff746251104b6c1ce3ddd933e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat, MultiAssayExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides a flexible representation of copy number, mutation, and other data that fit into the ragged array schema for genomic location data. The basic representation of such data provides a rectangular flat table interface to the user with range information in the rows and samples/specimen in the columns.' - +extra: + parent_recipe: + name: bioconductor-raggedexperiment + path: recipes/bioconductor-raggedexperiment + version: 1.4.0 diff --git a/recipes/bioconductor-rain/build.sh b/recipes/bioconductor-rain/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rain/build.sh +++ b/recipes/bioconductor-rain/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rain/meta.yaml b/recipes/bioconductor-rain/meta.yaml index 60d09328fec25..9c4a482051eb8 100644 --- a/recipes/bioconductor-rain/meta.yaml +++ b/recipes/bioconductor-rain/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "rain" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d379e73af167fb35d1046e9a0c0af8248de837ed62105bdd6e463a11e584fa05 + md5: f2ec7a42028c930beb3857c0e1292817 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: lattice, BiocStyle requirements: host: - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-gmp run: - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base - r-gmp test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package uses non-parametric methods to detect rhythms in time series. It deals with outliers, missing values and is optimized for time series comprising 10-100 measurements. As it does not assume expect any distinct waveform it is optimal or detecting oscillating behavior (e.g. circadian or cell cycle) in e.g. genome- or proteome-wide biological measurements such as: micro arrays, proteome mass spectrometry, or metabolome measurements.' extra: identifiers: - biotools:rain + parent_recipe: + name: bioconductor-rain + path: recipes/bioconductor-rain + version: 1.14.0 + diff --git a/recipes/bioconductor-rama/build.sh b/recipes/bioconductor-rama/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rama/build.sh +++ b/recipes/bioconductor-rama/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rama/meta.yaml b/recipes/bioconductor-rama/meta.yaml index 36a51e769f1c9..22b4a2ef014e9 100644 --- a/recipes/bioconductor-rama/meta.yaml +++ b/recipes/bioconductor-rama/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "rama" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e76746a1a360ab02ce12bd63fde642e294f75982ce8940621b8a9f0e9dd5d7c8 + md5: 698c5d694e8e08c717ab7e0f7a6495d9 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Robust estimation of cDNA microarray intensities with replicates. The package uses a Bayesian hierarchical model for the robust estimation. Outliers are modeled explicitly using a t-distribution, and the model also addresses classical issues such as design effects, normalization, transformation, and nonconstant variance.' extra: identifiers: - biotools:rama - doi:10.1198/016214505000001096 + parent_recipe: + name: bioconductor-rama + path: recipes/bioconductor-rama + version: 1.54.0 + diff --git a/recipes/bioconductor-ramwas/build.sh b/recipes/bioconductor-ramwas/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ramwas/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ramwas/meta.yaml b/recipes/bioconductor-ramwas/meta.yaml new file mode 100644 index 0000000000000..9839b469e11b8 --- /dev/null +++ b/recipes/bioconductor-ramwas/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "ramwas" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 63327d48803487a400eea7b0dcb09611 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, pander, BiocStyle, BSgenome.Ecoli.NCBI.20080805 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-digest + - r-filematrix + - r-glmnet + - r-kernsmooth + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-digest + - r-filematrix + - r-glmnet + - r-kernsmooth + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'A complete toolset for methylome-wide association studies (MWAS). It is specifically designed for data from enrichment based methylation assays, but can be applied to other data as well. The analysis pipeline includes seven steps: (1) scanning aligned reads from BAM files, (2) calculation of quality control measures, (3) creation of methylation score (coverage) matrix, (4) principal component analysis for capturing batch effects and detection of outliers, (5) association analysis with respect to phenotypes of interest while correcting for top PCs and known covariates, (6) annotation of significant findings, and (7) multi-marker analysis (methylation risk score) using elastic net. Additionally, RaMWAS include tools for joint analysis of methlyation and genotype data. This work is published in Bioinformatics, Shabalin et al. (2018) .' + diff --git a/recipes/bioconductor-randomwalkrestartmh/build.sh b/recipes/bioconductor-randomwalkrestartmh/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-randomwalkrestartmh/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-randomwalkrestartmh/meta.yaml b/recipes/bioconductor-randomwalkrestartmh/meta.yaml new file mode 100644 index 0000000000000..4fd637f929c06 --- /dev/null +++ b/recipes/bioconductor-randomwalkrestartmh/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.2.0" %} +{% set name = "RandomWalkRestartMH" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 351404a67f4b115a3d24314cb60f9d20 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat +requirements: + host: + - r-base + - r-dnet + - r-igraph + - r-matrix + run: + - r-base + - r-dnet + - r-igraph + - r-matrix +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package performs Random Walk with Restart on multiplex and heterogeneous networks. It is described in the following article: "Random Walk With Restart On Multiplex And Heterogeneous Biological Networks". https://www.biorxiv.org/content/early/2017/08/30/134734 .' + diff --git a/recipes/bioconductor-randpack/build.sh b/recipes/bioconductor-randpack/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-randpack/build.sh +++ b/recipes/bioconductor-randpack/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-randpack/meta.yaml b/recipes/bioconductor-randpack/meta.yaml index f3fd6352897c8..e06bc2b218bac 100644 --- a/recipes/bioconductor-randpack/meta.yaml +++ b/recipes/bioconductor-randpack/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "randPack" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d7d8e7875308441c68431f7654a354e64380cbcd3d3be94ad291cc16cb3d05f3 + md5: 92c6a0d2bee12aa5cc9fae2882ac72f1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic 2.0' summary: 'A suite of classes and functions for randomizing patients in clinical trials.' extra: identifiers: - biotools:randpack - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-randpack + path: recipes/bioconductor-randpack + version: 1.26.0 + diff --git a/recipes/bioconductor-rankprod/build.sh b/recipes/bioconductor-rankprod/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rankprod/build.sh +++ b/recipes/bioconductor-rankprod/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rankprod/meta.yaml b/recipes/bioconductor-rankprod/meta.yaml index 209cd691ef05c..5207123a975b0 100644 --- a/recipes/bioconductor-rankprod/meta.yaml +++ b/recipes/bioconductor-rankprod/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "3.6.0" %} +{% set version = "3.8.0" %} {% set name = "RankProd" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b05409063bef40dd0e321fb9b0ed9ec94b09968232a8585504938324bdc8f372 + md5: 86e2a46efa5edd1ad7ecaf7556b18208 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Non-parametric method for identifying differentially expressed (up- or down- regulated) genes based on the estimated percentage of false predictions (pfp). The method can combine data sets from different origins (meta-analysis) to increase the power of the identification.' extra: identifiers: - biotools:rankprod - doi:10.1093/bioinformatics/btl476 + parent_recipe: + name: bioconductor-rankprod + path: recipes/bioconductor-rankprod + version: 3.6.0 + diff --git a/recipes/bioconductor-rarevariantvis/build.sh b/recipes/bioconductor-rarevariantvis/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rarevariantvis/build.sh +++ b/recipes/bioconductor-rarevariantvis/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rarevariantvis/conda_build_config.yaml b/recipes/bioconductor-rarevariantvis/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rarevariantvis/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rarevariantvis/meta.yaml b/recipes/bioconductor-rarevariantvis/meta.yaml index 200920625fac0..6da8c4cb49ac2 100644 --- a/recipes/bioconductor-rarevariantvis/meta.yaml +++ b/recipes/bioconductor-rarevariantvis/meta.yaml @@ -1,53 +1,55 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "RareVariantVis" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ee65a6eda36b3f776e3e333c6080b8389f93929971a335d6922321e2a9c5e381 + md5: 193cfc429d07fdf039d3e2edea0893ae build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.2,<3.9.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-googlevis - r-gtools run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.2,<3.9.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-phastcons100way.ucsc.hg19 >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-googlevis - r-gtools @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Second version of RareVariantVis package aims to provide comprehensive information about rare variants for your genome data. It annotates, filters and presents genomic variants (especially rare ones) in a global, per chromosome way. For discovered rare variants CRISPR guide RNAs are designed, so the user can plan further functional studies. Large structural variants, including copy number variants are also supported. Package accepts variants directly from variant caller - for example GATK or Speedseq. Output of package are lists of variants together with adequate visualization. Visualization of variants is performed in two ways - standard that outputs png figures and interactive that uses JavaScript d3 package. Interactive visualization allows to analyze trio/family data, for example in search for causative variants in rare Mendelian diseases, in point-and-click interface. The package includes homozygous region caller and allows to analyse whole human genomes in less than 30 minutes on a desktop computer. RareVariantVis disclosed novel causes of several rare monogenic disorders, including one with non-coding causative variant - keratolythic winter erythema.' extra: identifiers: - biotools:rarevariantvis - doi:10.1093/bioinformatics/btw359 + parent_recipe: + name: bioconductor-rarevariantvis + path: recipes/bioconductor-rarevariantvis + version: 2.8.0 + diff --git a/recipes/bioconductor-rariant/build.sh b/recipes/bioconductor-rariant/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rariant/build.sh +++ b/recipes/bioconductor-rariant/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rariant/conda_build_config.yaml b/recipes/bioconductor-rariant/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rariant/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rariant/meta.yaml b/recipes/bioconductor-rariant/meta.yaml index ea1024f149efa..41f62dacb896c 100644 --- a/recipes/bioconductor-rariant/meta.yaml +++ b/recipes/bioconductor-rariant/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "Rariant" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: da698f812d7a8bfac97043800a7f3f95eed9f7a8697b90cf3426ecc89f5517d9 + md5: cc3ad6548566082286949d086014730c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: h5vcData, testthat, knitr, optparse, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-dplyr - r-ggplot2 @@ -35,16 +37,16 @@ requirements: - r-shiny - r-vgam run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-exomecopy >=1.26.0,<1.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-dplyr - r-ggplot2 @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The ''Rariant'' package identifies single nucleotide variants from sequencing data based on the difference of binomially distributed mismatch rates between matched samples.' extra: identifiers: - biotools:rariant - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rariant + path: recipes/bioconductor-rariant + version: 1.16.0 + diff --git a/recipes/bioconductor-rat.db0/meta.yaml b/recipes/bioconductor-rat.db0/meta.yaml new file mode 100644 index 0000000000000..a185a2d0a7c8a --- /dev/null +++ b/recipes/bioconductor-rat.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "rat.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 356c5e1a7c24d7e3f1d6785c59af1016 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for rat, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-rat.db0/post-link.sh b/recipes/bioconductor-rat.db0/post-link.sh new file mode 100644 index 0000000000000..96abc9b36c44e --- /dev/null +++ b/recipes/bioconductor-rat.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rat.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/rat.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat.db0/bioconductor-rat.db0_3.7.1_src_all.tar.gz" +) +MD5="356c5e1a7c24d7e3f1d6785c59af1016" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rat.db0/pre-unlink.sh b/recipes/bioconductor-rat.db0/pre-unlink.sh new file mode 100644 index 0000000000000..89926a46f4ddf --- /dev/null +++ b/recipes/bioconductor-rat.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rat.db0 diff --git a/recipes/bioconductor-rat2302.db/meta.yaml b/recipes/bioconductor-rat2302.db/meta.yaml new file mode 100644 index 0000000000000..2481b77bcddb7 --- /dev/null +++ b/recipes/bioconductor-rat2302.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rat2302.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bcd325ab88de497001867a7cae4501cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Genome 230 2.0 Array annotation data (chip rat2302) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rat2302.db/post-link.sh b/recipes/bioconductor-rat2302.db/post-link.sh new file mode 100644 index 0000000000000..3da5b5189776d --- /dev/null +++ b/recipes/bioconductor-rat2302.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rat2302.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rat2302.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302.db/bioconductor-rat2302.db_3.2.3_src_all.tar.gz" +) +MD5="bcd325ab88de497001867a7cae4501cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rat2302.db/pre-unlink.sh b/recipes/bioconductor-rat2302.db/pre-unlink.sh new file mode 100644 index 0000000000000..8b015a86b10c4 --- /dev/null +++ b/recipes/bioconductor-rat2302.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rat2302.db diff --git a/recipes/bioconductor-rat2302cdf/meta.yaml b/recipes/bioconductor-rat2302cdf/meta.yaml new file mode 100644 index 0000000000000..eeb64cb13d5b2 --- /dev/null +++ b/recipes/bioconductor-rat2302cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rat2302cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a033730f79a11d45b4cd7e7c520f8052 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Rat230_2.cdf file.' + diff --git a/recipes/bioconductor-rat2302cdf/post-link.sh b/recipes/bioconductor-rat2302cdf/post-link.sh new file mode 100644 index 0000000000000..8e3c967cdc9a8 --- /dev/null +++ b/recipes/bioconductor-rat2302cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rat2302cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rat2302cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302cdf/bioconductor-rat2302cdf_2.18.0_src_all.tar.gz" +) +MD5="a033730f79a11d45b4cd7e7c520f8052" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rat2302cdf/pre-unlink.sh b/recipes/bioconductor-rat2302cdf/pre-unlink.sh new file mode 100644 index 0000000000000..0794670b1e4f9 --- /dev/null +++ b/recipes/bioconductor-rat2302cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rat2302cdf diff --git a/recipes/bioconductor-rat2302probe/meta.yaml b/recipes/bioconductor-rat2302probe/meta.yaml new file mode 100644 index 0000000000000..e1d7e83abdf14 --- /dev/null +++ b/recipes/bioconductor-rat2302probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rat2302probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d1d9215e52b9e845cc4d7c902536e0d6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rat230\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-rat2302probe/post-link.sh b/recipes/bioconductor-rat2302probe/post-link.sh new file mode 100644 index 0000000000000..3146429141a53 --- /dev/null +++ b/recipes/bioconductor-rat2302probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rat2302probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rat2302probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rat2302probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rat2302probe/bioconductor-rat2302probe_2.18.0_src_all.tar.gz" +) +MD5="d1d9215e52b9e845cc4d7c902536e0d6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rat2302probe/pre-unlink.sh b/recipes/bioconductor-rat2302probe/pre-unlink.sh new file mode 100644 index 0000000000000..5de74b49b41c1 --- /dev/null +++ b/recipes/bioconductor-rat2302probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rat2302probe diff --git a/recipes/bioconductor-ratchrloc/meta.yaml b/recipes/bioconductor-ratchrloc/meta.yaml new file mode 100644 index 0000000000000..7612b172c684e --- /dev/null +++ b/recipes/bioconductor-ratchrloc/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "2.1.6" %} +{% set name = "ratCHRLOC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6fecff4821a5a47e3bd38a2ff78173d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'Annotation data file for ratCHRLOC assembled using data from public data repositories' + diff --git a/recipes/bioconductor-ratchrloc/post-link.sh b/recipes/bioconductor-ratchrloc/post-link.sh new file mode 100644 index 0000000000000..8f4441d3e9074 --- /dev/null +++ b/recipes/bioconductor-ratchrloc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ratCHRLOC_2.1.6.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ratCHRLOC_2.1.6.tar.gz" + "https://bioarchive.galaxyproject.org/ratCHRLOC_2.1.6.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ratchrloc/bioconductor-ratchrloc_2.1.6_src_all.tar.gz" +) +MD5="6fecff4821a5a47e3bd38a2ff78173d5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ratchrloc/pre-unlink.sh b/recipes/bioconductor-ratchrloc/pre-unlink.sh new file mode 100644 index 0000000000000..ec7a730a9c50f --- /dev/null +++ b/recipes/bioconductor-ratchrloc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ratCHRLOC diff --git a/recipes/bioconductor-rattoxfxcdf/meta.yaml b/recipes/bioconductor-rattoxfxcdf/meta.yaml new file mode 100644 index 0000000000000..dd65a93a7708f --- /dev/null +++ b/recipes/bioconductor-rattoxfxcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rattoxfxcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 912d0fa424615fcd92773ed174d5efdd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RatToxFX.cdf file.' + diff --git a/recipes/bioconductor-rattoxfxcdf/post-link.sh b/recipes/bioconductor-rattoxfxcdf/post-link.sh new file mode 100644 index 0000000000000..6aef9d95287bf --- /dev/null +++ b/recipes/bioconductor-rattoxfxcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rattoxfxcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rattoxfxcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rattoxfxcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattoxfxcdf/bioconductor-rattoxfxcdf_2.18.0_src_all.tar.gz" +) +MD5="912d0fa424615fcd92773ed174d5efdd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rattoxfxcdf/pre-unlink.sh b/recipes/bioconductor-rattoxfxcdf/pre-unlink.sh new file mode 100644 index 0000000000000..697f53a350029 --- /dev/null +++ b/recipes/bioconductor-rattoxfxcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rattoxfxcdf diff --git a/recipes/bioconductor-rattoxfxprobe/meta.yaml b/recipes/bioconductor-rattoxfxprobe/meta.yaml new file mode 100644 index 0000000000000..327ace06090ef --- /dev/null +++ b/recipes/bioconductor-rattoxfxprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rattoxfxprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 202791c72e8c956b9854fa4d9ba67a24 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RatToxFX\_probe\_tab.' + diff --git a/recipes/bioconductor-rattoxfxprobe/post-link.sh b/recipes/bioconductor-rattoxfxprobe/post-link.sh new file mode 100644 index 0000000000000..5788be0de840c --- /dev/null +++ b/recipes/bioconductor-rattoxfxprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rattoxfxprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rattoxfxprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rattoxfxprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattoxfxprobe/bioconductor-rattoxfxprobe_2.18.0_src_all.tar.gz" +) +MD5="202791c72e8c956b9854fa4d9ba67a24" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rattoxfxprobe/pre-unlink.sh b/recipes/bioconductor-rattoxfxprobe/pre-unlink.sh new file mode 100644 index 0000000000000..5c7d23b1e021c --- /dev/null +++ b/recipes/bioconductor-rattoxfxprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rattoxfxprobe diff --git a/recipes/bioconductor-rattus.norvegicus/meta.yaml b/recipes/bioconductor-rattus.norvegicus/meta.yaml new file mode 100644 index 0000000000000..8a013fe1473a9 --- /dev/null +++ b/recipes/bioconductor-rattus.norvegicus/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.3.1" %} +{% set name = "Rattus.norvegicus" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5692fdeb0bc7f94e1db35f097cad99a9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.4.0,<3.5.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-organismdbi >=1.24.0,<1.25.0' + - 'bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene >=3.4.0,<3.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the Rattus.norvegicus object to access data from several related annotation packages.' + diff --git a/recipes/bioconductor-rattus.norvegicus/post-link.sh b/recipes/bioconductor-rattus.norvegicus/post-link.sh new file mode 100644 index 0000000000000..df34ef1ad5b70 --- /dev/null +++ b/recipes/bioconductor-rattus.norvegicus/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Rattus.norvegicus_1.3.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Rattus.norvegicus_1.3.1.tar.gz" + "https://bioarchive.galaxyproject.org/Rattus.norvegicus_1.3.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rattus.norvegicus/bioconductor-rattus.norvegicus_1.3.1_src_all.tar.gz" +) +MD5="5692fdeb0bc7f94e1db35f097cad99a9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rattus.norvegicus/pre-unlink.sh b/recipes/bioconductor-rattus.norvegicus/pre-unlink.sh new file mode 100644 index 0000000000000..6adfa2634642d --- /dev/null +++ b/recipes/bioconductor-rattus.norvegicus/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Rattus.norvegicus diff --git a/recipes/bioconductor-rbcbook1/build.sh b/recipes/bioconductor-rbcbook1/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbcbook1/build.sh +++ b/recipes/bioconductor-rbcbook1/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbcbook1/meta.yaml b/recipes/bioconductor-rbcbook1/meta.yaml index 8fae8eef80e3c..dfa0c44c5c887 100644 --- a/recipes/bioconductor-rbcbook1/meta.yaml +++ b/recipes/bioconductor-rbcbook1/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "RbcBook1" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c71579d58e40a18bb50f645e9af6355567e9b45d30155fa6df8202e5b58a5f77 + md5: ab688a83dd3cb0dacea22caacd02c9cc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-rpart run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-rpart test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'tools for building book' extra: identifiers: - biotools:rbcbook1 - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbcbook1 + path: recipes/bioconductor-rbcbook1 + version: 1.48.0 + diff --git a/recipes/bioconductor-rbgl/build.sh b/recipes/bioconductor-rbgl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbgl/build.sh +++ b/recipes/bioconductor-rbgl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbgl/meta.yaml b/recipes/bioconductor-rbgl/meta.yaml index 75e4e633cd54f..f6dca0df6ae0d 100644 --- a/recipes/bioconductor-rbgl/meta.yaml +++ b/recipes/bioconductor-rbgl/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.1" %} {% set name = "RBGL" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0e5a056a1a63e711bf73ec9978b525dfb7adb49f63e01cba2bd15f5cab384942 + md5: 39204954255e7e33c3595f00bc8bbe72 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Rgraphviz, XML, RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} @@ -32,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A fairly extensive and comprehensive interface to the graph algorithms contained in the BOOST library.' extra: identifiers: - biotools:rbgl - doi:10.1093/bioinformatics/bth458 + parent_recipe: + name: bioconductor-rbgl + path: recipes/bioconductor-rbgl + version: 1.56.0 + diff --git a/recipes/bioconductor-rbioinf/build.sh b/recipes/bioconductor-rbioinf/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbioinf/build.sh +++ b/recipes/bioconductor-rbioinf/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbioinf/meta.yaml b/recipes/bioconductor-rbioinf/meta.yaml index 185ecf6af5aef..903a40c044080 100644 --- a/recipes/bioconductor-rbioinf/meta.yaml +++ b/recipes/bioconductor-rbioinf/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "RBioinf" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78df3c853398434730b46bca69b43f1eff9947149bde054f889fe6d0b57ab52e + md5: ccc0e1c81f86882eef47cef5b74b94d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Rgraphviz requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Functions and datasets and examples to accompany the monograph R For Bioinformatics.' extra: identifiers: - biotools:rbioinf - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbioinf + path: recipes/bioconductor-rbioinf + version: 1.40.0 + diff --git a/recipes/bioconductor-rbiopaxparser/build.sh b/recipes/bioconductor-rbiopaxparser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbiopaxparser/build.sh +++ b/recipes/bioconductor-rbiopaxparser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbiopaxparser/meta.yaml b/recipes/bioconductor-rbiopaxparser/meta.yaml index 7725448ccb2ff..26e81cdc53444 100644 --- a/recipes/bioconductor-rbiopaxparser/meta.yaml +++ b/recipes/bioconductor-rbiopaxparser/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "rBiopaxParser" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5356f663cf55e8c1432d3c4b046aa74c1e7b5e2fc6f9b9e595061c66f7c76223 + md5: d83ba9fc20daeefc0ec70a01a4a99c07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz, RCurl, graph, RUnit, BiocGenerics, nem, RBGL, igraph requirements: host: - r-base @@ -29,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Parses BioPAX files and represents them in R, at the moment BioPAX level 2 and level 3 are supported.' extra: identifiers: - biotools:rbiopaxparser + parent_recipe: + name: bioconductor-rbiopaxparser + path: recipes/bioconductor-rbiopaxparser + version: 2.20.0 + diff --git a/recipes/bioconductor-rbm/build.sh b/recipes/bioconductor-rbm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbm/build.sh +++ b/recipes/bioconductor-rbm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbm/meta.yaml b/recipes/bioconductor-rbm/meta.yaml index 3929ba4916aeb..159c63c02b35b 100644 --- a/recipes/bioconductor-rbm/meta.yaml +++ b/recipes/bioconductor-rbm/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RBM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 09e17448d6c2bb6cf86a0fc9a43f4059a57f6d4fe609b4dcae3330f1b1dc993b + md5: 3606f3c75a1198316189c26f7ea7ba85 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Use A Resampling-Based Empirical Bayes Approach to Assess Differential Expression in Two-Color Microarrays and RNA-Seq data sets.' extra: identifiers: - biotools:rbm - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbm + path: recipes/bioconductor-rbm + version: 1.12.0 + diff --git a/recipes/bioconductor-rbowtie/build.sh b/recipes/bioconductor-rbowtie/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbowtie/build.sh +++ b/recipes/bioconductor-rbowtie/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbowtie/meta.yaml b/recipes/bioconductor-rbowtie/meta.yaml index e0d66fe096f84..8be861b313c6e 100644 --- a/recipes/bioconductor-rbowtie/meta.yaml +++ b/recipes/bioconductor-rbowtie/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "Rbowtie" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 80b1b576de6afc0b4efe90e70bc56f246468d0a5cf94859069d21e8d70322a04 + md5: 4c1a3ec981370710eb6d526043a31965 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, BiocStyle, knitr, rmarkdown +# SystemRequirements: GNU make requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-1.0 | file LICENSE' summary: 'This package provides an R wrapper around the popular bowtie short read aligner and around SpliceMap, a de novo splice junction discovery and alignment tool. The package is used by the QuasR bioconductor package. We recommend to use the QuasR package instead of using Rbowtie directly.' extra: identifiers: - biotools:rbowtie - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rbowtie + path: recipes/bioconductor-rbowtie + version: 1.20.0 + diff --git a/recipes/bioconductor-rbowtie2/build.sh b/recipes/bioconductor-rbowtie2/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rbowtie2/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbowtie2/meta.yaml b/recipes/bioconductor-rbowtie2/meta.yaml new file mode 100644 index 0000000000000..42c5516b911c3 --- /dev/null +++ b/recipes/bioconductor-rbowtie2/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.4.0" %} +{% set name = "Rbowtie2" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8c6f2b4f4cf420132402458cc0431d96 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr +# SystemRequirements: C++11 +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package provides an R wrapper of the popular bowtie2 sequencing reads aligner and AdapterRemoval, a convenient tool for rapid adapter trimming, identification, and read merging.' + diff --git a/recipes/bioconductor-rbsurv/build.sh b/recipes/bioconductor-rbsurv/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rbsurv/build.sh +++ b/recipes/bioconductor-rbsurv/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rbsurv/meta.yaml b/recipes/bioconductor-rbsurv/meta.yaml index b427c5b201445..2d7af98a801cb 100644 --- a/recipes/bioconductor-rbsurv/meta.yaml +++ b/recipes/bioconductor-rbsurv/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "rbsurv" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d463f2bc1d08b234530a4181e3812501bda3bcbebee55b81dd8cb1712554876d + md5: 1e470e032da134db83ae929adb8ff66a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-survival run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-survival test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package selects genes associated with survival.' extra: identifiers: - biotools:rbsurv - doi:10.18637/jss.v029.i01 + parent_recipe: + name: bioconductor-rbsurv + path: recipes/bioconductor-rbsurv + version: 2.38.0 + diff --git a/recipes/bioconductor-rcade/build.sh b/recipes/bioconductor-rcade/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcade/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcade/meta.yaml b/recipes/bioconductor-rcade/meta.yaml new file mode 100644 index 0000000000000..a5065ab1c1ac2 --- /dev/null +++ b/recipes/bioconductor-rcade/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.24.0" %} +{% set name = "Rcade" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 33e6f9f825b0dabf32897a4044af6f7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: limma, biomaRt, RUnit, BiocGenerics, BiocStyle +requirements: + host: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-plotrix + - r-rgl + run: + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-plotrix + - r-rgl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Rcade (which stands for "R-based analysis of ChIP-seq And Differential Expression") is a tool for integrating ChIP-seq data with differential expression summary data, through a Bayesian framework. A key application is in identifing the genes targeted by a transcription factor of interest - that is, we collect genes that are associated with a ChIP-seq peak, and differential expression under some perturbation related to that TF.' + diff --git a/recipes/bioconductor-rcas/build.sh b/recipes/bioconductor-rcas/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rcas/build.sh +++ b/recipes/bioconductor-rcas/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcas/meta.yaml b/recipes/bioconductor-rcas/meta.yaml index dcc2feb45c7c3..7f4671eeb6cee 100644 --- a/recipes/bioconductor-rcas/meta.yaml +++ b/recipes/bioconductor-rcas/meta.yaml @@ -1,37 +1,40 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "RCAS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a53507c0f0f831e9124205720b1d2459680dad6ac5e5ae26b06a899a813ab66e + md5: 2146754031cbc929a628de63e7088388 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg38, BSgenome.Mmusculus.UCSC.mm10, BSgenome.Mmusculus.UCSC.mm9, BSgenome.Celegans.UCSC.ce10, BSgenome.Dmelanogaster.UCSC.dm3, org.Mm.eg.db, org.Ce.eg.db, org.Dm.eg.db, testthat, covr +# SystemRequirements: pandoc (>= 1.12.3) requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-motifrg >=1.24.0,<1.26.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-motifrg >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-cowplot - r-data.table @@ -48,20 +51,20 @@ requirements: - 'r-rmarkdown >=0.9.5' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomation >=1.12.0,<1.14.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-motifrg >=1.24.0,<1.26.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomation >=1.14.0,<1.15.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-motifrg >=1.26.0,<1.27.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-cowplot - r-data.table @@ -81,9 +84,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'RCAS is an automated system that provides dynamic genome annotations for custom input files that contain transcriptomic regions. Such transcriptomic regions could be, for instance, peak regions detected by CLIP-Seq analysis that detect protein-RNA interactions, RNA modifications (alias the epitranscriptome), CAGE-tag locations, or any other collection of target regions at the level of the transcriptome. RCAS is designed as a reporting tool for the functional analysis of RNA-binding sites detected by high-throughput experiments. It takes as input a BED format file containing the genomic coordinates of the RNA binding sites and a GTF file that contains the genomic annotation features usually provided by publicly available databases such as Ensembl and UCSC. RCAS performs overlap operations between the genomic coordinates of the RNA binding sites and the genomic annotation features and produces in-depth annotation summaries such as the distribution of binding sites with respect to gene features (exons, introns, 5''/3'' UTR regions, exon-intron boundaries, promoter regions, and whole transcripts). Moreover, by detecting the collection of targeted transcripts, RCAS can carry out functional annotation tables for enriched gene sets (annotated by the Molecular Signatures Database) and GO terms. As one of the most important questions that arise during protein-RNA interaction analysis; RCAS has a module for detecting sequence motifs enriched in the targeted regions of the transcriptome. A full interactive report in HTML format can be generated that contains interactive figures and tables that are ready for publication purposes.' extra: identifiers: - biotools:rcas + parent_recipe: + name: bioconductor-rcas + path: recipes/bioconductor-rcas + version: 1.6.0 + diff --git a/recipes/bioconductor-rcaspar/build.sh b/recipes/bioconductor-rcaspar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rcaspar/build.sh +++ b/recipes/bioconductor-rcaspar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcaspar/meta.yaml b/recipes/bioconductor-rcaspar/meta.yaml index 83e34182188f7..1911f4a19f275 100644 --- a/recipes/bioconductor-rcaspar/meta.yaml +++ b/recipes/bioconductor-rcaspar/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "RCASPAR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c64f4052b272075854b06c831d4ff054f5ea36b5552d1ee680d9cbed058eaa61 + md5: e479b18cfbc19c9ff633add554d85c2f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'The package is the R-version of the C-based software \bold{CASPAR} (Kaderali,2006: \url{http://bioinformatics.oxfordjournals.org/content/22/12/1495}). It is meant to help predict survival times in the presence of high-dimensional explanatory covariates. The model is a piecewise baseline hazard Cox regression model with an Lq-norm based prior that selects for the most important regression coefficients, and in turn the most relevant covariates for survival analysis. It was primarily tried on gene expression and aCGH data, but can be used on any other type of high-dimensional data and in disciplines other than biology and medicine.' extra: identifiers: - biotools:rcaspar - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rcaspar + path: recipes/bioconductor-rcaspar + version: 1.26.0 + diff --git a/recipes/bioconductor-rcellminer/build.sh b/recipes/bioconductor-rcellminer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcellminer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcellminer/meta.yaml b/recipes/bioconductor-rcellminer/meta.yaml new file mode 100644 index 0000000000000..050ab39792704 --- /dev/null +++ b/recipes/bioconductor-rcellminer/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "2.4.0" %} +{% set name = "rcellminer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b4cc81cd0e95c5987a8bb9780abdf85c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RColorBrewer, sqldf, BiocGenerics, testthat, BiocStyle, jsonlite, d3heatmap, glmnet, foreach, doSNOW, parallel +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-rcellminerdata >=2.4.0,<2.5.0' + - r-base + - r-fingerprint + - r-ggplot2 + - r-gplots + - r-rcdk + - r-shiny + - r-stringr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-rcellminerdata >=2.4.0,<2.5.0' + - r-base + - r-fingerprint + - r-ggplot2 + - r-gplots + - r-rcdk + - r-shiny + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL-3 + file LICENSE' + summary: 'The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.' + diff --git a/recipes/bioconductor-rcellminerdata/meta.yaml b/recipes/bioconductor-rcellminerdata/meta.yaml new file mode 100644 index 0000000000000..7bf2795c40198 --- /dev/null +++ b/recipes/bioconductor-rcellminerdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "2.4.0" %} +{% set name = "rcellminerData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7259b2817b463847c17e2d6f1d85fe04 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, BiocStyle, rcellminer +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL-3 + file LICENSE' + summary: 'The NCI-60 cancer cell line panel has been used over the course of several decades as an anti-cancer drug screen. This panel was developed as part of the Developmental Therapeutics Program (DTP, http://dtp.nci.nih.gov/) of the U.S. National Cancer Institute (NCI). Thousands of compounds have been tested on the NCI-60, which have been extensively characterized by many platforms for gene and protein expression, copy number, mutation, and others (Reinhold, et al., 2012). The purpose of the CellMiner project (http://discover.nci.nih.gov/ cellminer) has been to integrate data from multiple platforms used to analyze the NCI-60 and to provide a powerful suite of tools for exploration of NCI-60 data.' + diff --git a/recipes/bioconductor-rcellminerdata/post-link.sh b/recipes/bioconductor-rcellminerdata/post-link.sh new file mode 100644 index 0000000000000..22a0e5c20ba80 --- /dev/null +++ b/recipes/bioconductor-rcellminerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rcellminerData_2.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rcellminerData_2.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/rcellminerData_2.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rcellminerdata/bioconductor-rcellminerdata_2.4.0_src_all.tar.gz" +) +MD5="7259b2817b463847c17e2d6f1d85fe04" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rcellminerdata/pre-unlink.sh b/recipes/bioconductor-rcellminerdata/pre-unlink.sh new file mode 100644 index 0000000000000..9b697aa294832 --- /dev/null +++ b/recipes/bioconductor-rcellminerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rcellminerData diff --git a/recipes/bioconductor-rcgh/build.sh b/recipes/bioconductor-rcgh/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rcgh/build.sh +++ b/recipes/bioconductor-rcgh/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcgh/conda_build_config.yaml b/recipes/bioconductor-rcgh/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rcgh/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rcgh/meta.yaml b/recipes/bioconductor-rcgh/meta.yaml index 9e835b5de5e68..00b942296defd 100644 --- a/recipes/bioconductor-rcgh/meta.yaml +++ b/recipes/bioconductor-rcgh/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rCGH" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a1e5429e1be9fa134e3527bf760b3dca74819313fd72db8a7e563b56278c58d0 + md5: eae2203e032108c2873331c9de08161e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, BiocGenerics, RUnit requirements: host: - - 'bioconductor-acgh >=1.58.0,<1.60.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.6.0' + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-ggplot2 - r-lattice @@ -38,19 +40,19 @@ requirements: - r-plyr - 'r-shiny >=0.11.1' run: - - 'bioconductor-acgh >=1.58.0,<1.60.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.2,<3.4.0' - - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.6.0' + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg18.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' - r-base - r-ggplot2 - r-lattice @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A comprehensive pipeline for analyzing and interactively visualizing genomic profiles generated through commercial or custom aCGH arrays. As inputs, rCGH supports Agilent dual-color Feature Extraction files (.txt), from 44 to 400K, Affymetrix SNP6.0 and cytoScanHD probeset.txt, cychp.txt, and cnchp.txt files exported from ChAS or Affymetrix Power Tools. rCGH also supports custom arrays, provided data complies with the expected format. This package takes over all the steps required for individual genomic profiles analysis, from reading files to profiles segmentation and gene annotations. This package also provides several visualization functions (static or interactive) which facilitate individual profiles interpretation. Input files can be in compressed format, e.g. .bz2 or .gz.' extra: identifiers: - biotools:rcgh - doi:10.1093/bioinformatics/btv718 + parent_recipe: + name: bioconductor-rcgh + path: recipes/bioconductor-rcgh + version: 1.10.0 + diff --git a/recipes/bioconductor-rchemcpp/build.sh b/recipes/bioconductor-rchemcpp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rchemcpp/build.sh +++ b/recipes/bioconductor-rchemcpp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rchemcpp/meta.yaml b/recipes/bioconductor-rchemcpp/meta.yaml index 6d8981ed5b915..637fcf7cc7b70 100644 --- a/recipes/bioconductor-rchemcpp/meta.yaml +++ b/recipes/bioconductor-rchemcpp/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "Rchemcpp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f47733f4a375f15e60dfbd1f6bd04a835c66a80d6308a5dbcde7a4266e018139 + md5: a3749cf4b057d518ad1deeff788368f4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: apcluster, kernlab +# SystemRequirements: GNU make requirements: host: - - 'bioconductor-chemminer >=3.32.1,<3.34.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' - r-base - 'r-rcpp >=0.11.1' run: - - 'bioconductor-chemminer >=3.32.1,<3.34.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' - r-base - 'r-rcpp >=0.11.1' build: @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2.1)' summary: 'The Rchemcpp package implements the marginalized graph kernel and extensions, Tanimoto kernels, graph kernels, pharmacophore and 3D kernels suggested for measuring the similarity of molecules.' extra: identifiers: - biotools:rchemcpp + parent_recipe: + name: bioconductor-rchemcpp + path: recipes/bioconductor-rchemcpp + version: 2.18.0 + diff --git a/recipes/bioconductor-rchyoptimyx/build.sh b/recipes/bioconductor-rchyoptimyx/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rchyoptimyx/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rchyoptimyx/meta.yaml b/recipes/bioconductor-rchyoptimyx/meta.yaml new file mode 100644 index 0000000000000..1d457eb9594f4 --- /dev/null +++ b/recipes/bioconductor-rchyoptimyx/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "2.22.0" %} +{% set name = "RchyOptimyx" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: da60b35d34e9ca50d24128210ea043cd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: flowCore +requirements: + host: + - 'bioconductor-flowtype >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-sfsmisc + run: + - 'bioconductor-flowtype >=2.20.0,<2.21.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-sfsmisc + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Constructs a hierarchy of cells using flow cytometry for maximization of an external variable (e.g., a clinical outcome or a cytokine response).' + diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml new file mode 100644 index 0000000000000..f8ce7287009e4 --- /dev/null +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "RcisTarget.hg19.motifDBs.cisbpOnly.500bp" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a43b2fd762e2ea0d13283c4c7fa5221c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + - r-data.table + run: + - r-base + - r-data.table + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'RcisTarget databases: Gene-based motif rankings and annotation to transcription factors. This package contains a subset of 4.6k motifs (cisbp motifs), scored only within 500bp upstream and the TSS. See RcisTarget tutorial to download the full databases, containing 20k motifs and search space up to 10kbp around the TSS.' + diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh new file mode 100644 index 0000000000000..1ff243153d5bc --- /dev/null +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RcisTarget.hg19.motifDBs.cisbpOnly.500bp_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp_1.2.0_src_all.tar.gz" +) +MD5="a43b2fd762e2ea0d13283c4c7fa5221c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/pre-unlink.sh b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/pre-unlink.sh new file mode 100644 index 0000000000000..48501e759fe1e --- /dev/null +++ b/recipes/bioconductor-rcistarget.hg19.motifdbs.cisbponly.500bp/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RcisTarget.hg19.motifDBs.cisbpOnly.500bp diff --git a/recipes/bioconductor-rcistarget/build.sh b/recipes/bioconductor-rcistarget/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcistarget/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcistarget/meta.yaml b/recipes/bioconductor-rcistarget/meta.yaml new file mode 100644 index 0000000000000..6d61b68806043 --- /dev/null +++ b/recipes/bioconductor-rcistarget/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.2.0" %} +{% set name = "RcisTarget" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 063f34a6f8346f2b88ad9e290a3ea709 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocStyle, BiocParallel, doParallel, DT, foreach, igraph, knitr, RcisTarget.hg19.motifDBs.cisbpOnly.500bp, rmarkdown, testthat, visNetwork +requirements: + host: + - 'bioconductor-aucell >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-feather + - r-r.utils + run: + - 'bioconductor-aucell >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-feather + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'RcisTarget identifies transcription factor binding motifs (TFBS) over-represented on a gene list. In a first step, RcisTarget selects DNA motifs that are significantly over-represented in the surroundings of the transcription start site (TSS) of the genes in the gene-set. This is achieved by using a database that contains genome-wide cross-species rankings for each motif. The motifs that are then annotated to TFs and those that have a high Normalized Enrichment Score (NES) are retained. Finally, for each motif and gene-set, RcisTarget predicts the candidate target genes (i.e. genes in the gene-set that are ranked above the leading edge).' + diff --git a/recipes/bioconductor-rcpi/build.sh b/recipes/bioconductor-rcpi/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcpi/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcpi/meta.yaml b/recipes/bioconductor-rcpi/meta.yaml new file mode 100644 index 0000000000000..6a5571a4f25eb --- /dev/null +++ b/recipes/bioconductor-rcpi/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.18.1" %} +{% set name = "Rcpi" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ee46e5f6fe8d72cb137d8f2bbf37c7f9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-fmcsr >=1.24.0,<1.25.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - r-base + - r-doparallel + - r-foreach + - 'r-rcdk >=3.3.8' + - r-rcurl + - r-rjson + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chemminer >=3.34.0,<3.35.0' + - 'bioconductor-fmcsr >=1.24.0,<1.25.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - r-base + - r-doparallel + - r-foreach + - 'r-rcdk >=3.3.8' + - r-rcurl + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic-2.0 | file LICENSE' + summary: 'Rcpi offers a molecular informatics toolkit with a comprehensive integration of bioinformatics and chemoinformatics tools for drug discovery.' + diff --git a/recipes/bioconductor-rcy3/build.sh b/recipes/bioconductor-rcy3/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rcy3/build.sh +++ b/recipes/bioconductor-rcy3/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcy3/meta.yaml b/recipes/bioconductor-rcy3/meta.yaml index c4c801d277827..fa885c0dd2f36 100644 --- a/recipes/bioconductor-rcy3/meta.yaml +++ b/recipes/bioconductor-rcy3/meta.yaml @@ -1,33 +1,36 @@ -{% set version = "2.0.88" %} +{% set version = "2.2.5" %} {% set name = "RCy3" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 84e5eaa3077b08a54481c9c617118491343ab824c74a6826a1defde02b2ef74b + md5: 54b8d5ad530cff11d5ec97476d92373b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, RColorBrewer, BiocStyle, knitr, rmarkdown +# SystemRequirements: Cytoscape (>= 3.7.0), CyREST (>= 3.8.0) requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-httr - r-igraph - r-rjsonio - r-xml run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-httr - r-igraph @@ -37,8 +40,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Vizualize, analyze and explore networks using Cytoscape via R.' - +extra: + parent_recipe: + name: bioconductor-rcy3 + path: recipes/bioconductor-rcy3 + version: 2.0.88 diff --git a/recipes/bioconductor-rcyjs/build.sh b/recipes/bioconductor-rcyjs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rcyjs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rcyjs/meta.yaml b/recipes/bioconductor-rcyjs/meta.yaml new file mode 100644 index 0000000000000..e1416d9510b49 --- /dev/null +++ b/recipes/bioconductor-rcyjs/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.4.0" %} +{% set name = "RCyjs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 19c7f00c1017e0322bca3036a696fc66 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, RefNet, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-browserviz >=2.4.0,<2.5.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-base64enc + - 'r-httpuv >=1.4.0' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-browserviz >=2.4.0,<2.5.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - r-base64enc + - 'r-httpuv >=1.4.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Interactive viewing and exploration of graphs, connecting R to Cytoscape.js, using websockets.' + diff --git a/recipes/bioconductor-rdavidwebservice/build.sh b/recipes/bioconductor-rdavidwebservice/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rdavidwebservice/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rdavidwebservice/meta.yaml b/recipes/bioconductor-rdavidwebservice/meta.yaml new file mode 100644 index 0000000000000..afde7ac7c629d --- /dev/null +++ b/recipes/bioconductor-rdavidwebservice/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.20.0" %} +{% set name = "RDAVIDWebService" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 21a1209b7e43d5753dcf84a4590d06e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Rgraphviz +requirements: + host: + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-ggplot2 + - r-rjava + run: + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-ggplot2 + - r-rjava +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Tools for retrieving data from the Database for Annotation, Visualization and Integrated Discovery (DAVID) using Web Services into R objects. This package offers the main functionalities of DAVID website including: i) user friendly connectivity to upload gene/background list/s, change gene/background position, select current specie/s, select annotations, etc. ii) Reports of the submitted Gene List, Annotation Category Summary, Gene/Term Clusters, Functional Annotation Chart, Functional Annotation Table' + diff --git a/recipes/bioconductor-rdgidb/build.sh b/recipes/bioconductor-rdgidb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rdgidb/build.sh +++ b/recipes/bioconductor-rdgidb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rdgidb/meta.yaml b/recipes/bioconductor-rdgidb/meta.yaml index e61e905dc34fa..60eccba952eeb 100644 --- a/recipes/bioconductor-rdgidb/meta.yaml +++ b/recipes/bioconductor-rdgidb/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "rDGIdb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3c4930b2695455d29a8b9fc3cbff92197d75dd38fa4282b1e573bce40bf69d7a + md5: b08e5cd64ac2af2f3fd05a7ec4472b1c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle,knitr,testthat requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'The rDGIdb package provides a wrapper for the Drug Gene Interaction Database (DGIdb). For simplicity, the wrapper query function and output resembles the user interface and results format provided on the DGIdb website (http://www.dgidb.org/).' extra: identifiers: - biotools:rdgidb - doi:10.12688/f1000research.9357.1 + parent_recipe: + name: bioconductor-rdgidb + path: recipes/bioconductor-rdgidb + version: 1.6.0 + diff --git a/recipes/bioconductor-rdisop/build.sh b/recipes/bioconductor-rdisop/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rdisop/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rdisop/meta.yaml b/recipes/bioconductor-rdisop/meta.yaml new file mode 100644 index 0000000000000..88e396c487e95 --- /dev/null +++ b/recipes/bioconductor-rdisop/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.42.0" %} +{% set name = "Rdisop" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e22c4c75e68685c797a063b2f59a9ae2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit +# SystemRequirements: None +requirements: + host: + - r-base + - r-rcpp + - r-rcppclassic + run: + - r-base + - r-rcpp + - r-rcppclassic + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Identification of metabolites using high precision mass spectrometry. MS Peaks are used to derive a ranked list of sum formulae, alternatively for a given sum formula the theoretical isotope distribution can be calculated to search in MS peak lists.' + diff --git a/recipes/bioconductor-rdrtoolbox/build.sh b/recipes/bioconductor-rdrtoolbox/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rdrtoolbox/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rdrtoolbox/meta.yaml b/recipes/bioconductor-rdrtoolbox/meta.yaml new file mode 100644 index 0000000000000..4fb4f856510df --- /dev/null +++ b/recipes/bioconductor-rdrtoolbox/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.32.0" %} +{% set name = "RDRToolbox" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4878943bca03a276c3ad77772ae786cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: golubEsets +requirements: + host: + - r-base + - r-mass + - r-rgl + run: + - r-base + - r-mass + - r-rgl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'A package for nonlinear dimension reduction using the Isomap and LLE algorithm. It also includes a routine for computing the Davis-Bouldin-Index for cluster validation, a plotting tool and a data generator for microarray gene expression data and for the Swiss Roll dataset.' + diff --git a/recipes/bioconductor-reactome.db/meta.yaml b/recipes/bioconductor-reactome.db/meta.yaml index 5eb5aaeb9dcae..4d4818a1196bb 100644 --- a/recipes/bioconductor-reactome.db/meta.yaml +++ b/recipes/bioconductor-reactome.db/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.64.0" %} +{% set version = "1.66.0" %} {% set name = "reactome.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2da0eb17b5fce58cf4ee97d414f0c03b22f8b9487f7e31b4e5a02b9479898ff3 + md5: 986cbb0b2f951b57c682364213f5016e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RSQLite requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'CC BY 4.0' summary: 'A set of annotation maps for reactome assembled using data from reactome' - +extra: + parent_recipe: + name: bioconductor-reactome.db + path: recipes/bioconductor-reactome.db + version: 1.64.0 diff --git a/recipes/bioconductor-reactome.db/post-link.sh b/recipes/bioconductor-reactome.db/post-link.sh index a8955bee48571..735e7cee27dea 100644 --- a/recipes/bioconductor-reactome.db/post-link.sh +++ b/recipes/bioconductor-reactome.db/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="reactome.db_1.64.0.tar.gz" +FN="reactome.db_1.66.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/reactome.db_1.64.0.tar.gz" - "https://bioarchive.galaxyproject.org/reactome.db_1.64.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.64.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/reactome.db_1.66.0.tar.gz" + "https://bioarchive.galaxyproject.org/reactome.db_1.66.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-reactome.db/bioconductor-reactome.db_1.66.0_src_all.tar.gz" ) -MD5="4dfc5160ef8673ff4a892cb4146d1eeb" +MD5="986cbb0b2f951b57c682364213f5016e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-reactomepa/build.sh b/recipes/bioconductor-reactomepa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-reactomepa/build.sh +++ b/recipes/bioconductor-reactomepa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-reactomepa/meta.yaml b/recipes/bioconductor-reactomepa/meta.yaml index afa5c10238c4f..62b0a5f14473f 100644 --- a/recipes/bioconductor-reactomepa/meta.yaml +++ b/recipes/bioconductor-reactomepa/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ReactomePA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ef9896f14944f43514cc57cd3518e3e8060ed1f86274b84cef3939bfd8170a16 + md5: b240608152ce98d954046ecd1e14ba7b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, clusterProfiler, knitr, org.Hs.eg.db, prettydoc, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-graphite >=1.26.1,<1.28.0' - - 'bioconductor-reactome.db >=1.64.0,<1.66.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - r-base - r-ggplot2 - r-ggraph - r-igraph run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-dose >=3.6.1,<3.8.0' - - 'bioconductor-enrichplot >=1.0.2,<1.2.0' - - 'bioconductor-graphite >=1.26.1,<1.28.0' - - 'bioconductor-reactome.db >=1.64.0,<1.66.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-enrichplot >=1.2.0,<1.3.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' - r-base - r-ggplot2 - r-ggraph @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides functions for pathway analysis based on REACTOME pathway database. It implements enrichment analysis, gene set enrichment analysis and several functions for visualization.' extra: identifiers: - biotools:reactomepa + parent_recipe: + name: bioconductor-reactomepa + path: recipes/bioconductor-reactomepa + version: 1.24.0 + diff --git a/recipes/bioconductor-readat/build.sh b/recipes/bioconductor-readat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-readat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-readat/meta.yaml b/recipes/bioconductor-readat/meta.yaml new file mode 100644 index 0000000000000..d79436b5f9486 --- /dev/null +++ b/recipes/bioconductor-readat/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.8.0" %} +{% set name = "readat" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 5997fc86272923223432b715e16ba7be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, MSnbase, rmarkdown, withr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'r-assertive.base >=0.0-7' + - 'r-assertive.files >=0.0-2' + - 'r-assertive.numbers >=0.0-2' + - 'r-assertive.properties >=0.0-4' + - 'r-assertive.sets >=0.0-3' + - 'r-assertive.types >=0.0-3' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.5.0' + - 'r-magrittr >=1.5' + - 'r-openxlsx >=4.0.17' + - 'r-pathological >=0.1-2' + - 'r-reshape2 >=1.4.2' + - 'r-stringi >=1.1.5' + - 'r-testthat >=1.0.2' + - 'r-tidyr >=0.6.2' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'r-assertive.base >=0.0-7' + - 'r-assertive.files >=0.0-2' + - 'r-assertive.numbers >=0.0-2' + - 'r-assertive.properties >=0.0-4' + - 'r-assertive.sets >=0.0-3' + - 'r-assertive.types >=0.0-3' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.5.0' + - 'r-magrittr >=1.5' + - 'r-openxlsx >=4.0.17' + - 'r-pathological >=0.1-2' + - 'r-reshape2 >=1.4.2' + - 'r-stringi >=1.1.5' + - 'r-testthat >=1.0.2' + - 'r-tidyr >=0.6.2' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package contains functionality to import, transform and annotate data from ADAT files generated by the SomaLogic SOMAscan platform.' + diff --git a/recipes/bioconductor-readqpcr/build.sh b/recipes/bioconductor-readqpcr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-readqpcr/build.sh +++ b/recipes/bioconductor-readqpcr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-readqpcr/conda_build_config.yaml b/recipes/bioconductor-readqpcr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-readqpcr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-readqpcr/meta.yaml b/recipes/bioconductor-readqpcr/meta.yaml index 360ed34443308..fd5f2c733f927 100644 --- a/recipes/bioconductor-readqpcr/meta.yaml +++ b/recipes/bioconductor-readqpcr/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "ReadqPCR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 760a54616ab9113dbaea7ca981443f25793d5308c2cfd1c6ca2aea42cdf074ae + md5: dff61efd77bb86fb720acd7c63b32976 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: qpcR requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'The package provides functions to read raw RT-qPCR data of different platforms.' extra: identifiers: - biotools:readqpcr + parent_recipe: + name: bioconductor-readqpcr + path: recipes/bioconductor-readqpcr + version: 1.26.0 + diff --git a/recipes/bioconductor-reb/build.sh b/recipes/bioconductor-reb/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-reb/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-reb/meta.yaml b/recipes/bioconductor-reb/meta.yaml new file mode 100644 index 0000000000000..3fd3edf15047d --- /dev/null +++ b/recipes/bioconductor-reb/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.60.0" %} +{% set name = "reb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b4e0632e5c9173414286e0dba2af409a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-idiogram >=1.58.0,<1.59.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-idiogram >=1.58.0,<1.59.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A set of functions to dentify regional expression biases' + diff --git a/recipes/bioconductor-rebet/build.sh b/recipes/bioconductor-rebet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rebet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rebet/meta.yaml b/recipes/bioconductor-rebet/meta.yaml new file mode 100644 index 0000000000000..065ee7a92e0c0 --- /dev/null +++ b/recipes/bioconductor-rebet/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.0.0" %} +{% set name = "REBET" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f48ce39437f7c86e3685d0426ba8083c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-asset >=2.0.0,<2.1.0' + - r-base + run: + - 'bioconductor-asset >=2.0.0,<2.1.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'There is an increasing focus to investigate the association between rare variants and diseases. The REBET package implements the subREgion-based BurdEn Test which is a powerful burden test that simultaneously identifies susceptibility loci and sub-regions.' + diff --git a/recipes/bioconductor-recount/build.sh b/recipes/bioconductor-recount/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-recount/build.sh +++ b/recipes/bioconductor-recount/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-recount/conda_build_config.yaml b/recipes/bioconductor-recount/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-recount/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-recount/meta.yaml b/recipes/bioconductor-recount/meta.yaml index e92599b61abc5..b0a0f175f8e5e 100644 --- a/recipes/bioconductor-recount/meta.yaml +++ b/recipes/bioconductor-recount/meta.yaml @@ -1,46 +1,48 @@ -{% set version = "1.6.3" %} +{% set version = "1.8.1" %} {% set name = "recount" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1ab27e802bfae64af83cd10d97c40bee50fa3eb97184e627b018778d81d1907c + md5: b2277eb66cef0baf558f8b9a3fbc9d7e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: AnnotationDbi, BiocManager, BiocStyle (>= 2.5.19), DESeq2, sessioninfo, EnsDb.Hsapiens.v79, GenomicFeatures, knitcitations, knitr (>= 1.6), org.Hs.eg.db, RefManageR, regionReport (>= 1.9.4), rmarkdown (>= 0.9.5), testthat requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-derfinder >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-downloader - r-rcurl - r-rentrez run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-derfinder >=1.14.0,<1.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-downloader - r-rcurl @@ -49,8 +51,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Explore and download data from the recount project available at https://jhubiostatistics.shinyapps.io/recount/. Using the recount package you can download RangedSummarizedExperiment objects at the gene, exon or exon-exon junctions level, the raw counts, the phenotype metadata used, the urls to the sample coverage bigWig files or the mean coverage bigWig file for a particular study. The RangedSummarizedExperiment objects can be used by different packages for performing differential expression analysis. Using http://bioconductor.org/packages/derfinder you can perform annotation-agnostic differential expression analyses with the data from the recount project as described at http://www.nature.com/nbt/journal/v35/n4/full/nbt.3838.html.' - +extra: + parent_recipe: + name: bioconductor-recount + path: recipes/bioconductor-recount + version: 1.6.3 diff --git a/recipes/bioconductor-recoup/build.sh b/recipes/bioconductor-recoup/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-recoup/build.sh +++ b/recipes/bioconductor-recoup/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-recoup/meta.yaml b/recipes/bioconductor-recoup/meta.yaml index 5a1ff9ae97135..a6b5275d96ec4 100644 --- a/recipes/bioconductor-recoup/meta.yaml +++ b/recipes/bioconductor-recoup/meta.yaml @@ -1,40 +1,42 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "recoup" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0aec44ef2f910c4d1d77709d551b9605e7f715f8e9649391e224ceb2e564a541 + md5: 01f46bb984f1c8a7370d9405565609d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: grid, GenomeInfoDb, Rsamtools, BiocStyle, knitr, rmarkdown, zoo, RUnit, BiocManager, BSgenome, RSQLite, RMySQL requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-circlize - r-ggplot2 - r-plyr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' - r-base - r-circlize - r-ggplot2 @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'recoup calculates and plots signal profiles created from short sequence reads derived from Next Generation Sequencing technologies. The profiles provided are either sumarized curve profiles or heatmap profiles. Currently, recoup supports genomic profile plots for reads derived from ChIP-Seq and RNA-Seq experiments. The package uses ggplot2 and ComplexHeatmap graphics facilities for curve and heatmap coverage profiles respectively.' extra: identifiers: - biotools:recoup - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-recoup + path: recipes/bioconductor-recoup + version: 1.8.0 + diff --git a/recipes/bioconductor-reder/build.sh b/recipes/bioconductor-reder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-reder/build.sh +++ b/recipes/bioconductor-reder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-reder/meta.yaml b/recipes/bioconductor-reder/meta.yaml index 44c936d7b10d2..30c6f0c7aace6 100644 --- a/recipes/bioconductor-reder/meta.yaml +++ b/recipes/bioconductor-reder/meta.yaml @@ -1,21 +1,24 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RedeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78ddf06627aac2d18dd49022aeee9abda15853ad6ac8e3fd55042140d3d4a670 + md5: feec78beaad4c43950605f9fb6af3f9d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pvclust, BiocStyle, knitr, rmarkdown +# SystemRequirements: Java Runtime Environment (>= 6) requirements: host: - r-base @@ -27,9 +30,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'RedeR is an R-based package combined with a stand-alone Java application for interactive visualization and manipulation of modular structures, nested networks and multiple levels of hierarchical associations.' extra: identifiers: - biotools:reder + parent_recipe: + name: bioconductor-reder + path: recipes/bioconductor-reder + version: 1.28.0 + diff --git a/recipes/bioconductor-redseq/build.sh b/recipes/bioconductor-redseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-redseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-redseq/meta.yaml b/recipes/bioconductor-redseq/meta.yaml new file mode 100644 index 0000000000000..807a5519ca735 --- /dev/null +++ b/recipes/bioconductor-redseq/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.28.0" %} +{% set name = "REDseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 77974694af5810b7e9cbec3c126cc814 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.celegans.ucsc.ce2 >=1.4.0,<1.5.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'The package includes functions to build restriction enzyme cut site (RECS) map, distribute mapped sequences on the map with five different approaches, find enriched/depleted RECSs for a sample, and identify differentially enriched/depleted RECSs between samples.' + diff --git a/recipes/bioconductor-refnet/build.sh b/recipes/bioconductor-refnet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-refnet/build.sh +++ b/recipes/bioconductor-refnet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-refnet/conda_build_config.yaml b/recipes/bioconductor-refnet/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-refnet/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-refnet/meta.yaml b/recipes/bioconductor-refnet/meta.yaml index 20bd8634948b6..dc0baeb1b9d4f 100644 --- a/recipes/bioconductor-refnet/meta.yaml +++ b/recipes/bioconductor-refnet/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "RefNet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7b3ee3bcdb4ba12dcf66a8df6429c26626aaeaf676351a4dd1365e03fe2881a6 + md5: 5f543dd88c9275d0decf135bffa552dd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, org.Hs.eg.db requirements: host: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-psicquic >=1.18.1,<1.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-psicquic >=1.20.0,<1.21.0' - r-base - r-rcurl - r-shiny run: - - 'bioconductor-annotationhub >=2.12.1,<2.14.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-psicquic >=1.18.1,<1.20.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-psicquic >=1.20.0,<1.21.0' - r-base - r-rcurl - r-shiny @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Molecular interactions with metadata, some archived, some dynamically obtained' extra: identifiers: - biotools:refnet - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-refnet + path: recipes/bioconductor-refnet + version: 1.16.0 + diff --git a/recipes/bioconductor-refplus/build.sh b/recipes/bioconductor-refplus/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-refplus/build.sh +++ b/recipes/bioconductor-refplus/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-refplus/conda_build_config.yaml b/recipes/bioconductor-refplus/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-refplus/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-refplus/meta.yaml b/recipes/bioconductor-refplus/meta.yaml index b56a45e6a7af6..8b54cee2d1f86 100644 --- a/recipes/bioconductor-refplus/meta.yaml +++ b/recipes/bioconductor-refplus/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "RefPlus" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 90233d707debd7503960345dddd5a8c245a18dd981bd09d34258aeeea323e5a2 + md5: 1f3f27dfeccc81b91cef120849de5d1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyplm >=1.56.0,<1.58.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyplm >=1.56.0,<1.58.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyplm >=1.58.0,<1.59.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains functions for pre-processing Affymetrix data using the RMA+ and the RMA++ methods.' extra: identifiers: - biotools:refplus - doi:10.1093/bioinformatics/btm357 + parent_recipe: + name: bioconductor-refplus + path: recipes/bioconductor-refplus + version: 1.50.0 + diff --git a/recipes/bioconductor-regioner/build.sh b/recipes/bioconductor-regioner/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-regioner/build.sh +++ b/recipes/bioconductor-regioner/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regioner/meta.yaml b/recipes/bioconductor-regioner/meta.yaml index 6b57e0559e5cd..ae7d2b900b559 100644 --- a/recipes/bioconductor-regioner/meta.yaml +++ b/recipes/bioconductor-regioner/meta.yaml @@ -1,47 +1,56 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "regioneR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4b7758319a8dc7db5b57d7d21e693da081a29af089fde1e9affcf8d7b0a27f25 + md5: 526f133b01e3b43e3e1e72a1c34b4076 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, BSgenome.Hsapiens.UCSC.hg19.masked, testthat requirements: host: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-memoise run: - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-memoise test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'regioneR offers a statistical framework based on customizable permutation tests to assess the association between genomic region sets and other genomic features.' extra: identifiers: - biotools:regioner + parent_recipe: + name: bioconductor-regioner + path: recipes/bioconductor-regioner + version: 1.12.0 + diff --git a/recipes/bioconductor-regionreport/build.sh b/recipes/bioconductor-regionreport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-regionreport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regionreport/meta.yaml b/recipes/bioconductor-regionreport/meta.yaml new file mode 100644 index 0000000000000..2333b2cd421a6 --- /dev/null +++ b/recipes/bioconductor-regionreport/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.16.1" %} +{% set name = "regionReport" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 52d87e72b67f0cbe611fbf647ccbff39 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocManager, biovizBase, bumphunter (>= 1.7.6), derfinderPlot (>= 1.3.2), sessioninfo, DT, DESeq, edgeR, ggbio (>= 1.13.13), ggplot2, grid, gridExtra, IRanges, mgcv, pasilla, pheatmap, RColorBrewer, TxDb.Hsapiens.UCSC.hg19.knownGene, whisker +requirements: + host: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deformats >=1.10.0,<1.11.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-knitcitations >=1.0.1' + - 'r-knitr >=1.6' + - 'r-knitrbootstrap >=0.9.0' + - r-refmanager + - 'r-rmarkdown >=0.9.5' + run: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deformats >=1.10.0,<1.11.0' + - 'bioconductor-derfinder >=1.16.0,<1.17.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - 'r-knitcitations >=1.0.1' + - 'r-knitr >=1.6' + - 'r-knitrbootstrap >=0.9.0' + - r-refmanager + - 'r-rmarkdown >=0.9.5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Generate HTML or PDF reports to explore a set of regions such as the results from annotation-agnostic expression analysis of RNA-seq data at base-pair resolution performed by derfinder. You can also create reports for DESeq2 or edgeR results.' + diff --git a/recipes/bioconductor-regparallel/meta.yaml b/recipes/bioconductor-regparallel/meta.yaml new file mode 100644 index 0000000000000..1e1defc858ade --- /dev/null +++ b/recipes/bioconductor-regparallel/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.0.0" %} +{% set name = "RegParallel" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dbfebc547b8aaf83e060210498e8492a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, DESeq2, airway, magrittr, Biobase, GEOquery, biomaRt, survminer +requirements: + host: + - r-arm + - r-base + - r-data.table + - r-doparallel + - r-foreach + - r-iterators + - r-mass + - r-stringr + - r-survival + run: + - r-arm + - r-base + - r-data.table + - r-doparallel + - r-foreach + - r-iterators + - r-mass + - r-stringr + - r-survival + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'In many analyses, a large amount of variables have to be tested independently against the trait/endpoint of interest, and also adjusted for covariates and confounding factors at the same time. The major bottleneck in these is the amount of time that it takes to complete these analyses. With RegParallel, a large number of tests can be performed simultaneously. On a 12-core system, 144 variables can be tested simultaneously, with 1000s of variables processed in a matter of seconds via ''nested'' parallel processing. Works for logistic regression, linear regression, conditional logistic regression, Cox proportional hazards and survival models, Bayesian logistic regression, and negative binomial regression.' + diff --git a/recipes/bioconductor-regparallel/post-link.sh b/recipes/bioconductor-regparallel/post-link.sh new file mode 100644 index 0000000000000..1a3d4b0b7b7d7 --- /dev/null +++ b/recipes/bioconductor-regparallel/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RegParallel_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RegParallel_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/RegParallel_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-regparallel/bioconductor-regparallel_1.0.0_src_all.tar.gz" +) +MD5="dbfebc547b8aaf83e060210498e8492a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-regparallel/pre-unlink.sh b/recipes/bioconductor-regparallel/pre-unlink.sh new file mode 100644 index 0000000000000..890c882d52831 --- /dev/null +++ b/recipes/bioconductor-regparallel/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RegParallel diff --git a/recipes/bioconductor-regsplice/build.sh b/recipes/bioconductor-regsplice/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-regsplice/build.sh +++ b/recipes/bioconductor-regsplice/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-regsplice/meta.yaml b/recipes/bioconductor-regsplice/meta.yaml index 7b684590dc286..ad0f7064abc5a 100644 --- a/recipes/bioconductor-regsplice/meta.yaml +++ b/recipes/bioconductor-regsplice/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "regsplice" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 4031a2ddf1e35f3a9dee96596786d3b461c706aa4e0c419fc9520bd9506fcfbd + md5: b16a6d2c1bf9d695e268a1d515fe9230 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-glmnet - r-pbapply run: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-glmnet - r-pbapply @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Statistical methods for detection of differential splicing (differential exon usage) in RNA-seq and exon microarray data, using L1-regularization (lasso) to improve power.' extra: identifiers: - biotools:regsplice - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-regsplice + path: recipes/bioconductor-regsplice + version: 1.6.0 + diff --git a/recipes/bioconductor-remp/build.sh b/recipes/bioconductor-remp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-remp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-remp/meta.yaml b/recipes/bioconductor-remp/meta.yaml new file mode 100644 index 0000000000000..216e82f435df3 --- /dev/null +++ b/recipes/bioconductor-remp/meta.yaml @@ -0,0 +1,77 @@ +{% set version = "1.6.0" %} +{% set name = "REMP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b0b025520740209fff8d5ea2e3f3ce22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, minfiDataEPIC +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-caret + - r-doparallel + - r-foreach + - r-iterators + - r-kernlab + - r-ranger + - r-settings + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-caret + - r-doparallel + - r-foreach + - r-iterators + - r-kernlab + - r-ranger + - r-settings +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Machine learning-based tools to predict DNA methylation of locus-specific repetitive elements (RE) by learning surrounding genetic and epigenetic information. These tools provide genomewide and single-base resolution of DNA methylation prediction on RE that are difficult to measure using array-based or sequencing-based platforms, which enables epigenome-wide association study (EWAS) and differentially methylated region (DMR) analysis on RE.' + diff --git a/recipes/bioconductor-repitools/build.sh b/recipes/bioconductor-repitools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-repitools/build.sh +++ b/recipes/bioconductor-repitools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-repitools/conda_build_config.yaml b/recipes/bioconductor-repitools/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-repitools/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-repitools/meta.yaml b/recipes/bioconductor-repitools/meta.yaml index 490f7ba99eb25..bf30bcf12acde 100644 --- a/recipes/bioconductor-repitools/meta.yaml +++ b/recipes/bioconductor-repitools/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Repitools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cc74a0f353877f2ddb9f013fd969dec74fa0f9605701c96c159248704e653932 + md5: 59c4e8b79e061909762b5e6d25f55510 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: ShortRead, BSgenome.Hsapiens.UCSC.hg18 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-aroma.affymetrix - r-base - r-cluster @@ -39,19 +40,19 @@ requirements: - r-mass - r-rsolnp run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-dnacopy >=1.54.0,<1.56.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-aroma.affymetrix - r-base - r-cluster @@ -66,9 +67,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Tools for the analysis of enrichment-based epigenomic data. Features include summarization and visualization of epigenomic data across promoters according to gene expression context, finding regions of differential methylation/binding, BayMeth for quantifying methylation etc.' extra: identifiers: - biotools:repitools + parent_recipe: + name: bioconductor-repitools + path: recipes/bioconductor-repitools + version: 1.26.0 + diff --git a/recipes/bioconductor-reportingtools/build.sh b/recipes/bioconductor-reportingtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-reportingtools/build.sh +++ b/recipes/bioconductor-reportingtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-reportingtools/conda_build_config.yaml b/recipes/bioconductor-reportingtools/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-reportingtools/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-reportingtools/meta.yaml b/recipes/bioconductor-reportingtools/meta.yaml index 6a9143751fd01..cebb0bd767aa0 100644 --- a/recipes/bioconductor-reportingtools/meta.yaml +++ b/recipes/bioconductor-reportingtools/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "ReportingTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 78fbf2d6b98f7683f303c551de46ec75077b35459febebcb827286b391c57e6d + md5: 0e52900be927455f8033469f28d8b492 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, ALL, hgu95av2.db, org.Mm.eg.db, shiny, pasilla, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pfam.db >=3.6.0,<3.8.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pfam.db >=3.7.0,<3.8.0' - r-base - r-ggplot2 - r-hwriter @@ -39,19 +41,19 @@ requirements: - r-r.utils - r-xml run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-category >=2.46.0,<2.48.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-pfam.db >=3.6.0,<3.8.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-category >=2.48.0,<2.49.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-pfam.db >=3.7.0,<3.8.0' - r-base - r-ggplot2 - r-hwriter @@ -63,9 +65,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The ReportingTools software package enables users to easily display reports of analysis results generated from sources such as microarray and sequencing data. The package allows users to create HTML pages that may be viewed on a web browser such as Safari, or in other formats readable by programs such as Excel. Users can generate tables with sortable and filterable columns, make and display plots, and link table entries to other data sources such as NCBI or larger plots within the HTML page. Using the package, users can also produce a table of contents page to link various reports together for a particular project that can be viewed in a web browser. For more examples, please visit our site: http:// research-pub.gene.com/ReportingTools.' extra: identifiers: - biotools:reportingtools + parent_recipe: + name: bioconductor-reportingtools + path: recipes/bioconductor-reportingtools + version: 2.20.0 + diff --git a/recipes/bioconductor-reqon/build.sh b/recipes/bioconductor-reqon/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-reqon/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-reqon/meta.yaml b/recipes/bioconductor-reqon/meta.yaml new file mode 100644 index 0000000000000..37249ec3ccbbc --- /dev/null +++ b/recipes/bioconductor-reqon/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.28.0" %} +{% set name = "ReQON" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4e9e1fd5a4b1c189e039a97dff587ccb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +# SystemRequirements: Java version >= 1.6 +requirements: + host: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-seqbias >=1.30.0,<1.31.0' + - r-base + - r-rjava + run: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-seqbias >=1.30.0,<1.31.0' + - r-base + - r-rjava +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Algorithm for recalibrating the base quality scores for aligned sequencing data in BAM format.' + diff --git a/recipes/bioconductor-restfulse/build.sh b/recipes/bioconductor-restfulse/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-restfulse/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-restfulse/meta.yaml b/recipes/bioconductor-restfulse/meta.yaml new file mode 100644 index 0000000000000..23f15ed36f356 --- /dev/null +++ b/recipes/bioconductor-restfulse/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.4.0" %} +{% set name = "restfulSE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 71a91f399fd3f3cbfc5a7b2009c15696 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, Rtsne, org.Mm.eg.db, org.Hs.eg.db, BiocStyle +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-rhdf5client >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bigrquery + - r-dbi + - 'r-dplyr >=0.7.1' + - r-magrittr + - r-reshape2 + - r-rlang + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-rhdf5client >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bigrquery + - r-dbi + - 'r-dplyr >=0.7.1' + - r-magrittr + - r-reshape2 + - r-rlang +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides functions and classes to interface with remote data stores by operating on SummarizedExperiment-like objects.' + diff --git a/recipes/bioconductor-restfulsedata/meta.yaml b/recipes/bioconductor-restfulsedata/meta.yaml new file mode 100644 index 0000000000000..63b4b9345e411 --- /dev/null +++ b/recipes/bioconductor-restfulsedata/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.4.0" %} +{% set name = "restfulSEData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a4008a223e2c5417f8f164fb3b2d3752 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Metadata RangedSummarizedExperiment shell for use with restfulSE.' + diff --git a/recipes/bioconductor-restfulsedata/post-link.sh b/recipes/bioconductor-restfulsedata/post-link.sh new file mode 100644 index 0000000000000..cf47f0955f61d --- /dev/null +++ b/recipes/bioconductor-restfulsedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="restfulSEData_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/restfulSEData_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/restfulSEData_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-restfulsedata/bioconductor-restfulsedata_1.4.0_src_all.tar.gz" +) +MD5="a4008a223e2c5417f8f164fb3b2d3752" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-restfulsedata/pre-unlink.sh b/recipes/bioconductor-restfulsedata/pre-unlink.sh new file mode 100644 index 0000000000000..89c984be2d60d --- /dev/null +++ b/recipes/bioconductor-restfulsedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ restfulSEData diff --git a/recipes/bioconductor-rexposome/build.sh b/recipes/bioconductor-rexposome/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rexposome/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rexposome/meta.yaml b/recipes/bioconductor-rexposome/meta.yaml new file mode 100644 index 0000000000000..0d0f27774ebab --- /dev/null +++ b/recipes/bioconductor-rexposome/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.4.0" %} +{% set name = "rexposome" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ba602e53b72ac2e89c0206164a9f6df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: mclust, flexmix, testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-circlize + - r-corrplot + - r-factominer + - r-ggplot2 + - r-ggrepel + - r-glmnet + - r-gplots + - r-gridextra + - r-gtools + - r-hmisc + - r-imputelcmd + - r-lme4 + - r-lsr + - r-mice + - r-pryr + - r-reshape2 + - r-scales + - r-scatterplot3d + - r-stringr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-circlize + - r-corrplot + - r-factominer + - r-ggplot2 + - r-ggrepel + - r-glmnet + - r-gplots + - r-gridextra + - r-gtools + - r-hmisc + - r-imputelcmd + - r-lme4 + - r-lsr + - r-mice + - r-pryr + - r-reshape2 + - r-scales + - r-scatterplot3d + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Package that allows to explore the exposome and to perform association analyses between exposures and health outcomes.' + diff --git a/recipes/bioconductor-rforproteomics/meta.yaml b/recipes/bioconductor-rforproteomics/meta.yaml new file mode 100644 index 0000000000000..3df3f684c0071 --- /dev/null +++ b/recipes/bioconductor-rforproteomics/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.20.0" %} +{% set name = "RforProteomics" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c2df3edec11e6ebf57e0c7b7c19c3e14 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: AnnotationDbi, rpx, DT, knitr, rmarkdown, BiocStyle, mzR, xcms, msdata, isobar, MALDIquant (>= 1.12), MALDIquantForeign, readBrukerFlexData, rTANDEM, synapter, synapterdata, IPPD, Rdisop, OrgMassSpecR, SummarizedExperiment, BRAIN, rols, hpar, GO.db, org.Hs.eg.db, e1071, biomaRt, RColorBrewer, ggplot2, reshape2, xtable, lattice, mzID, pRoloc, pRolocdata, MSGFplus, MSGFgui, MSnID, msmsTests, msmsEDA, DEP, corrplot, beanplot, Heatplus, gplots, VennDiagram, protViz, genefilter, plotly, gridExtra, dplyr, lubridate +requirements: + host: + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + - r-biocmanager + - r-r.utils + - r-shiny + run: + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - r-base + - r-biocmanager + - r-r.utils + - r-shiny + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains code to illustrate the ''Using R and Bioconductor for proteomics data analysis'' and ''Visualisation of proteomics data using R and Bioconductor'' manuscripts. The vignettes describe the code and data needed to reproduce the examples and figures described in the paper and functionality for proteomics visualisation. It also contain various function to discover R software for mass spectrometry and proteomics.' + diff --git a/recipes/bioconductor-rforproteomics/post-link.sh b/recipes/bioconductor-rforproteomics/post-link.sh new file mode 100644 index 0000000000000..2afce6ddc2630 --- /dev/null +++ b/recipes/bioconductor-rforproteomics/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RforProteomics_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RforProteomics_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/RforProteomics_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rforproteomics/bioconductor-rforproteomics_1.20.0_src_all.tar.gz" +) +MD5="c2df3edec11e6ebf57e0c7b7c19c3e14" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rforproteomics/pre-unlink.sh b/recipes/bioconductor-rforproteomics/pre-unlink.sh new file mode 100644 index 0000000000000..20dad66e74a7c --- /dev/null +++ b/recipes/bioconductor-rforproteomics/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RforProteomics diff --git a/recipes/bioconductor-rfpred/build.sh b/recipes/bioconductor-rfpred/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rfpred/build.sh +++ b/recipes/bioconductor-rfpred/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rfpred/meta.yaml b/recipes/bioconductor-rfpred/meta.yaml index 7fd4bc6e649a8..15446b9b6fdb3 100644 --- a/recipes/bioconductor-rfpred/meta.yaml +++ b/recipes/bioconductor-rfpred/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "rfPred" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9515489fd5b14bd5e694569e9c25abd978c9f16f91a2125ee834441fda42efde + md5: 9d76d084ffbc2c95925accca4d39888b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-data.table run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-data.table build: @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2 )' summary: 'Based on external numerous data files where rfPred scores are pre-calculated on all genomic positions of the human exome, the package gives rfPred scores to missense variants identified by the chromosome, the position (hg19 version), the referent and alternative nucleotids and the uniprot identifier of the protein. Note that for using the package, the user has to be connected on the Internet or to download the TabixFile and index (approximately 3.3 Go).' extra: identifiers: - biotools:rfpred - doi:10.1101/037127 + parent_recipe: + name: bioconductor-rfpred + path: recipes/bioconductor-rfpred + version: 1.18.0 + diff --git a/recipes/bioconductor-rgadem/build.sh b/recipes/bioconductor-rgadem/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgadem/build.sh +++ b/recipes/bioconductor-rgadem/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgadem/meta.yaml b/recipes/bioconductor-rgadem/meta.yaml index fe93954dddeae..ba53a7e1c4ec0 100644 --- a/recipes/bioconductor-rgadem/meta.yaml +++ b/recipes/bioconductor-rgadem/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "rGADEM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4110213eb8d289cb19976c6a7242ec5b456675b8694e25c721f1566c33616dd6 + md5: 6c91a120a1451994f8a92d7a61b55662 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base build: - {{ compiler('c') }} @@ -37,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'rGADEM is an efficient de novo motif discovery tool for large-scale genomic sequence data. It is an open-source R package, which is based on the GADEM software.' extra: identifiers: - biotools:rgadem - doi:10.1371/journal.pone.0016432 + parent_recipe: + name: bioconductor-rgadem + path: recipes/bioconductor-rgadem + version: 2.28.0 + diff --git a/recipes/bioconductor-rgalaxy/build.sh b/recipes/bioconductor-rgalaxy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgalaxy/build.sh +++ b/recipes/bioconductor-rgalaxy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgalaxy/meta.yaml b/recipes/bioconductor-rgalaxy/meta.yaml index 22133654f98ed..84e9c60f8f4ca 100644 --- a/recipes/bioconductor-rgalaxy/meta.yaml +++ b/recipes/bioconductor-rgalaxy/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "RGalaxy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d6af5d039da3df327100f7400be4697ec0341d4a361222856a15b0dcf5719a91 + md5: b88c6f6f410d2f852096e69ebbe040d1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, hgu95av2.db, AnnotationDbi, knitr, formatR, Rserve requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-optparse - r-roxygen2 - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-optparse - r-roxygen2 @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Given an R function and its manual page, make the documented function available in Galaxy.' extra: identifiers: - biotools:rgalaxy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgalaxy + path: recipes/bioconductor-rgalaxy + version: 1.24.0 + diff --git a/recipes/bioconductor-rgin/build.sh b/recipes/bioconductor-rgin/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rgin/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgin/meta.yaml b/recipes/bioconductor-rgin/meta.yaml new file mode 100644 index 0000000000000..3eb8ee1324e27 --- /dev/null +++ b/recipes/bioconductor-rgin/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.2.0" %} +{% set name = "Rgin" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2d535bbeb2ba5810a0112f6c211a27a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - 'r-rcppeigen >=0.3.3.3.0' + run: + - r-base + - 'r-rcppeigen >=0.3.3.3.0' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'C++ implementation of SConES.' + diff --git a/recipes/bioconductor-rgmql/build.sh b/recipes/bioconductor-rgmql/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rgmql/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgmql/meta.yaml b/recipes/bioconductor-rgmql/meta.yaml new file mode 100644 index 0000000000000..173c170e72163 --- /dev/null +++ b/recipes/bioconductor-rgmql/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "RGMQL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ecee8f65b339090d4a4d9a0db3311424 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rgmqllib >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-dplyr + - r-glue + - r-httr + - r-plyr + - r-rjava + - r-xml2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rgmqllib >=1.2.0,<1.3.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-dplyr + - r-glue + - r-httr + - r-plyr + - r-rjava + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package brings the GenoMetric Query Language (GMQL) functionalities into the R environment. GMQL is a high-level, declarative language to manage heterogeneous genomic datasets for biomedical purposes, using simple queries to process genomic regions and their metadata and properties. GMQL adopts algorithms efficiently designed for big data using cloud-computing technologies (like Apache Hadoop and Spark) allowing GMQL to run on modern infrastructures, in order to achieve scalability and high performance. It allows to create, manipulate and extract genomic data from different data sources both locally and remotely. Our RGMQL functions allow complex queries and processing leveraging on the R idiomatic paradigm. The RGMQL package also provides a rich set of ancillary classes that allow sophisticated input/output management and sorting, such as: ASC, DESC, BAG, MIN, MAX, SUM, AVG, MEDIAN, STD, Q1, Q2, Q3 (and many others). Note that many RGMQL functions are not directly executed in R environment, but are deferred until real execution is issued.' + diff --git a/recipes/bioconductor-rgmqllib/meta.yaml b/recipes/bioconductor-rgmqllib/meta.yaml new file mode 100644 index 0000000000000..0acab165e663c --- /dev/null +++ b/recipes/bioconductor-rgmqllib/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "RGMQLlib" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 71eae8b46e7104c9733252c6162002f6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package that contains scala libraries to call GMQL from R used by RGMQL package. It contains a scalable data management engine written in Scala programming language.' + diff --git a/recipes/bioconductor-rgmqllib/post-link.sh b/recipes/bioconductor-rgmqllib/post-link.sh new file mode 100644 index 0000000000000..a09d31b2f8db2 --- /dev/null +++ b/recipes/bioconductor-rgmqllib/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RGMQLlib_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RGMQLlib_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RGMQLlib_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgmqllib/bioconductor-rgmqllib_1.2.0_src_all.tar.gz" +) +MD5="71eae8b46e7104c9733252c6162002f6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgmqllib/pre-unlink.sh b/recipes/bioconductor-rgmqllib/pre-unlink.sh new file mode 100644 index 0000000000000..bef2439754672 --- /dev/null +++ b/recipes/bioconductor-rgmqllib/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RGMQLlib diff --git a/recipes/bioconductor-rgraph2js/build.sh b/recipes/bioconductor-rgraph2js/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgraph2js/build.sh +++ b/recipes/bioconductor-rgraph2js/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgraph2js/meta.yaml b/recipes/bioconductor-rgraph2js/meta.yaml index effb2ac392ad1..0fe766ef516b3 100644 --- a/recipes/bioconductor-rgraph2js/meta.yaml +++ b/recipes/bioconductor-rgraph2js/meta.yaml @@ -1,30 +1,33 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RGraph2js" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2dbf5f4f599396ccbe9ffffe1ed0576db16d94d0cf2ca62637a7a7c98ffbef88 + md5: e407635c0ffbdb22152a1313025a8b4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, BiocGenerics, xtable, sna +# SystemRequirements: jQuery, jQueryUI, qTip2, D3js and Raphael are required Javascript libraries made available via the online CDNJS service (http://cdnjs.cloudflare.com). requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-digest - r-rjson - r-whisker run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-digest - r-rjson @@ -33,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Generator of web pages which display interactive network/graph visualizations with D3js, jQuery and Raphael.' extra: identifiers: - biotools:rgraph2js - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgraph2js + path: recipes/bioconductor-rgraph2js + version: 1.8.0 + diff --git a/recipes/bioconductor-rgraphviz/build.sh b/recipes/bioconductor-rgraphviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgraphviz/build.sh +++ b/recipes/bioconductor-rgraphviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgraphviz/meta.yaml b/recipes/bioconductor-rgraphviz/meta.yaml index 37163f0428505..bb5b6a44147e3 100644 --- a/recipes/bioconductor-rgraphviz/meta.yaml +++ b/recipes/bioconductor-rgraphviz/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "Rgraphviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7ee16deb1c30f60bb5ad1382b99006b2472be61c9523e40d37c4b2dedd876780 + md5: 148a37430c6f20d15b1564cb91796f00 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, XML +# SystemRequirements: optionally Graphviz (>= 2.16) requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base build: - {{ compiler('c') }} @@ -32,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: EPL summary: 'Interfaces R with the AT and T graphviz library for plotting R graph objects from the graph package.' extra: identifiers: - biotools:rgraphviz - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgraphviz + path: recipes/bioconductor-rgraphviz + version: 2.24.0 + diff --git a/recipes/bioconductor-rgreat/build.sh b/recipes/bioconductor-rgreat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgreat/build.sh +++ b/recipes/bioconductor-rgreat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgreat/meta.yaml b/recipes/bioconductor-rgreat/meta.yaml index 413a2c1a58bb4..e60c21f2d70cd 100644 --- a/recipes/bioconductor-rgreat/meta.yaml +++ b/recipes/bioconductor-rgreat/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "rGREAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 21004917b590ea5a9b5146d90980f3c0ec37a752b74a2975f8e6f6a4dc0b899a + md5: c7e906676ad1d4ce133a2d285e10b053 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat (>= 0.3), knitr, circlize requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl - r-rjson run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - 'r-getoptlong >=0.0.9' - r-rcurl @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'MIT + LICENSE' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' summary: 'This package makes GREAT (Genomic Regions Enrichment of Annotations Tool) analysis automatic by constructing a HTTP POST request according to user''s input and automatically retrieving results from GREAT web server.' extra: identifiers: - biotools:rgreat - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgreat + path: recipes/bioconductor-rgreat + version: 1.12.1 + diff --git a/recipes/bioconductor-rgsea/build.sh b/recipes/bioconductor-rgsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgsea/build.sh +++ b/recipes/bioconductor-rgsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgsea/meta.yaml b/recipes/bioconductor-rgsea/meta.yaml index 22fadc3f6fb9d..7f0bcaaa14e91 100644 --- a/recipes/bioconductor-rgsea/meta.yaml +++ b/recipes/bioconductor-rgsea/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RGSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 39d3e7677fe0fcdf0afb8629463be11b917fcf9421d3875802a7e18d943945a2 + md5: 7e45c90d4e1335e8fcc983f9a86e0ac0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, GEOquery, knitr, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=3) summary: 'Combining bootstrap aggregating and Gene set enrichment analysis (GSEA), RGSEA is a classfication algorithm with high robustness and no over-fitting problem. It performs well especially for the data generated from different exprements.' extra: identifiers: - biotools:rgsea - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgsea + path: recipes/bioconductor-rgsea + version: 1.14.0 + diff --git a/recipes/bioconductor-rgsepd/build.sh b/recipes/bioconductor-rgsepd/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rgsepd/build.sh +++ b/recipes/bioconductor-rgsepd/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rgsepd/conda_build_config.yaml b/recipes/bioconductor-rgsepd/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rgsepd/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rgsepd/meta.yaml b/recipes/bioconductor-rgsepd/meta.yaml index 649d805841464..7fd5958a3ac78 100644 --- a/recipes/bioconductor-rgsepd/meta.yaml +++ b/recipes/bioconductor-rgsepd/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "rgsepd" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ff51af7f5824f951b219c0b62ed0ca9d8c1fde7a47526885b55c498c14df72bd + md5: 88a18b7f1243982774b8acfa3c3716f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: boot, tools, BiocGenerics, knitr, xtable requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-gplots - r-hash run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-gplots - r-hash @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R/GSEPD is a bioinformatics package for R to help disambiguate transcriptome samples (a matrix of RNA-Seq counts at RefSeq IDs) by automating differential expression (with DESeq2), then gene set enrichment (with GOSeq), and finally a N-dimensional projection to quantify in which ways each sample is like either treatment group.' extra: identifiers: - biotools:rgsepd - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rgsepd + path: recipes/bioconductor-rgsepd + version: 1.12.0 + diff --git a/recipes/bioconductor-rgu34a.db/meta.yaml b/recipes/bioconductor-rgu34a.db/meta.yaml new file mode 100644 index 0000000000000..89d6e3e20b9e5 --- /dev/null +++ b/recipes/bioconductor-rgu34a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgu34a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b8e7fec45ef9e1423cda3171bb12e34c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Genome U34 Set annotation data (chip rgu34a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgu34a.db/post-link.sh b/recipes/bioconductor-rgu34a.db/post-link.sh new file mode 100644 index 0000000000000..20b52fdb618c2 --- /dev/null +++ b/recipes/bioconductor-rgu34a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34a.db/bioconductor-rgu34a.db_3.2.3_src_all.tar.gz" +) +MD5="b8e7fec45ef9e1423cda3171bb12e34c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34a.db/pre-unlink.sh b/recipes/bioconductor-rgu34a.db/pre-unlink.sh new file mode 100644 index 0000000000000..8bf1dcb4c6d4a --- /dev/null +++ b/recipes/bioconductor-rgu34a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34a.db diff --git a/recipes/bioconductor-rgu34acdf/meta.yaml b/recipes/bioconductor-rgu34acdf/meta.yaml new file mode 100644 index 0000000000000..f5bcef17f6831 --- /dev/null +++ b/recipes/bioconductor-rgu34acdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34acdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: dcfa7ecce00e529f93809759ed837b8d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RG_U34A.cdf file.' + diff --git a/recipes/bioconductor-rgu34acdf/post-link.sh b/recipes/bioconductor-rgu34acdf/post-link.sh new file mode 100644 index 0000000000000..d4cec3b060c3c --- /dev/null +++ b/recipes/bioconductor-rgu34acdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34acdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34acdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34acdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34acdf/bioconductor-rgu34acdf_2.18.0_src_all.tar.gz" +) +MD5="dcfa7ecce00e529f93809759ed837b8d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34acdf/pre-unlink.sh b/recipes/bioconductor-rgu34acdf/pre-unlink.sh new file mode 100644 index 0000000000000..ee52fc97df9b7 --- /dev/null +++ b/recipes/bioconductor-rgu34acdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34acdf diff --git a/recipes/bioconductor-rgu34aprobe/meta.yaml b/recipes/bioconductor-rgu34aprobe/meta.yaml new file mode 100644 index 0000000000000..017a6d4b6fac8 --- /dev/null +++ b/recipes/bioconductor-rgu34aprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34aprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 902aee259a2894fa8713c4bf9266c0e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34A\_probe\_tab.' + diff --git a/recipes/bioconductor-rgu34aprobe/post-link.sh b/recipes/bioconductor-rgu34aprobe/post-link.sh new file mode 100644 index 0000000000000..cf60e0459e448 --- /dev/null +++ b/recipes/bioconductor-rgu34aprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34aprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34aprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34aprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34aprobe/bioconductor-rgu34aprobe_2.18.0_src_all.tar.gz" +) +MD5="902aee259a2894fa8713c4bf9266c0e2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34aprobe/pre-unlink.sh b/recipes/bioconductor-rgu34aprobe/pre-unlink.sh new file mode 100644 index 0000000000000..1fcb002b4cee7 --- /dev/null +++ b/recipes/bioconductor-rgu34aprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34aprobe diff --git a/recipes/bioconductor-rgu34b.db/meta.yaml b/recipes/bioconductor-rgu34b.db/meta.yaml new file mode 100644 index 0000000000000..b51bc01826666 --- /dev/null +++ b/recipes/bioconductor-rgu34b.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgu34b.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d2ad468820c1cfbe94297d423237f5bb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Genome U34 Set annotation data (chip rgu34b) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgu34b.db/post-link.sh b/recipes/bioconductor-rgu34b.db/post-link.sh new file mode 100644 index 0000000000000..a3f3bac85f4c1 --- /dev/null +++ b/recipes/bioconductor-rgu34b.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34b.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34b.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34b.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34b.db/bioconductor-rgu34b.db_3.2.3_src_all.tar.gz" +) +MD5="d2ad468820c1cfbe94297d423237f5bb" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34b.db/pre-unlink.sh b/recipes/bioconductor-rgu34b.db/pre-unlink.sh new file mode 100644 index 0000000000000..85c0b20b19407 --- /dev/null +++ b/recipes/bioconductor-rgu34b.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34b.db diff --git a/recipes/bioconductor-rgu34bcdf/meta.yaml b/recipes/bioconductor-rgu34bcdf/meta.yaml new file mode 100644 index 0000000000000..2395056e66a11 --- /dev/null +++ b/recipes/bioconductor-rgu34bcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34bcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 428b3a39f0d8addd7d863539b8cda6ea +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RG_U34B.cdf file.' + diff --git a/recipes/bioconductor-rgu34bcdf/post-link.sh b/recipes/bioconductor-rgu34bcdf/post-link.sh new file mode 100644 index 0000000000000..6b1a967eca3d1 --- /dev/null +++ b/recipes/bioconductor-rgu34bcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34bcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34bcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34bcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34bcdf/bioconductor-rgu34bcdf_2.18.0_src_all.tar.gz" +) +MD5="428b3a39f0d8addd7d863539b8cda6ea" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34bcdf/pre-unlink.sh b/recipes/bioconductor-rgu34bcdf/pre-unlink.sh new file mode 100644 index 0000000000000..b41cc52ef1689 --- /dev/null +++ b/recipes/bioconductor-rgu34bcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34bcdf diff --git a/recipes/bioconductor-rgu34bprobe/meta.yaml b/recipes/bioconductor-rgu34bprobe/meta.yaml new file mode 100644 index 0000000000000..e0d2aff1aea67 --- /dev/null +++ b/recipes/bioconductor-rgu34bprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34bprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2d6488309c5e54231a18e2ecf5608bb1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34B\_probe\_tab.' + diff --git a/recipes/bioconductor-rgu34bprobe/post-link.sh b/recipes/bioconductor-rgu34bprobe/post-link.sh new file mode 100644 index 0000000000000..8bc4e109e4215 --- /dev/null +++ b/recipes/bioconductor-rgu34bprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34bprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34bprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34bprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34bprobe/bioconductor-rgu34bprobe_2.18.0_src_all.tar.gz" +) +MD5="2d6488309c5e54231a18e2ecf5608bb1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34bprobe/pre-unlink.sh b/recipes/bioconductor-rgu34bprobe/pre-unlink.sh new file mode 100644 index 0000000000000..1f239a9aac229 --- /dev/null +++ b/recipes/bioconductor-rgu34bprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34bprobe diff --git a/recipes/bioconductor-rgu34c.db/meta.yaml b/recipes/bioconductor-rgu34c.db/meta.yaml new file mode 100644 index 0000000000000..df1ae92bb9bff --- /dev/null +++ b/recipes/bioconductor-rgu34c.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgu34c.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 59b66663b8d419599d48301661bfa2c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Genome U34 Set annotation data (chip rgu34c) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgu34c.db/post-link.sh b/recipes/bioconductor-rgu34c.db/post-link.sh new file mode 100644 index 0000000000000..97988923a70e5 --- /dev/null +++ b/recipes/bioconductor-rgu34c.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34c.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34c.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34c.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34c.db/bioconductor-rgu34c.db_3.2.3_src_all.tar.gz" +) +MD5="59b66663b8d419599d48301661bfa2c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34c.db/pre-unlink.sh b/recipes/bioconductor-rgu34c.db/pre-unlink.sh new file mode 100644 index 0000000000000..49b5811caddaa --- /dev/null +++ b/recipes/bioconductor-rgu34c.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34c.db diff --git a/recipes/bioconductor-rgu34ccdf/meta.yaml b/recipes/bioconductor-rgu34ccdf/meta.yaml new file mode 100644 index 0000000000000..38103e88314a5 --- /dev/null +++ b/recipes/bioconductor-rgu34ccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34ccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 556a7130086004d26095594da31c6410 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RG_U34C.cdf file.' + diff --git a/recipes/bioconductor-rgu34ccdf/post-link.sh b/recipes/bioconductor-rgu34ccdf/post-link.sh new file mode 100644 index 0000000000000..d02087f9bb019 --- /dev/null +++ b/recipes/bioconductor-rgu34ccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34ccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34ccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34ccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34ccdf/bioconductor-rgu34ccdf_2.18.0_src_all.tar.gz" +) +MD5="556a7130086004d26095594da31c6410" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34ccdf/pre-unlink.sh b/recipes/bioconductor-rgu34ccdf/pre-unlink.sh new file mode 100644 index 0000000000000..ee8e9bdb6748d --- /dev/null +++ b/recipes/bioconductor-rgu34ccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34ccdf diff --git a/recipes/bioconductor-rgu34cprobe/meta.yaml b/recipes/bioconductor-rgu34cprobe/meta.yaml new file mode 100644 index 0000000000000..4cd1904c9eba2 --- /dev/null +++ b/recipes/bioconductor-rgu34cprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rgu34cprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d1a6c433acd30b95fa7be89147105b74 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RG-U34C\_probe\_tab.' + diff --git a/recipes/bioconductor-rgu34cprobe/post-link.sh b/recipes/bioconductor-rgu34cprobe/post-link.sh new file mode 100644 index 0000000000000..3e41e281ab3ba --- /dev/null +++ b/recipes/bioconductor-rgu34cprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgu34cprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgu34cprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rgu34cprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgu34cprobe/bioconductor-rgu34cprobe_2.18.0_src_all.tar.gz" +) +MD5="d1a6c433acd30b95fa7be89147105b74" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgu34cprobe/pre-unlink.sh b/recipes/bioconductor-rgu34cprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3b3c27f7b5ad8 --- /dev/null +++ b/recipes/bioconductor-rgu34cprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgu34cprobe diff --git a/recipes/bioconductor-rguatlas4k.db/meta.yaml b/recipes/bioconductor-rguatlas4k.db/meta.yaml new file mode 100644 index 0000000000000..01f2a45cb39a1 --- /dev/null +++ b/recipes/bioconductor-rguatlas4k.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rguatlas4k.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6a360676e08319ec5465c47c758110bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Clontech BD Atlas Long Oligos Rat 4K annotation data (chip rguatlas4k) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rguatlas4k.db/post-link.sh b/recipes/bioconductor-rguatlas4k.db/post-link.sh new file mode 100644 index 0000000000000..a6d1413d132fe --- /dev/null +++ b/recipes/bioconductor-rguatlas4k.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rguatlas4k.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rguatlas4k.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rguatlas4k.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rguatlas4k.db/bioconductor-rguatlas4k.db_3.2.3_src_all.tar.gz" +) +MD5="6a360676e08319ec5465c47c758110bd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rguatlas4k.db/pre-unlink.sh b/recipes/bioconductor-rguatlas4k.db/pre-unlink.sh new file mode 100644 index 0000000000000..1fd60692a818d --- /dev/null +++ b/recipes/bioconductor-rguatlas4k.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rguatlas4k.db diff --git a/recipes/bioconductor-rgug4105a.db/meta.yaml b/recipes/bioconductor-rgug4105a.db/meta.yaml new file mode 100644 index 0000000000000..65ce9e572cd0f --- /dev/null +++ b/recipes/bioconductor-rgug4105a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgug4105a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ccf354083ae36a7ae687fb8209c4e5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent annotation data (chip rgug4105a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgug4105a.db/post-link.sh b/recipes/bioconductor-rgug4105a.db/post-link.sh new file mode 100644 index 0000000000000..bc2be09f2757e --- /dev/null +++ b/recipes/bioconductor-rgug4105a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgug4105a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4105a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgug4105a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4105a.db/bioconductor-rgug4105a.db_3.2.3_src_all.tar.gz" +) +MD5="3ccf354083ae36a7ae687fb8209c4e5b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgug4105a.db/pre-unlink.sh b/recipes/bioconductor-rgug4105a.db/pre-unlink.sh new file mode 100644 index 0000000000000..f4937f6046069 --- /dev/null +++ b/recipes/bioconductor-rgug4105a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgug4105a.db diff --git a/recipes/bioconductor-rgug4130a.db/meta.yaml b/recipes/bioconductor-rgug4130a.db/meta.yaml new file mode 100644 index 0000000000000..9f9be92b5032e --- /dev/null +++ b/recipes/bioconductor-rgug4130a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgug4130a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 13643ac109aaf12590a5b6e379609b79 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Rat annotation data (chip rgug4130a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgug4130a.db/post-link.sh b/recipes/bioconductor-rgug4130a.db/post-link.sh new file mode 100644 index 0000000000000..a8ce3eb976c3d --- /dev/null +++ b/recipes/bioconductor-rgug4130a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgug4130a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4130a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgug4130a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4130a.db/bioconductor-rgug4130a.db_3.2.3_src_all.tar.gz" +) +MD5="13643ac109aaf12590a5b6e379609b79" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgug4130a.db/pre-unlink.sh b/recipes/bioconductor-rgug4130a.db/pre-unlink.sh new file mode 100644 index 0000000000000..7da19bebf7852 --- /dev/null +++ b/recipes/bioconductor-rgug4130a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgug4130a.db diff --git a/recipes/bioconductor-rgug4131a.db/meta.yaml b/recipes/bioconductor-rgug4131a.db/meta.yaml new file mode 100644 index 0000000000000..2cba9ee23c501 --- /dev/null +++ b/recipes/bioconductor-rgug4131a.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rgug4131a.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1168d4906fb8ce60cbc0fa6cfa3b8ec6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent "Rat Genome, Whole" annotation data (chip rgug4131a) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rgug4131a.db/post-link.sh b/recipes/bioconductor-rgug4131a.db/post-link.sh new file mode 100644 index 0000000000000..c20034ba70469 --- /dev/null +++ b/recipes/bioconductor-rgug4131a.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rgug4131a.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rgug4131a.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rgug4131a.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rgug4131a.db/bioconductor-rgug4131a.db_3.2.3_src_all.tar.gz" +) +MD5="1168d4906fb8ce60cbc0fa6cfa3b8ec6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rgug4131a.db/pre-unlink.sh b/recipes/bioconductor-rgug4131a.db/pre-unlink.sh new file mode 100644 index 0000000000000..0de44aaa24eab --- /dev/null +++ b/recipes/bioconductor-rgug4131a.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rgug4131a.db diff --git a/recipes/bioconductor-rhdf5/build.sh b/recipes/bioconductor-rhdf5/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rhdf5/build.sh +++ b/recipes/bioconductor-rhdf5/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhdf5/meta.yaml b/recipes/bioconductor-rhdf5/meta.yaml index 85a82ee88c089..2c0b64fb1695e 100644 --- a/recipes/bioconductor-rhdf5/meta.yaml +++ b/recipes/bioconductor-rhdf5/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "2.24.0" %} +{% set version = "2.26.0" %} {% set name = "rhdf5" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a6bb589b3f785661965df73713f62c5db6ef719a1fbcfe48ba76a10921ab9595 + md5: 75cedfb5317f0d5e835779722a453fd7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: bit64, BiocStyle, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - r-base run: - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' - r-base build: - {{ compiler('c') }} @@ -31,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package provides an interface between HDF5 and R. HDF5''s main features are the ability to store and access very large and/or complex datasets and a wide variety of metadata on mass storage (disk) through a completely portable file format. The rhdf5 package is thus suited for the exchange of large and/or complex datasets between R and other software package, and for letting R applications work on datasets that are larger than the available RAM.' extra: identifiers: - biotools:rhdf5 + parent_recipe: + name: bioconductor-rhdf5 + path: recipes/bioconductor-rhdf5 + version: 2.24.0 + diff --git a/recipes/bioconductor-rhdf5client/build.sh b/recipes/bioconductor-rhdf5client/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rhdf5client/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhdf5client/meta.yaml b/recipes/bioconductor-rhdf5client/meta.yaml new file mode 100644 index 0000000000000..d643f988ef000 --- /dev/null +++ b/recipes/bioconductor-rhdf5client/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "rhdf5client" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b4457b3af9a3d99673584ff9444eaeca +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, testthat, BiocStyle, DT, reticulate +requirements: + host: + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-httr + - r-r6 + - r-rjson + run: + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-httr + - r-r6 + - r-rjson + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides functionality for reading data from h5serv server from within R.' + diff --git a/recipes/bioconductor-rhdf5lib/build.sh b/recipes/bioconductor-rhdf5lib/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rhdf5lib/build.sh +++ b/recipes/bioconductor-rhdf5lib/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhdf5lib/meta.yaml b/recipes/bioconductor-rhdf5lib/meta.yaml index cb88e9dafa167..531370cddb78e 100644 --- a/recipes/bioconductor-rhdf5lib/meta.yaml +++ b/recipes/bioconductor-rhdf5lib/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.2" %} {% set name = "Rhdf5lib" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c74f2f3acd9119af339412aa67aef295aed62b2f03d8236cc106dc31453a9f8 + md5: 05dbaf6e2c8cebfe41e4e5a98f8a75ed build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, rmarkdown +# SystemRequirements: GNU make requirements: host: - r-base @@ -29,8 +31,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Provides C and C++ hdf5 libraries.' - +extra: + parent_recipe: + name: bioconductor-rhdf5lib + path: recipes/bioconductor-rhdf5lib + version: 1.2.1 diff --git a/recipes/bioconductor-rhesus.db0/meta.yaml b/recipes/bioconductor-rhesus.db0/meta.yaml new file mode 100644 index 0000000000000..420e79f1bda21 --- /dev/null +++ b/recipes/bioconductor-rhesus.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "rhesus.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c93d15f3864b15368d896db0961b0b35 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for rhesus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-rhesus.db0/post-link.sh b/recipes/bioconductor-rhesus.db0/post-link.sh new file mode 100644 index 0000000000000..86ff40bc912a4 --- /dev/null +++ b/recipes/bioconductor-rhesus.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rhesus.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesus.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/rhesus.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesus.db0/bioconductor-rhesus.db0_3.7.1_src_all.tar.gz" +) +MD5="c93d15f3864b15368d896db0961b0b35" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rhesus.db0/pre-unlink.sh b/recipes/bioconductor-rhesus.db0/pre-unlink.sh new file mode 100644 index 0000000000000..431ffefb487bb --- /dev/null +++ b/recipes/bioconductor-rhesus.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rhesus.db0 diff --git a/recipes/bioconductor-rhesuscdf/meta.yaml b/recipes/bioconductor-rhesuscdf/meta.yaml new file mode 100644 index 0000000000000..5a074bf79b966 --- /dev/null +++ b/recipes/bioconductor-rhesuscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rhesuscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 994e16da5dd31bc2796d0da40aa2634f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Rhesus.cdf file.' + diff --git a/recipes/bioconductor-rhesuscdf/post-link.sh b/recipes/bioconductor-rhesuscdf/post-link.sh new file mode 100644 index 0000000000000..1f77c9ec4e245 --- /dev/null +++ b/recipes/bioconductor-rhesuscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rhesuscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesuscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rhesuscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesuscdf/bioconductor-rhesuscdf_2.18.0_src_all.tar.gz" +) +MD5="994e16da5dd31bc2796d0da40aa2634f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rhesuscdf/pre-unlink.sh b/recipes/bioconductor-rhesuscdf/pre-unlink.sh new file mode 100644 index 0000000000000..56b48aa8cc304 --- /dev/null +++ b/recipes/bioconductor-rhesuscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rhesuscdf diff --git a/recipes/bioconductor-rhesusprobe/meta.yaml b/recipes/bioconductor-rhesusprobe/meta.yaml new file mode 100644 index 0000000000000..f9fd6da246bc5 --- /dev/null +++ b/recipes/bioconductor-rhesusprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rhesusprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4169c1c997c4c08b027bc7489533e11e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rhesus\_probe\_tab.' + diff --git a/recipes/bioconductor-rhesusprobe/post-link.sh b/recipes/bioconductor-rhesusprobe/post-link.sh new file mode 100644 index 0000000000000..b7229a0358346 --- /dev/null +++ b/recipes/bioconductor-rhesusprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rhesusprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rhesusprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rhesusprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rhesusprobe/bioconductor-rhesusprobe_2.18.0_src_all.tar.gz" +) +MD5="4169c1c997c4c08b027bc7489533e11e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rhesusprobe/pre-unlink.sh b/recipes/bioconductor-rhesusprobe/pre-unlink.sh new file mode 100644 index 0000000000000..b01ec911700c8 --- /dev/null +++ b/recipes/bioconductor-rhesusprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rhesusprobe diff --git a/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml new file mode 100644 index 0000000000000..beb10caca7856 --- /dev/null +++ b/recipes/bioconductor-rheumaticconditionwollbold/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "rheumaticConditionWOLLBOLD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8e65dd2904480c3e37fa19cec75c15c9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: genefilter, Biobase, hgu133plus2.db +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Normalized gene expression data from rheumatic diseases from study published by Wollbold et al. in 2009, provided as an eSet.' + diff --git a/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh new file mode 100644 index 0000000000000..f834b9d124c82 --- /dev/null +++ b/recipes/bioconductor-rheumaticconditionwollbold/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rheumaticConditionWOLLBOLD_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rheumaticConditionWOLLBOLD_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/rheumaticConditionWOLLBOLD_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rheumaticconditionwollbold/bioconductor-rheumaticconditionwollbold_1.20.0_src_all.tar.gz" +) +MD5="8e65dd2904480c3e37fa19cec75c15c9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rheumaticconditionwollbold/pre-unlink.sh b/recipes/bioconductor-rheumaticconditionwollbold/pre-unlink.sh new file mode 100644 index 0000000000000..051b123a61573 --- /dev/null +++ b/recipes/bioconductor-rheumaticconditionwollbold/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rheumaticConditionWOLLBOLD diff --git a/recipes/bioconductor-rhtslib/build.sh b/recipes/bioconductor-rhtslib/build.sh index db15136537a5f..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rhtslib/build.sh +++ b/recipes/bioconductor-rhtslib/build.sh @@ -1,6 +1,11 @@ #!/bin/bash -export C_INCLUDE_PATH=${PREFIX}/include -export LIBRARY_PATH=${PREFIX}/lib mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhtslib/meta.yaml b/recipes/bioconductor-rhtslib/meta.yaml index 362a62785cf70..890c6656def7f 100644 --- a/recipes/bioconductor-rhtslib/meta.yaml +++ b/recipes/bioconductor-rhtslib/meta.yaml @@ -1,42 +1,46 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "Rhtslib" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3f0dc503b927187ea309db17b197eb87c7efb2482b8818da525de4cad0b2dc9b + md5: 0e1ce5e3e5894b9d120087dd9dc40cd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr requirements: - build: - - {{ compiler('c') }} - - automake - - make host: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - - zlib run: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - - zlib + build: + - {{ compiler('c') }} + - automake + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'This package provides version 1.7 of the ''HTSlib'' C library for high-throughput sequence analysis. The package is primarily useful to developers of other R packages who wish to make use of HTSlib. Motivation and instructions for use of this package are in the vignette, vignette(package="Rhtslib", "Rhtslib").' extra: identifiers: - biotools:rhtslib - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rhtslib + path: recipes/bioconductor-rhtslib + version: 1.12.1 + diff --git a/recipes/bioconductor-rhvdm/build.sh b/recipes/bioconductor-rhvdm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rhvdm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rhvdm/meta.yaml b/recipes/bioconductor-rhvdm/meta.yaml new file mode 100644 index 0000000000000..44dce1f6c6b7a --- /dev/null +++ b/recipes/bioconductor-rhvdm/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.48.0" %} +{% set name = "rHVDM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 03b3afcc36d32af3e5f32f14cbbdf79a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-minpack.lm >=1.0-5' + - 'r-r2html >=1.5' + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - 'r-minpack.lm >=1.0-5' + - 'r-r2html >=1.5' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'A R implementation of HVDM (Genome Biol 2006, V7(3) R25)' + diff --git a/recipes/bioconductor-ri16cod.db/meta.yaml b/recipes/bioconductor-ri16cod.db/meta.yaml new file mode 100644 index 0000000000000..18a532f2ddabb --- /dev/null +++ b/recipes/bioconductor-ri16cod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "ri16cod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: cd01b429295fdbba21dbe566effacbdd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Rat Inflammation 16 Bioarray annotation data (chip ri16cod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ri16cod.db/post-link.sh b/recipes/bioconductor-ri16cod.db/post-link.sh new file mode 100644 index 0000000000000..62d920fe1c6b0 --- /dev/null +++ b/recipes/bioconductor-ri16cod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ri16cod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ri16cod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/ri16cod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ri16cod.db/bioconductor-ri16cod.db_3.4.0_src_all.tar.gz" +) +MD5="cd01b429295fdbba21dbe566effacbdd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ri16cod.db/pre-unlink.sh b/recipes/bioconductor-ri16cod.db/pre-unlink.sh new file mode 100644 index 0000000000000..ed819a4acbd82 --- /dev/null +++ b/recipes/bioconductor-ri16cod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ri16cod.db diff --git a/recipes/bioconductor-riboprofiling/build.sh b/recipes/bioconductor-riboprofiling/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-riboprofiling/build.sh +++ b/recipes/bioconductor-riboprofiling/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-riboprofiling/conda_build_config.yaml b/recipes/bioconductor-riboprofiling/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-riboprofiling/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-riboprofiling/meta.yaml b/recipes/bioconductor-riboprofiling/meta.yaml index df78b6291285b..f214be59a31b4 100644 --- a/recipes/bioconductor-riboprofiling/meta.yaml +++ b/recipes/bioconductor-riboprofiling/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RiboProfiling" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 20529dc4f37161a5f8fbae56c1b7f3ddf35a81db9e8de9bb3f354ed9309dd213 + md5: bde2fcd441936a57773f4c14fe283ffe build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, TxDb.Hsapiens.UCSC.hg19.knownGene, BSgenome.Hsapiens.UCSC.hg19, testthat, SummarizedExperiment requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-ggplot2 @@ -36,17 +38,17 @@ requirements: - r-reshape2 - r-sqldf run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-data.table - r-ggplot2 @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Starting with a BAM file, this package provides the necessary functions for quality assessment, read start position recalibration, the counting of reads on CDS, 3''UTR, and 5''UTR, plotting of count data: pairs, log fold-change, codon frequency and coverage assessment, principal component analysis on codon coverage.' extra: identifiers: - biotools:riboprofiling - doi:10.12688/f1000research.8964.1 + parent_recipe: + name: bioconductor-riboprofiling + path: recipes/bioconductor-riboprofiling + version: 1.10.0 + diff --git a/recipes/bioconductor-riboseqr/build.sh b/recipes/bioconductor-riboseqr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-riboseqr/build.sh +++ b/recipes/bioconductor-riboseqr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-riboseqr/meta.yaml b/recipes/bioconductor-riboseqr/meta.yaml index bc4762ed02d14..746fc428d7d64 100644 --- a/recipes/bioconductor-riboseqr/meta.yaml +++ b/recipes/bioconductor-riboseqr/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "riboSeqR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 76db293ebfe2942f9f08df94bd9b0f589ae7a983120695ac741845d858685b75 + md5: 48f5aad232a33ca5f3ab9766c1b246f2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-abind - r-base run: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-abind - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Plotting functions, frameshift detection and parsing of sequencing data from ribosome profiling experiments.' extra: identifiers: - biotools:riboseqr - doi:10.1080/15476286.2016.1141862 + parent_recipe: + name: bioconductor-riboseqr + path: recipes/bioconductor-riboseqr + version: 1.14.0 + diff --git a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml new file mode 100644 index 0000000000000..8b81fc87b0bf3 --- /dev/null +++ b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.00.0" %} +{% set name = "ribosomaldatabaseproject11.5MgDb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b50b3dedc5ed906df4f335c80ad072cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + run: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Metagenome annotation package with for the Ribosomal Database Project 16S rRNA Database version 11.5, Bacterial and Archeal sequences. Contains a MgDb-class object, defined in the metagenomeFeatures package.' + diff --git a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh new file mode 100644 index 0000000000000..792b40118d5e8 --- /dev/null +++ b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" + "https://bioarchive.galaxyproject.org/ribosomaldatabaseproject11.5MgDb_1.00.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ribosomaldatabaseproject11.5mgdb/bioconductor-ribosomaldatabaseproject11.5mgdb_1.00.0_src_all.tar.gz" +) +MD5="b50b3dedc5ed906df4f335c80ad072cf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/pre-unlink.sh b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/pre-unlink.sh new file mode 100644 index 0000000000000..d41a777570fa3 --- /dev/null +++ b/recipes/bioconductor-ribosomaldatabaseproject11.5mgdb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ribosomaldatabaseproject11.5MgDb diff --git a/recipes/bioconductor-ricecdf/meta.yaml b/recipes/bioconductor-ricecdf/meta.yaml new file mode 100644 index 0000000000000..fcdc6205c1dc6 --- /dev/null +++ b/recipes/bioconductor-ricecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ricecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 51db6f51f4adcfb7f4940d07668db8b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Rice.cdf file.' + diff --git a/recipes/bioconductor-ricecdf/post-link.sh b/recipes/bioconductor-ricecdf/post-link.sh new file mode 100644 index 0000000000000..a4a4cb0c0670d --- /dev/null +++ b/recipes/bioconductor-ricecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ricecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ricecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ricecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ricecdf/bioconductor-ricecdf_2.18.0_src_all.tar.gz" +) +MD5="51db6f51f4adcfb7f4940d07668db8b8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ricecdf/pre-unlink.sh b/recipes/bioconductor-ricecdf/pre-unlink.sh new file mode 100644 index 0000000000000..902ced06aea36 --- /dev/null +++ b/recipes/bioconductor-ricecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ricecdf diff --git a/recipes/bioconductor-riceprobe/meta.yaml b/recipes/bioconductor-riceprobe/meta.yaml new file mode 100644 index 0000000000000..4732e479eff40 --- /dev/null +++ b/recipes/bioconductor-riceprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "riceprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2fac7746c343546cf30e6d54bc1e2019 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Rice\_probe\_tab.' + diff --git a/recipes/bioconductor-riceprobe/post-link.sh b/recipes/bioconductor-riceprobe/post-link.sh new file mode 100644 index 0000000000000..46c42cfcc9358 --- /dev/null +++ b/recipes/bioconductor-riceprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="riceprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/riceprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/riceprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-riceprobe/bioconductor-riceprobe_2.18.0_src_all.tar.gz" +) +MD5="2fac7746c343546cf30e6d54bc1e2019" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-riceprobe/pre-unlink.sh b/recipes/bioconductor-riceprobe/pre-unlink.sh new file mode 100644 index 0000000000000..1caa88c175006 --- /dev/null +++ b/recipes/bioconductor-riceprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ riceprobe diff --git a/recipes/bioconductor-rimmport/build.sh b/recipes/bioconductor-rimmport/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rimmport/build.sh +++ b/recipes/bioconductor-rimmport/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rimmport/meta.yaml b/recipes/bioconductor-rimmport/meta.yaml index 44cde35a45cde..e1f3272a3c205 100644 --- a/recipes/bioconductor-rimmport/meta.yaml +++ b/recipes/bioconductor-rimmport/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RImmPort" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f86e5fbf0353d1dba24d22cbf4b5d048793baf67d0534fc60e0937eb011de5a2 + md5: 6912d86ace8499a7be8bbcd2f2496ec5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The RImmPort package simplifies access to ImmPort data for analysis in the R environment. It provides a standards-based interface to the ImmPort study data that is in a proprietary format.' extra: identifiers: - biotools:rimmport - doi:10.1093/bioinformatics/btw719 + parent_recipe: + name: bioconductor-rimmport + path: recipes/bioconductor-rimmport + version: 1.8.0 + diff --git a/recipes/bioconductor-ringo/build.sh b/recipes/bioconductor-ringo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ringo/build.sh +++ b/recipes/bioconductor-ringo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ringo/conda_build_config.yaml b/recipes/bioconductor-ringo/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-ringo/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-ringo/meta.yaml b/recipes/bioconductor-ringo/meta.yaml index dae378b386dd1..cd1b5cd4ae841 100644 --- a/recipes/bioconductor-ringo/meta.yaml +++ b/recipes/bioconductor-ringo/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "Ringo" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d19a7ee45bdd075c73d3c1b9edea43fb83d53386bb29f78062d7832bb27945f9 + md5: 3436818ae4313f8dfab65d0db0e0b86f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: rtracklayer (>= 1.3.1), mclust, topGO (>= 1.15.0) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-lattice - r-matrix - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base - r-lattice - r-matrix @@ -45,9 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.' + summary: 'The package Ringo facilitates the primary analysis of ChIP-chip data. The main functionalities of the package are data read-in, quality assessment, data visualisation and identification of genomic regions showing enrichment in ChIP-chip. The package has functions to deal with two-color oligonucleotide microarrays from NimbleGen used in ChIP-chip projects, but also contains more general functions for ChIP-chip data analysis, given that the data is supplied as RGList (raw) or ExpressionSet (pre- processed). The package employs functions from various other packages of the Bioconductor project and provides additional ChIP-chip-specific and NimbleGen-specific functionalities.' extra: identifiers: - biotools:ringo + parent_recipe: + name: bioconductor-ringo + path: recipes/bioconductor-ringo + version: 1.44.0 + diff --git a/recipes/bioconductor-ripseeker/build.sh b/recipes/bioconductor-ripseeker/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ripseeker/build.sh +++ b/recipes/bioconductor-ripseeker/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ripseeker/meta.yaml b/recipes/bioconductor-ripseeker/meta.yaml index f9afb44aae052..de32bbf146713 100644 --- a/recipes/bioconductor-ripseeker/meta.yaml +++ b/recipes/bioconductor-ripseeker/meta.yaml @@ -1,47 +1,54 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RIPSeeker" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d1f58470199d495f74f8a1a35e9ef0f302e7ecac875c5bd31fb23baaf1df2c79 + md5: ca82b8eb26b72bc28c55f133afcc7c2a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, ChIPpeakAnno, parallel, GenomicFeatures requirements: host: - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer and discriminate RIP peaks from RIP-seq alignments using two-state HMM with negative binomial emission probability. While RIPSeeker is specifically tailored for RIP-seq data analysis, it also provides a suite of bioinformatics tools integrated within this self-contained software package comprehensively addressing issues ranging from post-alignments processing to visualization and annotation.' extra: identifiers: - biotools:ripseeker + parent_recipe: + name: bioconductor-ripseeker + path: recipes/bioconductor-ripseeker + version: 1.20.0 + diff --git a/recipes/bioconductor-ripseekerdata/meta.yaml b/recipes/bioconductor-ripseekerdata/meta.yaml new file mode 100644 index 0000000000000..0740095a0058b --- /dev/null +++ b/recipes/bioconductor-ripseekerdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.18.0" %} +{% set name = "RIPSeekerData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f81b8966e307327aeba0796f80f0e97a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-ripseeker >=1.22.0,<1.23.0' + - r-base + run: + - 'bioconductor-ripseeker >=1.22.0,<1.23.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'The RIP-seq data in BAM format are the test data for the package RIPSeeker. The data correspond to two RIP-seq experiments, namely PRC2 and CCNT1. Raw data from NCBI Gene Expression Omnibus under accession numbers GSE17064 for PRC2 and in-house for CCNT1.' + diff --git a/recipes/bioconductor-ripseekerdata/post-link.sh b/recipes/bioconductor-ripseekerdata/post-link.sh new file mode 100644 index 0000000000000..3a13eb32f60c8 --- /dev/null +++ b/recipes/bioconductor-ripseekerdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RIPSeekerData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RIPSeekerData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/RIPSeekerData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ripseekerdata/bioconductor-ripseekerdata_1.18.0_src_all.tar.gz" +) +MD5="f81b8966e307327aeba0796f80f0e97a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ripseekerdata/pre-unlink.sh b/recipes/bioconductor-ripseekerdata/pre-unlink.sh new file mode 100644 index 0000000000000..6e45c12de0b77 --- /dev/null +++ b/recipes/bioconductor-ripseekerdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RIPSeekerData diff --git a/recipes/bioconductor-risa/build.sh b/recipes/bioconductor-risa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-risa/build.sh +++ b/recipes/bioconductor-risa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-risa/conda_build_config.yaml b/recipes/bioconductor-risa/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-risa/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-risa/meta.yaml b/recipes/bioconductor-risa/meta.yaml index b2097996a8790..2d5f7a031718b 100644 --- a/recipes/bioconductor-risa/meta.yaml +++ b/recipes/bioconductor-risa/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "Risa" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 68e05f197833a1688c6afa66554cc7bb713ce3950eaf7964f20736bf8768ba9b + md5: 7e0030432ea9e984265b3326e1cc08f9 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: faahKO (>= 1.2.11) requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - 'r-rcpp >=0.9.13' run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocviews >=1.48.3,<1.50.0' - - 'bioconductor-xcms >=3.2.0,<3.4.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-xcms >=3.4.0,<3.5.0' - r-base - 'r-rcpp >=0.9.13' build: @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The Investigation / Study / Assay (ISA) tab-delimited format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from experiments employing a combination of technologies, spanning from traditional approaches to high-throughput techniques. Risa allows to access metadata/data in ISA-Tab format and build Bioconductor data structures. Currently, data generated from microarray, flow cytometry and metabolomics-based (i.e. mass spectrometry) assays are supported. The package is extendable and efforts are undergoing to support metadata associated to proteomics assays.' extra: identifiers: - biotools:risa + parent_recipe: + name: bioconductor-risa + path: recipes/bioconductor-risa + version: 1.22.0 + diff --git a/recipes/bioconductor-ritan/build.sh b/recipes/bioconductor-ritan/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ritan/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ritan/meta.yaml b/recipes/bioconductor-ritan/meta.yaml new file mode 100644 index 0000000000000..7de2ac2739299 --- /dev/null +++ b/recipes/bioconductor-ritan/meta.yaml @@ -0,0 +1,69 @@ +{% set version = "1.6.0" %} +{% set name = "RITAN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 922a970ba929bac0ecbc38e9f4496975 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rmarkdown +requirements: + host: + - 'bioconductor-bgeedb >=2.8.0,<2.9.0' + - 'bioconductor-ritandata >=1.6.0,<1.7.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-dynamictreecut + - r-ggplot2 + - r-gplots + - r-gridextra + - r-gsubfn + - r-hash + - r-igraph + - r-knitr + - r-linkcomm + - r-mcl + - r-plotrix + - r-png + - r-rcolorbrewer + - r-reshape2 + - r-sqldf + run: + - 'bioconductor-bgeedb >=2.8.0,<2.9.0' + - 'bioconductor-ritandata >=1.6.0,<1.7.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-dynamictreecut + - r-ggplot2 + - r-gplots + - r-gridextra + - r-gsubfn + - r-hash + - r-igraph + - r-knitr + - r-linkcomm + - r-mcl + - r-plotrix + - r-png + - r-rcolorbrewer + - r-reshape2 + - r-sqldf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Tools for comprehensive gene set enrichment and extraction of multi-resource high confidence subnetworks. RITAN facilitates bioinformatic tasks for enabling network biology research.' + diff --git a/recipes/bioconductor-ritandata/meta.yaml b/recipes/bioconductor-ritandata/meta.yaml new file mode 100644 index 0000000000000..0a0b1accbb6a6 --- /dev/null +++ b/recipes/bioconductor-ritandata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.6.0" %} +{% set name = "RITANdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2cf6bf4546fd2e53d870202ba8b33ad3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Data such as is contained in these two R data files in this package are required for the RITAN package. Users may use their own or additional resources in conjunction with RITANdata. See the RITAN vignettes for more information.' + diff --git a/recipes/bioconductor-ritandata/post-link.sh b/recipes/bioconductor-ritandata/post-link.sh new file mode 100644 index 0000000000000..d2ae9b8cae120 --- /dev/null +++ b/recipes/bioconductor-ritandata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RITANdata_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RITANdata_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/RITANdata_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ritandata/bioconductor-ritandata_1.6.0_src_all.tar.gz" +) +MD5="2cf6bf4546fd2e53d870202ba8b33ad3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ritandata/pre-unlink.sh b/recipes/bioconductor-ritandata/pre-unlink.sh new file mode 100644 index 0000000000000..d63692039fb7c --- /dev/null +++ b/recipes/bioconductor-ritandata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RITANdata diff --git a/recipes/bioconductor-river/build.sh b/recipes/bioconductor-river/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-river/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-river/meta.yaml b/recipes/bioconductor-river/meta.yaml new file mode 100644 index 0000000000000..e5c664f30297b --- /dev/null +++ b/recipes/bioconductor-river/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.0" %} +{% set name = "RIVER" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c71522aa5110c5e162019c2be4531ae +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-ggplot2 + - r-glmnet + - r-proc + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-ggplot2 + - r-glmnet + - r-proc +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'An implementation of a probabilistic modeling framework that jointly analyzes personal genome and transcriptome data to estimate the probability that a variant has regulatory impact in that individual. It is based on a generative model that assumes that genomic annotations, such as the location of a variant with respect to regulatory elements, determine the prior probability that variant is a functional regulatory variant, which is an unobserved variable. The functional regulatory variant status then influences whether nearby genes are likely to display outlier levels of gene expression in that person. See the RIVER website for more information, documentation and examples.' + diff --git a/recipes/bioconductor-rjmcmcnucleosomes/build.sh b/recipes/bioconductor-rjmcmcnucleosomes/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rjmcmcnucleosomes/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml new file mode 100644 index 0000000000000..a27ff3cafabab --- /dev/null +++ b/recipes/bioconductor-rjmcmcnucleosomes/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.6.0" %} +{% set name = "RJMCMCNucleosomes" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 969be4b78d5429790fe5921118ba8b7e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr, rmarkdown, nucleoSim, RUnit +# SystemRequirements: Rcpp +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-consensusseeker >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-rcpp >=0.12.5' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-consensusseeker >=1.10.0,<1.11.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-rcpp >=0.12.5' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package does nucleosome positioning using informative Multinomial-Dirichlet prior in a t-mixture with reversible jump estimation of nucleosome positions for genome-wide profiling.' + diff --git a/recipes/bioconductor-rlmm/build.sh b/recipes/bioconductor-rlmm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rlmm/build.sh +++ b/recipes/bioconductor-rlmm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rlmm/meta.yaml b/recipes/bioconductor-rlmm/meta.yaml index dc0c0e76eebcc..9e8d62277a8d9 100644 --- a/recipes/bioconductor-rlmm/meta.yaml +++ b/recipes/bioconductor-rlmm/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "RLMM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a4489271b863d660b8489cec6b6c947effe33bcdfe1ca52546cd29c9353ad0e7 + md5: 8421a9bb66653cde951b58562ce7aaaf build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# SystemRequirements: Internal files Xba.CQV, Xba.regions (or other regions file) requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'A classification algorithm, based on a multi-chip, multi-SNP approach for Affymetrix SNP arrays. Using a large training sample where the genotype labels are known, this aglorithm will obtain more accurate classification results on new data. RLMM is based on a robust, linear model and uses the Mahalanobis distance for classification. The chip-to-chip non-biological variation is removed through normalization. This model-based algorithm captures the similarities across genotype groups and probes, as well as thousands other SNPs for accurate classification. NOTE: 100K-Xba only at for now.' extra: identifiers: - biotools:rlmm - doi:10.1093/bioinformatics/bti741 + parent_recipe: + name: bioconductor-rlmm + path: recipes/bioconductor-rlmm + version: 1.42.0 + diff --git a/recipes/bioconductor-rmagpie/build.sh b/recipes/bioconductor-rmagpie/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rmagpie/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmagpie/meta.yaml b/recipes/bioconductor-rmagpie/meta.yaml new file mode 100644 index 0000000000000..e402003d45893 --- /dev/null +++ b/recipes/bioconductor-rmagpie/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.38.0" %} +{% set name = "Rmagpie" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dcc38ce1cc7a63089db512988d0e5611 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: xtable +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-e1071 + - r-kernlab + - r-pamr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-e1071 + - r-kernlab + - r-pamr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Microarray Classification is designed for both biologists and statisticians. It offers the ability to train a classifier on a labelled microarray dataset and to then use that classifier to predict the class of new observations. A range of modern classifiers are available, including support vector machines (SVMs), nearest shrunken centroids (NSCs)... Advanced methods are provided to estimate the predictive error rate and to report the subset of genes which appear essential in discriminating between classes.' + diff --git a/recipes/bioconductor-rmassbank/build.sh b/recipes/bioconductor-rmassbank/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rmassbank/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmassbank/meta.yaml b/recipes/bioconductor-rmassbank/meta.yaml new file mode 100644 index 0000000000000..9cf6aa614a6d4 --- /dev/null +++ b/recipes/bioconductor-rmassbank/meta.yaml @@ -0,0 +1,60 @@ +{% set version = "2.10.0" %} +{% set name = "RMassBank" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: be820644e8da8f88c16de86381fd518c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: gplots,RMassBankData, xcms (>= 1.37.1), CAMERA, RUnit, enviPat +# SystemRequirements: OpenBabel +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-digest + - r-httr + - r-rcdk + - r-rcpp + - r-rcurl + - r-rjson + - r-xml + - r-yaml + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-digest + - r-httr + - r-rcdk + - r-rcpp + - r-rcurl + - r-rjson + - r-xml + - r-yaml + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Workflow to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.' + diff --git a/recipes/bioconductor-rmassbankdata/meta.yaml b/recipes/bioconductor-rmassbankdata/meta.yaml new file mode 100644 index 0000000000000..651eeb73af54d --- /dev/null +++ b/recipes/bioconductor-rmassbankdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.20.0" %} +{% set name = "RMassBankData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 46d74376c499336ed7d6f2abbad99b73 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RMassBank +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Example spectra, example compound list(s) and an example annotation list for a narcotics dataset; required to test RMassBank. The package is described in the man page for RMassBankData. Includes new XCMS test data.' + diff --git a/recipes/bioconductor-rmassbankdata/post-link.sh b/recipes/bioconductor-rmassbankdata/post-link.sh new file mode 100644 index 0000000000000..76e9155168170 --- /dev/null +++ b/recipes/bioconductor-rmassbankdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RMassBankData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RMassBankData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/RMassBankData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rmassbankdata/bioconductor-rmassbankdata_1.20.0_src_all.tar.gz" +) +MD5="46d74376c499336ed7d6f2abbad99b73" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rmassbankdata/pre-unlink.sh b/recipes/bioconductor-rmassbankdata/pre-unlink.sh new file mode 100644 index 0000000000000..2bc21c4262c05 --- /dev/null +++ b/recipes/bioconductor-rmassbankdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RMassBankData diff --git a/recipes/bioconductor-rmat/build.sh b/recipes/bioconductor-rmat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rmat/build.sh +++ b/recipes/bioconductor-rmat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmat/meta.yaml b/recipes/bioconductor-rmat/meta.yaml index 5df528c344b2f..24be716e501c8 100644 --- a/recipes/bioconductor-rmat/meta.yaml +++ b/recipes/bioconductor-rmat/meta.yaml @@ -1,36 +1,36 @@ -{% set version = "3.30.0" %} +{% set version = "3.32.0" %} {% set name = "rMAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7c1af420fb92e41e920fda3d05558281986650012415b3ac733e5e35891cf6d3 + md5: c37de71a14cb83a43f58db7c6ce5cbf2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: GenomeGraphs, rtracklayer +# SystemRequirements: GSL (GNU Scientific Library) requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - - openblas run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - - openblas build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -40,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package is an R version of the package MAT and contains functions to parse and merge Affymetrix BPMAP and CEL tiling array files (using C++ based Fusion SDK and Bioconductor package affxparser), normalize tiling arrays using sequence specific models, detect enriched regions from ChIP-chip experiments. Note: users should have GSL and GenomeGraphs installed. Windows users: ''consult the README file available in the inst directory of the source distribution for necessary configuration instructions''. Snow Leopard users can take advantage of increase speed with Grand Central Dispatch!' extra: identifiers: - biotools:rmat - doi:10.1093/bioinformatics/btq023 + parent_recipe: + name: bioconductor-rmat + path: recipes/bioconductor-rmat + version: 3.30.0 + diff --git a/recipes/bioconductor-rmir.hs.mirna/meta.yaml b/recipes/bioconductor-rmir.hs.mirna/meta.yaml index 1d4c2e8f26ac8..111e225f157a9 100644 --- a/recipes/bioconductor-rmir.hs.mirna/meta.yaml +++ b/recipes/bioconductor-rmir.hs.mirna/meta.yaml @@ -1,35 +1,41 @@ {% set version = "1.0.7" %} {% set name = "RmiR.Hs.miRNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 649da235d09f1c8d8cbb0a84bce7085f70ac945b80410bf9d4d9d18a40e2cb5f + md5: 4aedac188382447d9907d2617aa2e8e6 build: - number: 2 + number: 3 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: methods, hgug4112a.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'The Artistic License, Version 2.0' summary: 'Various databases of microRNA Targets' - +extra: + parent_recipe: + name: bioconductor-rmir.hs.mirna + path: recipes/bioconductor-rmir.hs.mirna + version: 1.0.7 diff --git a/recipes/bioconductor-rmir.hs.mirna/post-link.sh b/recipes/bioconductor-rmir.hs.mirna/post-link.sh index 7c304f5c1f086..342ed67ad7746 100644 --- a/recipes/bioconductor-rmir.hs.mirna/post-link.sh +++ b/recipes/bioconductor-rmir.hs.mirna/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="RmiR.Hs.miRNA_1.0.7.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://bioarchive.galaxyproject.org/RmiR.Hs.miRNA_1.0.7.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-rmir.hs.mirna/bioconductor-rmir.hs.mirna_1.0.7_src_all.tar.gz" diff --git a/recipes/bioconductor-rmir.hsa/meta.yaml b/recipes/bioconductor-rmir.hsa/meta.yaml new file mode 100644 index 0000000000000..c3790a8942937 --- /dev/null +++ b/recipes/bioconductor-rmir.hsa/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.5" %} +{% set name = "RmiR.hsa" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f22a18d1a34d12f8fc4ba3daaf1379fd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: methods, hgug4112a.db +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'The Artistic License, Version 2.0' + summary: 'Various databases of microRNA Targets' + diff --git a/recipes/bioconductor-rmir.hsa/post-link.sh b/recipes/bioconductor-rmir.hsa/post-link.sh new file mode 100644 index 0000000000000..8a4983e94a4f4 --- /dev/null +++ b/recipes/bioconductor-rmir.hsa/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RmiR.hsa_1.0.5.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RmiR.hsa_1.0.5.tar.gz" + "https://bioarchive.galaxyproject.org/RmiR.hsa_1.0.5.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rmir.hsa/bioconductor-rmir.hsa_1.0.5_src_all.tar.gz" +) +MD5="f22a18d1a34d12f8fc4ba3daaf1379fd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rmir.hsa/pre-unlink.sh b/recipes/bioconductor-rmir.hsa/pre-unlink.sh new file mode 100644 index 0000000000000..2cc556073af16 --- /dev/null +++ b/recipes/bioconductor-rmir.hsa/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RmiR.hsa diff --git a/recipes/bioconductor-rmir/build.sh b/recipes/bioconductor-rmir/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rmir/build.sh +++ b/recipes/bioconductor-rmir/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmir/meta.yaml b/recipes/bioconductor-rmir/meta.yaml index 52281ef39e737..1b14333c1c8d0 100644 --- a/recipes/bioconductor-rmir/meta.yaml +++ b/recipes/bioconductor-rmir/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "RmiR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3c49c47be5407575d7ea446651fac7da4d0f4420601bf0eb926252498cb9920f + md5: f4320c1b98aa85b078b9b4c2c55ded07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: hgug4112a.db,org.Hs.eg.db requirements: host: - - 'bioconductor-rmir.hs.mirna >=1.0.7,<1.2.0' + - 'bioconductor-rmir.hs.mirna >=1.0.0,<1.1.0' - r-base - r-dbi - r-rsvgtipsdevice run: - - 'bioconductor-rmir.hs.mirna >=1.0.7,<1.2.0' + - 'bioconductor-rmir.hs.mirna >=1.0.0,<1.1.0' - r-base - r-dbi - r-rsvgtipsdevice @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 - summary: 'Useful functions to merge microRNA and respective targets using differents databases' + summary: 'Useful functions to merge microRNA and respective targets using differents databases' extra: identifiers: - biotools:rmir - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rmir + path: recipes/bioconductor-rmir + version: 1.36.0 + diff --git a/recipes/bioconductor-rmmquant/build.sh b/recipes/bioconductor-rmmquant/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rmmquant/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rmmquant/meta.yaml b/recipes/bioconductor-rmmquant/meta.yaml new file mode 100644 index 0000000000000..9e9b079aef065 --- /dev/null +++ b/recipes/bioconductor-rmmquant/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "Rmmquant" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c872cd62c9559b1d5c652be647d1ee5e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tbx20bamsubset >=1.18.0,<1.19.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-devtools + - 'r-rcpp >=0.12.8' + run: + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tbx20bamsubset >=1.18.0,<1.19.0' + - 'bioconductor-txdb.mmusculus.ucsc.mm9.knowngene >=3.2.0,<3.3.0' + - r-base + - r-devtools + - 'r-rcpp >=0.12.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'RNA-Seq is currently used routinely, and it provides accurate information on gene transcription. However, the method cannot accurately estimate duplicated genes expression. Several strategies have been previously used, but all of them provide biased results. With Rmmquant, if a read maps at different positions, the tool detects that the corresponding genes are duplicated; it merges the genes and creates a merged gene. The counts of ambiguous reads is then based on the input genes and the merged genes. Rmmquant is a drop-in replacement of the widely used tools findOverlaps and featureCounts that handles multi-mapping reads in an unabiased way.' + diff --git a/recipes/bioconductor-rnadecay/build.sh b/recipes/bioconductor-rnadecay/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rnadecay/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnadecay/meta.yaml b/recipes/bioconductor-rnadecay/meta.yaml new file mode 100644 index 0000000000000..20699f065aee4 --- /dev/null +++ b/recipes/bioconductor-rnadecay/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.2.0" %} +{% set name = "RNAdecay" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40be6b9afb6fdbcf854b481afacecbcc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: parallel, knitr, reshape2, rmarkdown +requirements: + host: + - r-base + - r-ggplot2 + - r-gplots + - r-nloptr + - r-tmb + run: + - r-base + - r-ggplot2 + - r-gplots + - r-nloptr + - r-tmb + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'RNA degradation is monitored through measurement of RNA abundance after inhibiting RNA synthesis. This package has functions and example scripts to facilitate (1) data normalization, (2) data modeling using constant decay rate or time-dependent decay rate models, (3) the evaluation of treatment or genotype effects, and (4) plotting of the data and models. Data Normalization: functions and scripts make easy the normalization to the initial (T0) RNA abundance, as well as a method to correct for artificial inflation of Reads per Million (RPM) abundance in global assessments as the total size of the RNA pool decreases. Modeling: Normalized data is then modeled using maximum likelihood to fit parameters. For making treatment or genotype comparisons (up to four), the modeling step models all possible treatment effects on each gene by repeating the modeling with constraints on the model parameters (i.e., the decay rate of treatments A and B are modeled once with them being equal and again allowing them to both vary independently). Model Selection: The AICc value is calculated for each model, and the model with the lowest AICc is chosen. Modeling results of selected models are then compiled into a single data frame. Graphical Plotting: a function is provided to easily visualize the data and the selected model using ggplot2 package functions.' + diff --git a/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml new file mode 100644 index 0000000000000..46c2bc3b3e2db --- /dev/null +++ b/recipes/bioconductor-rnagilentdesign028282.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "RnAgilentDesign028282.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 72cafb0f7514a81f462acb3248e21aa9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Agilent Chips that use Agilent design number 028282 annotation data (chip RnAgilentDesign028282) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh b/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh new file mode 100644 index 0000000000000..2e7fbe7a5976e --- /dev/null +++ b/recipes/bioconductor-rnagilentdesign028282.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RnAgilentDesign028282.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/RnAgilentDesign028282.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/RnAgilentDesign028282.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnagilentdesign028282.db/bioconductor-rnagilentdesign028282.db_3.2.3_src_all.tar.gz" +) +MD5="72cafb0f7514a81f462acb3248e21aa9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnagilentdesign028282.db/pre-unlink.sh b/recipes/bioconductor-rnagilentdesign028282.db/pre-unlink.sh new file mode 100644 index 0000000000000..e040f00b04418 --- /dev/null +++ b/recipes/bioconductor-rnagilentdesign028282.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RnAgilentDesign028282.db diff --git a/recipes/bioconductor-rnainteract/build.sh b/recipes/bioconductor-rnainteract/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnainteract/build.sh +++ b/recipes/bioconductor-rnainteract/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnainteract/conda_build_config.yaml b/recipes/bioconductor-rnainteract/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rnainteract/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rnainteract/meta.yaml b/recipes/bioconductor-rnainteract/meta.yaml index d7db0668fa53a..8dca983042178 100644 --- a/recipes/bioconductor-rnainteract/meta.yaml +++ b/recipes/bioconductor-rnainteract/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "RNAinteract" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a71c7861ce6aea6a8a825b787de415ca71d2ced8bfdc3ac65bf92462606935a3 + md5: b9aaf6f1cbb298ce83184334f93c5a5d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' - r-abind - r-base - r-gplots @@ -34,11 +35,11 @@ requirements: - r-locfit - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' - r-abind - r-base - r-gplots @@ -53,9 +54,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'RNAinteract estimates genetic interactions from multi-dimensional read-outs like features extracted from images. The screen is assumed to be performed in multi-well plates or similar designs. Starting from a list of features (e.g. cell number, area, fluorescence intensity) per well, genetic interactions are estimated. The packages provides functions for reporting interacting gene pairs, plotting heatmaps and double RNAi plots. An HTML report can be written for quality control and analysis.' extra: identifiers: - biotools:rnainteract + parent_recipe: + name: bioconductor-rnainteract + path: recipes/bioconductor-rnainteract + version: 1.28.0 + diff --git a/recipes/bioconductor-rnainteractmapk/meta.yaml b/recipes/bioconductor-rnainteractmapk/meta.yaml new file mode 100644 index 0000000000000..b156a4b79732c --- /dev/null +++ b/recipes/bioconductor-rnainteractmapk/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.20.0" %} +{% set name = "RNAinteractMAPK" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06d12d93a9a99709c6b5946fa4932486 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: qvalue, lattice +requirements: + host: + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-rnainteract >=1.30.0,<1.31.0' + - r-base + - r-fields + - r-gdata + - r-mass + - r-sparselda + run: + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-rnainteract >=1.30.0,<1.31.0' + - r-base + - r-fields + - r-gdata + - r-mass + - r-sparselda + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package includes all data used in the paper -Mapping of Signalling Networks through Synthetic Genetic Interaction Analysis by RNAi- by Horn, Sandmann, Fischer et al.., Nat. Methods, 2011. The package vignette shows the R code to reproduce all figures in the paper.' + diff --git a/recipes/bioconductor-rnainteractmapk/post-link.sh b/recipes/bioconductor-rnainteractmapk/post-link.sh new file mode 100644 index 0000000000000..246b206596d38 --- /dev/null +++ b/recipes/bioconductor-rnainteractmapk/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RNAinteractMAPK_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNAinteractMAPK_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNAinteractMAPK_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnainteractmapk/bioconductor-rnainteractmapk_1.20.0_src_all.tar.gz" +) +MD5="06d12d93a9a99709c6b5946fa4932486" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnainteractmapk/pre-unlink.sh b/recipes/bioconductor-rnainteractmapk/pre-unlink.sh new file mode 100644 index 0000000000000..5ed8625f4c898 --- /dev/null +++ b/recipes/bioconductor-rnainteractmapk/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RNAinteractMAPK diff --git a/recipes/bioconductor-rnaither/build.sh b/recipes/bioconductor-rnaither/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaither/build.sh +++ b/recipes/bioconductor-rnaither/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaither/meta.yaml b/recipes/bioconductor-rnaither/meta.yaml index 91a0b68befb7a..eefa0e0d77b87 100644 --- a/recipes/bioconductor-rnaither/meta.yaml +++ b/recipes/bioconductor-rnaither/meta.yaml @@ -1,50 +1,56 @@ -{% set version = "2.28.0" %} +{% set version = "2.30.0" %} {% set name = "RNAither" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 82ff30db93fc94eecb8b3e1ee11112d9f37e9ac8e79ed17165be0ce630098053 + md5: 0f8239609b46a02e35c85fb4e14aff89 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-prada >=1.56.0,<1.58.0' - - 'bioconductor-rankprod >=3.6.0,<3.8.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-car run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-geneplotter >=1.58.0,<1.60.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-prada >=1.56.0,<1.58.0' - - 'bioconductor-rankprod >=3.6.0,<3.8.0' - - 'bioconductor-splots >=1.46.0,<1.48.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-geneplotter >=1.60.0,<1.61.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-prada >=1.58.0,<1.59.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-splots >=1.48.0,<1.49.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-car test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'RNAither analyzes cell-based RNAi screens, and includes quality assessment, customizable normalization and statistical tests, leading to lists of significant genes and biological processes.' extra: identifiers: - biotools:rnaither - doi:10.1093/bioinformatics/btp014 + parent_recipe: + name: bioconductor-rnaither + path: recipes/bioconductor-rnaither + version: 2.28.0 + diff --git a/recipes/bioconductor-rnaprobr/build.sh b/recipes/bioconductor-rnaprobr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaprobr/build.sh +++ b/recipes/bioconductor-rnaprobr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaprobr/meta.yaml b/recipes/bioconductor-rnaprobr/meta.yaml index af327858fbcfb..1e5a928512de2 100644 --- a/recipes/bioconductor-rnaprobr/meta.yaml +++ b/recipes/bioconductor-rnaprobr/meta.yaml @@ -1,53 +1,60 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RNAprobR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9e5e217ccb0af15db7a1994ff74ab2f4ed76233e8d6842178f03d383571a1934 + md5: 7c4c5ed21a3b2594fe094e7b75f053bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-plyr >=1.8.1' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - 'r-plyr >=1.8.1' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package facilitates analysis of Next Generation Sequencing data for which positional information with a single nucleotide resolution is a key. It allows for applying different types of relevant normalizations, data visualization and export in a table or UCSC compatible bedgraph file.' extra: identifiers: - biotools:rnaprobr + parent_recipe: + name: bioconductor-rnaprobr + path: recipes/bioconductor-rnaprobr + version: 1.12.0 + diff --git a/recipes/bioconductor-rnaseqcomp/build.sh b/recipes/bioconductor-rnaseqcomp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaseqcomp/build.sh +++ b/recipes/bioconductor-rnaseqcomp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqcomp/meta.yaml b/recipes/bioconductor-rnaseqcomp/meta.yaml index 8d95466b6d210..4435f6c2f5377 100644 --- a/recipes/bioconductor-rnaseqcomp/meta.yaml +++ b/recipes/bioconductor-rnaseqcomp/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "rnaseqcomp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d7f106d539850825091ccc7bcbf51cb154fd743af5aed7c2ca1825c6118d50cc + md5: 42917eebae09b1408fd29f6e929793bc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - r-base @@ -27,9 +29,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Several quantitative and visualized benchmarks for RNA-seq quantification pipelines. Two-condition quantifications for genes, transcripts, junctions or exons by each pipeline with necessary meta information should be organized into numeric matrices in order to proceed the evaluation.' extra: identifiers: - biotools:rnaseqcomp + parent_recipe: + name: bioconductor-rnaseqcomp + path: recipes/bioconductor-rnaseqcomp + version: 1.10.0 + diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml new file mode 100644 index 0000000000000..f2082f397417e --- /dev/null +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.20.0" %} +{% set name = "RNAseqData.HNRNPC.bam.chr14" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 936faad52a796dfc487f2d104bfb91bd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicAlignments, BiocManager +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'The package contains 8 BAM files, 1 per sequencing run. Each BAM file was obtained by (1) aligning the reads (paired-end) to the full hg19 genome with TopHat2, and then (2) subsetting to keep only alignments on chr14. See accession number E-MTAB-1147 in the ArrayExpress database for details about the experiment, including links to the published study (by Zarnack et al., 2012) and to the FASTQ files.' + diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh new file mode 100644 index 0000000000000..07255ecd5ffd8 --- /dev/null +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNAseqData.HNRNPC.bam.chr14_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqdata.hnrnpc.bam.chr14/bioconductor-rnaseqdata.hnrnpc.bam.chr14_0.20.0_src_all.tar.gz" +) +MD5="936faad52a796dfc487f2d104bfb91bd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/pre-unlink.sh b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/pre-unlink.sh new file mode 100644 index 0000000000000..3b4fc6a585831 --- /dev/null +++ b/recipes/bioconductor-rnaseqdata.hnrnpc.bam.chr14/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RNAseqData.HNRNPC.bam.chr14 diff --git a/recipes/bioconductor-rnaseqmap/build.sh b/recipes/bioconductor-rnaseqmap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaseqmap/build.sh +++ b/recipes/bioconductor-rnaseqmap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqmap/meta.yaml b/recipes/bioconductor-rnaseqmap/meta.yaml index e4ce9e37a42ad..cd3cf43b42161 100644 --- a/recipes/bioconductor-rnaseqmap/meta.yaml +++ b/recipes/bioconductor-rnaseqmap/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.38.0" %} +{% set version = "2.40.0" %} {% set name = "rnaSeqMap" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 954e40aa612299bdbbbeead5a90b495216f9f65471a6af5e40a157d0c65b7f98 + md5: eb522f0cd8e74c18127295d42efe34fe build: number: 0 rpaths: @@ -18,23 +18,23 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-dbi run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-dbi build: @@ -44,10 +44,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rnaSeqMap library provides classes and functions to analyze the RNA-sequencing data using the coverage profiles in multiple samples at a time' extra: identifiers: - biotools:rnaseqmap - doi:10.1186/1471-2105-12-200 + parent_recipe: + name: bioconductor-rnaseqmap + path: recipes/bioconductor-rnaseqmap + version: 2.38.0 + diff --git a/recipes/bioconductor-rnaseqpower/build.sh b/recipes/bioconductor-rnaseqpower/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaseqpower/build.sh +++ b/recipes/bioconductor-rnaseqpower/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqpower/meta.yaml b/recipes/bioconductor-rnaseqpower/meta.yaml index 274e4c9d63cc6..9e0722e0eaa4a 100644 --- a/recipes/bioconductor-rnaseqpower/meta.yaml +++ b/recipes/bioconductor-rnaseqpower/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RNASeqPower" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1ee658caaef9d9e4fd8a1085e459b318438d763f0e271a45fb941d5ea6e45630 + md5: 7ec8d53cecbf22933b35197b8f36ca2e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'RNA-seq, sample size' extra: identifiers: - biotools:rnaseqpower - doi:10.1089/cmb.2012.0283 + parent_recipe: + name: bioconductor-rnaseqpower + path: recipes/bioconductor-rnaseqpower + version: 1.20.0 + diff --git a/recipes/bioconductor-rnaseqr/build.sh b/recipes/bioconductor-rnaseqr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rnaseqr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqr/meta.yaml b/recipes/bioconductor-rnaseqr/meta.yaml new file mode 100644 index 0000000000000..c674c0d422412 --- /dev/null +++ b/recipes/bioconductor-rnaseqr/meta.yaml @@ -0,0 +1,80 @@ +{% set version = "1.0.3" %} +{% set name = "RNASeqR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 41ef8cfd67effa33cca28f4a353edbd8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, png, grid, RNASeqRData +# SystemRequirements: RNASeqR only support Linux and macOS. Window is not supported. Python2 is highly recommended. If your machine is Python3, make sure '2to3' command is available. +requirements: + host: + - 'bioconductor-ballgown >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-systempiper >=1.16.0,<1.17.0' + - 'bioconductor-systempiperdata >=1.10.0,<1.11.0' + - r-base + - r-corrplot + - r-factoextra + - r-factominer + - r-ggplot2 + - r-gridextra + - r-performanceanalytics + - r-pheatmap + - r-rafalib + - r-reshape2 + - r-reticulate + - r-stringr + run: + - 'bioconductor-ballgown >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-dose >=3.8.0,<3.9.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-systempiper >=1.16.0,<1.17.0' + - 'bioconductor-systempiperdata >=1.10.0,<1.11.0' + - r-base + - r-corrplot + - r-factoextra + - r-factominer + - r-ggplot2 + - r-gridextra + - r-performanceanalytics + - r-pheatmap + - r-rafalib + - r-reshape2 + - r-reticulate + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This R package is designed for case-control RNA-Seq analysis (two-group). There are six steps: "RNASeqRParam S4 Object Creation", "Environment Setup", "Quality Assessment", "Reads Alignment & Quantification", "Gene-level Differential Analyses" and "Functional Analyses". Each step corresponds to a function in this package. After running functions in order, a basic RNASeq analysis would be done easily.' + diff --git a/recipes/bioconductor-rnaseqrdata/meta.yaml b/recipes/bioconductor-rnaseqrdata/meta.yaml new file mode 100644 index 0000000000000..995730a3f2964 --- /dev/null +++ b/recipes/bioconductor-rnaseqrdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.0.0" %} +{% set name = "RNASeqRData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aac4f4cb75fd142b66b9e954ac2652e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: png, grid +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'RNASeqRData is a helper experiment package for vignette demonstration purpose in RNASeqR software package.' + diff --git a/recipes/bioconductor-rnaseqrdata/post-link.sh b/recipes/bioconductor-rnaseqrdata/post-link.sh new file mode 100644 index 0000000000000..02180d718b314 --- /dev/null +++ b/recipes/bioconductor-rnaseqrdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RNASeqRData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RNASeqRData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/RNASeqRData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqrdata/bioconductor-rnaseqrdata_1.0.0_src_all.tar.gz" +) +MD5="aac4f4cb75fd142b66b9e954ac2652e3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnaseqrdata/pre-unlink.sh b/recipes/bioconductor-rnaseqrdata/pre-unlink.sh new file mode 100644 index 0000000000000..8cb3381aecc39 --- /dev/null +++ b/recipes/bioconductor-rnaseqrdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RNASeqRData diff --git a/recipes/bioconductor-rnaseqsamplesize/build.sh b/recipes/bioconductor-rnaseqsamplesize/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnaseqsamplesize/build.sh +++ b/recipes/bioconductor-rnaseqsamplesize/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnaseqsamplesize/meta.yaml b/recipes/bioconductor-rnaseqsamplesize/meta.yaml index 82a5600e9ad30..9adebc80ec02d 100644 --- a/recipes/bioconductor-rnaseqsamplesize/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesize/meta.yaml @@ -1,42 +1,55 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnaSeqSampleSize" %} -{% set bioc = "3.6" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'https://bioconductor.org/packages/release/bioc/src/contrib/RnaSeqSampleSize_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 60a3afc79a4ca2531adab6ea712a6ff6d5336ac24205036ffabfe8124a8b6202 + md5: 1613200808429e5e11933e889b3a7221 build: - number: 2 + number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr requirements: host: - - bioconductor-edgeR - - bioconductor-rnaseqsamplesizedata - - bioconductor-biomart + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rnaseqsamplesizedata >=1.14.0,<1.15.0' + - r-base - r-heatmap3 - r-matlab - - bioconductor-keggrest - - r-base + - 'r-rcpp >=0.11.2' run: - - bioconductor-edgeR - - bioconductor-rnaseqsamplesizedata - - bioconductor-biomart + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rnaseqsamplesizedata >=1.14.0,<1.15.0' + - r-base - r-heatmap3 - r-matlab - - bioconductor-keggrest - - r-base + - 'r-rcpp >=0.11.2' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL-2' - summary: 'RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data.' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'RnaSeqSampleSize package provides a sample size calculation method based on negative binomial model and the exact test for assessing differential expression analysis of RNA-seq data' +extra: + parent_recipe: + name: bioconductor-rnaseqsamplesize + path: recipes/bioconductor-rnaseqsamplesize + version: 1.12.0 + diff --git a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml index 8d91f97281f0c..cd8ed7b9d2df9 100644 --- a/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml +++ b/recipes/bioconductor-rnaseqsamplesizedata/meta.yaml @@ -1,32 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnaSeqSampleSizeData" %} -{% set bioc = "3.6" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/release/data/experiment/src/contrib/RnaSeqSampleSizeData_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1ee146d3992f06e442aad427bc8c0fd8b10991c2763dbed1638094832c2b0fcb + md5: faba578ad3a43e5fb8a72961dc17eef6 build: - number: 1 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr requirements: host: - - bioconductor-edgeR + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base run: - - bioconductor-edgeR + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base + - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPLv2' - summary: 'RnaSeqSampleSizeData: Read counts and dispersion distribution from real data for sample size estimation of RNA-seq experiments' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'RnaSeqSampleSizeData package provides the read counts and dispersion distribution from real RNA-seq experiments. It can be used by RnaSeqSampleSize package to estimate sample size and power for RNA-seq experiment design.' +extra: + parent_recipe: + name: bioconductor-rnaseqsamplesizedata + path: recipes/bioconductor-rnaseqsamplesizedata + version: 1.12.0 + diff --git a/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh new file mode 100644 index 0000000000000..ea641788d603a --- /dev/null +++ b/recipes/bioconductor-rnaseqsamplesizedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RnaSeqSampleSizeData_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnaSeqSampleSizeData_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnaSeqSampleSizeData_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnaseqsamplesizedata/bioconductor-rnaseqsamplesizedata_1.14.0_src_all.tar.gz" +) +MD5="faba578ad3a43e5fb8a72961dc17eef6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnaseqsamplesizedata/pre-unlink.sh b/recipes/bioconductor-rnaseqsamplesizedata/pre-unlink.sh new file mode 100644 index 0000000000000..fe0ff45415830 --- /dev/null +++ b/recipes/bioconductor-rnaseqsamplesizedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RnaSeqSampleSizeData diff --git a/recipes/bioconductor-rnbeads.hg19/meta.yaml b/recipes/bioconductor-rnbeads.hg19/meta.yaml index 6031857b22cd2..566f48d660353 100644 --- a/recipes/bioconductor-rnbeads.hg19/meta.yaml +++ b/recipes/bioconductor-rnbeads.hg19/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnBeads.hg19" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6546161385b2067afd17d4dd017a48810ec739743ece0d3e25a9ec273cc7db61 + md5: 4fc451cec743ae5482c90aa230bfbc05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly hg19.' - +extra: + parent_recipe: + name: bioconductor-rnbeads.hg19 + path: recipes/bioconductor-rnbeads.hg19 + version: 1.12.0 diff --git a/recipes/bioconductor-rnbeads.hg19/post-link.sh b/recipes/bioconductor-rnbeads.hg19/post-link.sh index e12ea3ef87d29..e29edf50cf25e 100644 --- a/recipes/bioconductor-rnbeads.hg19/post-link.sh +++ b/recipes/bioconductor-rnbeads.hg19/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.hg19_1.12.0.tar.gz" +FN="RnBeads.hg19_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.hg19_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.hg19_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.hg19_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg19/bioconductor-rnbeads.hg19_1.14.0_src_all.tar.gz" ) -MD5="836e7eef20499109e4bece34a7dbc8b3" +MD5="4fc451cec743ae5482c90aa230bfbc05" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-rnbeads.hg38/meta.yaml b/recipes/bioconductor-rnbeads.hg38/meta.yaml new file mode 100644 index 0000000000000..d8d0825a87ec1 --- /dev/null +++ b/recipes/bioconductor-rnbeads.hg38/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.14.0" %} +{% set name = "RnBeads.hg38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 184f7387ab19409cbb5eee2cbe0da8df +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RnBeads +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Automatically generated RnBeads annotation package for the assembly hg38.' + diff --git a/recipes/bioconductor-rnbeads.hg38/post-link.sh b/recipes/bioconductor-rnbeads.hg38/post-link.sh new file mode 100644 index 0000000000000..d823284a02098 --- /dev/null +++ b/recipes/bioconductor-rnbeads.hg38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RnBeads.hg38_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.hg38_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.hg38_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.hg38/bioconductor-rnbeads.hg38_1.14.0_src_all.tar.gz" +) +MD5="184f7387ab19409cbb5eee2cbe0da8df" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnbeads.hg38/pre-unlink.sh b/recipes/bioconductor-rnbeads.hg38/pre-unlink.sh new file mode 100644 index 0000000000000..ae2d543725737 --- /dev/null +++ b/recipes/bioconductor-rnbeads.hg38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RnBeads.hg38 diff --git a/recipes/bioconductor-rnbeads.mm10/meta.yaml b/recipes/bioconductor-rnbeads.mm10/meta.yaml index 08971550d58a9..709a14b4b07a5 100644 --- a/recipes/bioconductor-rnbeads.mm10/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm10/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnBeads.mm10" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b6d7862dfa9cf054096aece9de1b3abb709e201cda617eff3856997db3267b8 + md5: 94634f0b5fcea83c3c35545a7f097251 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly mm10.' - +extra: + parent_recipe: + name: bioconductor-rnbeads.mm10 + path: recipes/bioconductor-rnbeads.mm10 + version: 1.12.0 diff --git a/recipes/bioconductor-rnbeads.mm10/post-link.sh b/recipes/bioconductor-rnbeads.mm10/post-link.sh index 09713dbe84ac6..19e49e50e2af3 100644 --- a/recipes/bioconductor-rnbeads.mm10/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm10/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm10_1.12.0.tar.gz" +FN="RnBeads.mm10_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.mm10_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.mm10_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm10_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm10/bioconductor-rnbeads.mm10_1.14.0_src_all.tar.gz" ) -MD5="406fbbafb2bd367e01954fb63f9c07d7" +MD5="94634f0b5fcea83c3c35545a7f097251" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-rnbeads.mm9/meta.yaml b/recipes/bioconductor-rnbeads.mm9/meta.yaml index 4624b5d39db2c..c6a493b1be330 100644 --- a/recipes/bioconductor-rnbeads.mm9/meta.yaml +++ b/recipes/bioconductor-rnbeads.mm9/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnBeads.mm9" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 620042666b30174331df8e829ebec5d0c5da28237a4430fe5e4a0d7168d5055e + md5: 613c050b649b8ac4f8de05aff0df51ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly mm9.' - +extra: + parent_recipe: + name: bioconductor-rnbeads.mm9 + path: recipes/bioconductor-rnbeads.mm9 + version: 1.12.0 diff --git a/recipes/bioconductor-rnbeads.mm9/post-link.sh b/recipes/bioconductor-rnbeads.mm9/post-link.sh index 862b763953a33..86796faf87d3a 100644 --- a/recipes/bioconductor-rnbeads.mm9/post-link.sh +++ b/recipes/bioconductor-rnbeads.mm9/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.mm9_1.12.0.tar.gz" +FN="RnBeads.mm9_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.mm9_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.mm9_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.mm9_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.mm9/bioconductor-rnbeads.mm9_1.14.0_src_all.tar.gz" ) -MD5="1d101b3ded7f6f2b8ac287ff06dca07d" +MD5="613c050b649b8ac4f8de05aff0df51ad" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-rnbeads.rn5/meta.yaml b/recipes/bioconductor-rnbeads.rn5/meta.yaml index bdaa0a48b78c1..a22c8be62239f 100644 --- a/recipes/bioconductor-rnbeads.rn5/meta.yaml +++ b/recipes/bioconductor-rnbeads.rn5/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "RnBeads.rn5" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 800fc091bcecf71164140b5558f81f2b7d462096f03223159d9d6cb274200160 + md5: f3a037e9bd35824a15ceaededed22b6d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RnBeads requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Automatically generated RnBeads annotation package for the assembly rn5.' - +extra: + parent_recipe: + name: bioconductor-rnbeads.rn5 + path: recipes/bioconductor-rnbeads.rn5 + version: 1.12.0 diff --git a/recipes/bioconductor-rnbeads.rn5/post-link.sh b/recipes/bioconductor-rnbeads.rn5/post-link.sh index 65ffe2e09ac69..2df2eecdf8467 100644 --- a/recipes/bioconductor-rnbeads.rn5/post-link.sh +++ b/recipes/bioconductor-rnbeads.rn5/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RnBeads.rn5_1.12.0.tar.gz" +FN="RnBeads.rn5_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RnBeads.rn5_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RnBeads.rn5_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/RnBeads.rn5_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnbeads.rn5/bioconductor-rnbeads.rn5_1.14.0_src_all.tar.gz" ) -MD5="01f48fb32494406174cd2721cc95af7f" +MD5="f3a037e9bd35824a15ceaededed22b6d" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-rnbeads/build.sh b/recipes/bioconductor-rnbeads/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnbeads/build.sh +++ b/recipes/bioconductor-rnbeads/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnbeads/meta.yaml b/recipes/bioconductor-rnbeads/meta.yaml index db77dab6bae57..51c22c7db73f1 100644 --- a/recipes/bioconductor-rnbeads/meta.yaml +++ b/recipes/bioconductor-rnbeads/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.12.1" %} +{% set version = "2.0.0" %} {% set name = "RnBeads" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fb610fa5b63641311d1ce27789a8bdc220f864e84f02a34d11dfc0b4e3f4d80a + md5: 41a307928bc110ab23d901037ac523e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Category, GOstats, Gviz, IlluminaHumanMethylation450kmanifest, RPMM, RefFreeEWAS, RnBeads.hg19, XML, annotate, biomaRt, foreach, doParallel, ggbio, isva, mclust, mgcv, minfi, nlme, org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db, quadprog, rtracklayer, qvalue, sva, wateRmelon, wordcloud, qvalue, argparse, glmnet, GLAD, IlluminaHumanMethylation450kanno.ilmn12.hg19, scales, missMethyl, impute, shiny, shinyjs, plotrix, hexbin, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-cluster - r-ff @@ -36,13 +38,13 @@ requirements: - r-matrixstats - r-plyr run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-cluster - r-ff @@ -57,8 +59,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'RnBeads facilitates comprehensive analysis of various types of DNA methylation data at the genome scale.' - +extra: + parent_recipe: + name: bioconductor-rnbeads + path: recipes/bioconductor-rnbeads + version: 1.12.1 diff --git a/recipes/bioconductor-rnits/build.sh b/recipes/bioconductor-rnits/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rnits/build.sh +++ b/recipes/bioconductor-rnits/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rnits/conda_build_config.yaml b/recipes/bioconductor-rnits/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rnits/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rnits/meta.yaml b/recipes/bioconductor-rnits/meta.yaml index 1d552efcec1cd..dc3eff3969cb2 100644 --- a/recipes/bioconductor-rnits/meta.yaml +++ b/recipes/bioconductor-rnits/meta.yaml @@ -1,38 +1,40 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "Rnits" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 25baebc9454e10cdefafa34ae48dbd9a14bfde6ebf7d280bbdd1ed6d2ea0b1ab + md5: 47d6ced6ce9154da7718e97178123f13 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, GEOquery, stringr requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-boot - r-ggplot2 - r-reshape2 run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-impute >=1.54.0,<1.56.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-boot - r-ggplot2 @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'R/Bioconductor package for normalization, curve registration and inference in time course gene expression data' extra: identifiers: - biotools:rnits - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rnits + path: recipes/bioconductor-rnits + version: 1.14.0 + diff --git a/recipes/bioconductor-rnu34.db/meta.yaml b/recipes/bioconductor-rnu34.db/meta.yaml new file mode 100644 index 0000000000000..7f17dc25985ef --- /dev/null +++ b/recipes/bioconductor-rnu34.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rnu34.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a95920bb41a2f78da82f419b245ad1a9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Neurobiology U34 Array annotation data (chip rnu34) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rnu34.db/post-link.sh b/recipes/bioconductor-rnu34.db/post-link.sh new file mode 100644 index 0000000000000..2296d3a55b369 --- /dev/null +++ b/recipes/bioconductor-rnu34.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rnu34.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rnu34.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34.db/bioconductor-rnu34.db_3.2.3_src_all.tar.gz" +) +MD5="a95920bb41a2f78da82f419b245ad1a9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnu34.db/pre-unlink.sh b/recipes/bioconductor-rnu34.db/pre-unlink.sh new file mode 100644 index 0000000000000..0f59cae991312 --- /dev/null +++ b/recipes/bioconductor-rnu34.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rnu34.db diff --git a/recipes/bioconductor-rnu34cdf/meta.yaml b/recipes/bioconductor-rnu34cdf/meta.yaml new file mode 100644 index 0000000000000..5d96b63719319 --- /dev/null +++ b/recipes/bioconductor-rnu34cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rnu34cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0f2564fc6ac89de4d779faf253f23ce3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RN_U34.CDF file.' + diff --git a/recipes/bioconductor-rnu34cdf/post-link.sh b/recipes/bioconductor-rnu34cdf/post-link.sh new file mode 100644 index 0000000000000..62d24968b6429 --- /dev/null +++ b/recipes/bioconductor-rnu34cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rnu34cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rnu34cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34cdf/bioconductor-rnu34cdf_2.18.0_src_all.tar.gz" +) +MD5="0f2564fc6ac89de4d779faf253f23ce3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnu34cdf/pre-unlink.sh b/recipes/bioconductor-rnu34cdf/pre-unlink.sh new file mode 100644 index 0000000000000..2d39818e43fb6 --- /dev/null +++ b/recipes/bioconductor-rnu34cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rnu34cdf diff --git a/recipes/bioconductor-rnu34probe/meta.yaml b/recipes/bioconductor-rnu34probe/meta.yaml new file mode 100644 index 0000000000000..ece982a658fc3 --- /dev/null +++ b/recipes/bioconductor-rnu34probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rnu34probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c5ef9793a437f2bf990f6e84d31da0de +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RN-U34\_probe\_tab.' + diff --git a/recipes/bioconductor-rnu34probe/post-link.sh b/recipes/bioconductor-rnu34probe/post-link.sh new file mode 100644 index 0000000000000..08b0c99d8b4d8 --- /dev/null +++ b/recipes/bioconductor-rnu34probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rnu34probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rnu34probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rnu34probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rnu34probe/bioconductor-rnu34probe_2.18.0_src_all.tar.gz" +) +MD5="c5ef9793a437f2bf990f6e84d31da0de" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rnu34probe/pre-unlink.sh b/recipes/bioconductor-rnu34probe/pre-unlink.sh new file mode 100644 index 0000000000000..1a55087d1d057 --- /dev/null +++ b/recipes/bioconductor-rnu34probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rnu34probe diff --git a/recipes/bioconductor-roar/build.sh b/recipes/bioconductor-roar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-roar/build.sh +++ b/recipes/bioconductor-roar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-roar/meta.yaml b/recipes/bioconductor-roar/meta.yaml index 950574b60fa3a..2a8399fe9a954 100644 --- a/recipes/bioconductor-roar/meta.yaml +++ b/recipes/bioconductor-roar/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "roar" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 514556917357a0dff936eb20ecd3894615d34b0b870d2f61f86c77a92e692d59 + md5: af18fe575adeb3d3cddeea46774d9a07 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RNAseqData.HNRNPC.bam.chr14, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.' extra: identifiers: - biotools:roar - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-roar + path: recipes/bioconductor-roar + version: 1.16.0 + diff --git a/recipes/bioconductor-roberts2005annotation.db/meta.yaml b/recipes/bioconductor-roberts2005annotation.db/meta.yaml new file mode 100644 index 0000000000000..29bd2ed9c2934 --- /dev/null +++ b/recipes/bioconductor-roberts2005annotation.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "Roberts2005Annotation.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fb28aaf1a1e0c81cf936badc674b754a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Roberts2005Annotation Annotation Data (Roberts2005Annotation) assembled using data from public repositories' + diff --git a/recipes/bioconductor-roberts2005annotation.db/post-link.sh b/recipes/bioconductor-roberts2005annotation.db/post-link.sh new file mode 100644 index 0000000000000..88fa85fbefe93 --- /dev/null +++ b/recipes/bioconductor-roberts2005annotation.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Roberts2005Annotation.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/Roberts2005Annotation.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/Roberts2005Annotation.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-roberts2005annotation.db/bioconductor-roberts2005annotation.db_3.2.3_src_all.tar.gz" +) +MD5="fb28aaf1a1e0c81cf936badc674b754a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-roberts2005annotation.db/pre-unlink.sh b/recipes/bioconductor-roberts2005annotation.db/pre-unlink.sh new file mode 100644 index 0000000000000..0bfd475158bbb --- /dev/null +++ b/recipes/bioconductor-roberts2005annotation.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Roberts2005Annotation.db diff --git a/recipes/bioconductor-roc/build.sh b/recipes/bioconductor-roc/build.sh index 248d10a0bcfc4..b23b57398f093 100644 --- a/recipes/bioconductor-roc/build.sh +++ b/recipes/bioconductor-roc/build.sh @@ -2,9 +2,9 @@ mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION echo -e "CC=$CC -CXXFLAGS=$CXXFLAGS FC=$FC CXX=$CXX +CXXFLAGS=$CXXFLAGS CXX98=$CXX CXX11=$CXX CXX14=$CXX" > src/Makevars diff --git a/recipes/bioconductor-roleswitch/build.sh b/recipes/bioconductor-roleswitch/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-roleswitch/build.sh +++ b/recipes/bioconductor-roleswitch/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-roleswitch/meta.yaml b/recipes/bioconductor-roleswitch/meta.yaml index e3e71cdc8d856..221b388ca3c04 100644 --- a/recipes/bioconductor-roleswitch/meta.yaml +++ b/recipes/bioconductor-roleswitch/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Roleswitch" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 06377ed38e766b7e7b4aa17dccbf664763d685b2aee272d710fbbea026cbd647 + md5: e714b785159b4e22b1886d246a89adfc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ggplot2 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-microrna >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-microrna >=1.40.0,<1.41.0' - r-base - r-dbi - r-plotrix - r-pracma - r-reshape run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-microrna >=1.38.0,<1.40.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-microrna >=1.40.0,<1.41.0' - r-base - r-dbi - r-plotrix @@ -41,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer Probabilities of MiRNA-mRNA Interaction Signature (ProMISe) using paired expression data from a single sample. Roleswitch operates in two phases by inferring the probability of mRNA (miRNA) being the targets ("targets") of miRNA (mRNA), taking into account the expression of all of the mRNAs (miRNAs) due to their potential competition for the same miRNA (mRNA). Due to dynamic miRNA repression in the cell, Roleswitch assumes that the total transcribed mRNA levels are higher than the observed (equilibrium) mRNA levels and iteratively updates the total transcription of each mRNA targets based on the above inference. NB: in the paper, we used ProMISe as both the model name and inferred score name.' extra: identifiers: - biotools:roleswitch + parent_recipe: + name: bioconductor-roleswitch + path: recipes/bioconductor-roleswitch + version: 1.18.0 + diff --git a/recipes/bioconductor-rols/build.sh b/recipes/bioconductor-rols/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rols/build.sh +++ b/recipes/bioconductor-rols/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rols/meta.yaml b/recipes/bioconductor-rols/meta.yaml index 62df0168365aa..9e10683bcba0e 100644 --- a/recipes/bioconductor-rols/meta.yaml +++ b/recipes/bioconductor-rols/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "2.8.2" %} +{% set version = "2.10.0" %} {% set name = "rols" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 2dd9cc4130ed5ff62f712969f556a05ce6e9cb4483a1ad181db59f61725e96bc + md5: a16856e3b45badc273677be28eb16b71 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GO.db, knitr (>= 1.1.0), BiocStyle (>= 2.5.19), testthat, lubridate, DT, rmarkdown, requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-httr - r-jsonlite - r-progress run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-httr - r-jsonlite @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rols package is an interface to the Ontology Lookup Service (OLS) to access and query hundred of ontolgies directly from R.' extra: identifiers: - biotools:rols - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rols + path: recipes/bioconductor-rols + version: 2.8.2 + diff --git a/recipes/bioconductor-rontotools/build.sh b/recipes/bioconductor-rontotools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rontotools/build.sh +++ b/recipes/bioconductor-rontotools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rontotools/meta.yaml b/recipes/bioconductor-rontotools/meta.yaml index cc0fe8abba7eb..03f90a340f2d9 100644 --- a/recipes/bioconductor-rontotools/meta.yaml +++ b/recipes/bioconductor-rontotools/meta.yaml @@ -1,44 +1,51 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "ROntoTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 368956b887a88149dca733d933fef60d880990e015dca1126fdb9cf958d5dbcd + md5: 75691c4b8aa9bf7bd9a948c2bd0d36e3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-boot run: - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-boot test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'CC BY-NC-ND 4.0 + file LICENSE' summary: 'Suite of tools for functional analysis.' extra: identifiers: - biotools:rontotools - doi:10.1109/JPROC.2016.2531000 + parent_recipe: + name: bioconductor-rontotools + path: recipes/bioconductor-rontotools + version: 2.8.0 + diff --git a/recipes/bioconductor-ropls/build.sh b/recipes/bioconductor-ropls/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ropls/build.sh +++ b/recipes/bioconductor-ropls/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ropls/meta.yaml b/recipes/bioconductor-ropls/meta.yaml index c3f1fdb81be5e..0a38f0ed9ae50 100644 --- a/recipes/bioconductor-ropls/meta.yaml +++ b/recipes/bioconductor-ropls/meta.yaml @@ -1,35 +1,42 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "ropls" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a6fa8a4d7d2b1ebb69471b03f98f32e6c6dbd91f9b8aeed5182f8d150948c49f + md5: c554581b0ae01d061ce551f2a9fca08f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, knitr, multtest, rmarkdown, RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: CeCILL summary: 'Latent variable modeling with Principal Component Analysis(PCA) and Partial Least Squares (PLS) are powerful methods for visualization, regression, classification, and feature selection of omics data where the number of variables exceeds the number of samples and with multicollinearity among variables. Orthogonal Partial Least Squares (OPLS) enables to separately model the variation correlated (predictive) to the factor of interest and the uncorrelated (orthogonal) variation. While performing similarly to PLS, OPLS facilitates interpretation. Successful applications of these chemometrics techniques include spectroscopic data such as Raman spectroscopy, nuclear magnetic resonance (NMR), mass spectrometry (MS) in metabolomics and proteomics, but also transcriptomics data. In addition to scores, loadings and weights plots, the package provides metrics and graphics to determine the optimal number of components (e.g. with the R2 and Q2 coefficients), check the validity of the model by permutation testing, detect outliers, and perform feature selection (e.g. with Variable Importance in Projection or regression coefficients). The package can be accessed via a user interface on the Workflow4Metabolomics.org online resource for computational metabolomics (built upon the Galaxy environment).' extra: identifiers: - biotools:ropls + parent_recipe: + name: bioconductor-ropls + path: recipes/bioconductor-ropls + version: 1.12.0 + diff --git a/recipes/bioconductor-rots/build.sh b/recipes/bioconductor-rots/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rots/build.sh +++ b/recipes/bioconductor-rots/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rots/meta.yaml b/recipes/bioconductor-rots/meta.yaml index 593c26aeb62df..42c9c5a96f5cb 100644 --- a/recipes/bioconductor-rots/meta.yaml +++ b/recipes/bioconductor-rots/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "ROTS" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e3620525682a1e0c80efbeeab9e6035e881b7f01e152cf2e8c064d6f156e5b8a + md5: ce0bb4ba8baf6a5d94efb3c2d022547d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcpp run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rcpp build: @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Calculates the Reproducibility-Optimized Test Statistic (ROTS) for differential testing in omics data.' extra: identifiers: - biotools:rots - doi:10.1109/tcbb.2007.1078 + parent_recipe: + name: bioconductor-rots + path: recipes/bioconductor-rots + version: 1.8.0 + diff --git a/recipes/bioconductor-rpa/build.sh b/recipes/bioconductor-rpa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rpa/build.sh +++ b/recipes/bioconductor-rpa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rpa/conda_build_config.yaml b/recipes/bioconductor-rpa/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-rpa/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-rpa/meta.yaml b/recipes/bioconductor-rpa/meta.yaml index 6d53f98a80edf..97d04d8713698 100644 --- a/recipes/bioconductor-rpa/meta.yaml +++ b/recipes/bioconductor-rpa/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "RPA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b3b9d728cf632bbc752e6b44e3cd63096edf718024c0e00b504d592f51f93050 + md5: 7b2d727e06ee9202a906a384a1514c01 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata, knitr, parallel requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-phyloseq >=1.24.2,<1.26.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'Probabilistic analysis of probe reliability and differential gene expression on short oligonucleotide arrays.' extra: identifiers: - biotools:rpa + parent_recipe: + name: bioconductor-rpa + path: recipes/bioconductor-rpa + version: 1.36.0 + diff --git a/recipes/bioconductor-rprotobuflib/build.sh b/recipes/bioconductor-rprotobuflib/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rprotobuflib/build.sh +++ b/recipes/bioconductor-rprotobuflib/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rprotobuflib/meta.yaml b/recipes/bioconductor-rprotobuflib/meta.yaml index 14d88603da90a..d89523946a37d 100644 --- a/recipes/bioconductor-rprotobuflib/meta.yaml +++ b/recipes/bioconductor-rprotobuflib/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "RProtoBufLib" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 424e121ed7e573f8dbf7c9e2373f950f481967093ae20e1071c257d00fc7b04c + md5: 0aec534ff083127809f3313676f7b48e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# SystemRequirements: GNU make requirements: host: - r-base @@ -30,8 +31,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: BSD_3_clause summary: 'This package provides the headers and static library of Protocol buffers 2.6.0 for other R packages to compile and link against.' - +extra: + parent_recipe: + name: bioconductor-rprotobuflib + path: recipes/bioconductor-rprotobuflib + version: 1.2.0 diff --git a/recipes/bioconductor-rpsixml/build.sh b/recipes/bioconductor-rpsixml/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rpsixml/build.sh +++ b/recipes/bioconductor-rpsixml/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rpsixml/meta.yaml b/recipes/bioconductor-rpsixml/meta.yaml index f33e572138b4d..ee11f7c388873 100644 --- a/recipes/bioconductor-rpsixml/meta.yaml +++ b/recipes/bioconductor-rpsixml/meta.yaml @@ -1,48 +1,55 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "RpsiXML" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fc74073cddd42122c78423d997aff5cd3d325792f5267b0f15b259f98851a324 + md5: 7be74bec83e9b9afd74726a08f9e435b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, org.Mm.eg.db, org.Dm.eg.db, org.Rn.eg.db, org.Sc.sgd.db,hom.Hs.inp.db, hom.Mm.inp.db, hom.Dm.inp.db, hom.Rn.inp.db, hom.Sc.inp.db,Rgraphviz, ppiStats, ScISI requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - 'r-xml >=2.4.0' run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-hypergraph >=1.52.0,<1.54.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-hypergraph >=1.54.0,<1.55.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base - 'r-xml >=2.4.0' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Queries, data structure and interface to visualization of interaction datasets. This package inplements the PSI-MI 2.5 standard and supports up to now 8 databases. Further databases supporting PSI-MI 2.5 standard will be added continuously.' extra: identifiers: - biotools:rpsixml - doi:10.1007/978-1-60761-987-1_9 + parent_recipe: + name: bioconductor-rpsixml + path: recipes/bioconductor-rpsixml + version: 2.22.0 + diff --git a/recipes/bioconductor-rpx/build.sh b/recipes/bioconductor-rpx/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rpx/build.sh +++ b/recipes/bioconductor-rpx/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rpx/meta.yaml b/recipes/bioconductor-rpx/meta.yaml index f902add0d78d9..6806c7a854f1a 100644 --- a/recipes/bioconductor-rpx/meta.yaml +++ b/recipes/bioconductor-rpx/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "rpx" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a10a20d0e01568ae34a28352be193aa5e494378fadae3854fd0e77abb723f572 + md5: b09da2e7368c428e9220183e99ebbc56 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MSnbase, Biostrings, BiocStyle, testthat, knitr requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The rpx package implements an interface to proteomics data submitted to the ProteomeXchange consortium.' extra: identifiers: - biotools:rpx - doi:10.1038/nbt.2839 + parent_recipe: + name: bioconductor-rpx + path: recipes/bioconductor-rpx + version: 1.16.0 + diff --git a/recipes/bioconductor-rqc/build.sh b/recipes/bioconductor-rqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rqc/meta.yaml b/recipes/bioconductor-rqc/meta.yaml new file mode 100644 index 0000000000000..ebea1c4e87b88 --- /dev/null +++ b/recipes/bioconductor-rqc/meta.yaml @@ -0,0 +1,74 @@ +{% set version = "1.16.2" %} +{% set name = "Rqc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 58558b854ed79b3950d6f83db6cbf554 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-digest + - r-ggplot2 + - 'r-knitr >=1.7' + - r-markdown + - r-plyr + - 'r-rcpp >=0.11.6' + - r-reshape2 + - r-shiny + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-biovizbase >=1.30.0,<1.31.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - r-base + - r-digest + - r-ggplot2 + - 'r-knitr >=1.7' + - r-markdown + - r-plyr + - 'r-rcpp >=0.11.6' + - r-reshape2 + - r-shiny + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Rqc is an optimised tool designed for quality control and assessment of high-throughput sequencing data. It performs parallel processing of entire files and produces a report which contains a set of high-resolution graphics.' + diff --git a/recipes/bioconductor-rqt/build.sh b/recipes/bioconductor-rqt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rqt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rqt/meta.yaml b/recipes/bioconductor-rqt/meta.yaml new file mode 100644 index 0000000000000..880c054b23c5c --- /dev/null +++ b/recipes/bioconductor-rqt/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.8.0" %} +{% set name = "rqt" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7ce8c07744e2c70c68fb04ce7f7edab2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-car + - r-compquadform + - r-glmnet + - r-matrix + - r-metap + - r-pls + - r-runit + run: + - 'bioconductor-ropls >=1.14.0,<1.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-car + - r-compquadform + - r-glmnet + - r-matrix + - r-metap + - r-pls + - r-runit +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'Despite the recent advances of modern GWAS methods, it still remains an important problem of addressing calculation an effect size and corresponding p-value for the whole gene rather than for single variant. The R- package rqt offers gene-level GWAS meta-analysis. For more information, see: "Gene-set association tests for next-generation sequencing data" by Lee et al (2016), Bioinformatics, 32(17), i611-i619, .' + diff --git a/recipes/bioconductor-rqubic/build.sh b/recipes/bioconductor-rqubic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rqubic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rqubic/meta.yaml b/recipes/bioconductor-rqubic/meta.yaml new file mode 100644 index 0000000000000..e77ccba944fda --- /dev/null +++ b/recipes/bioconductor-rqubic/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.28.0" %} +{% set name = "rqubic" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9a57a107dffeee5d00f42aaaeab6400c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RColorBrewer +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-biclust + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - r-biclust + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package implements the QUBIC algorithm introduced by Li et al. for the qualitative biclustering with gene expression data.' + diff --git a/recipes/bioconductor-rrbsdata/meta.yaml b/recipes/bioconductor-rrbsdata/meta.yaml new file mode 100644 index 0000000000000..4d55287a61c61 --- /dev/null +++ b/recipes/bioconductor-rrbsdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "RRBSdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0b5b0c9b0b5dba4129cc67482eb24e58 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biseq >=1.22.0,<1.23.0' + - r-base + run: + - 'bioconductor-biseq >=1.22.0,<1.23.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-3 + summary: 'RRBS data set comprising 12 samples with simulated differentially methylated regions (DMRs).' + diff --git a/recipes/bioconductor-rrbsdata/post-link.sh b/recipes/bioconductor-rrbsdata/post-link.sh new file mode 100644 index 0000000000000..4db532fa3745e --- /dev/null +++ b/recipes/bioconductor-rrbsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RRBSdata_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RRBSdata_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RRBSdata_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rrbsdata/bioconductor-rrbsdata_1.2.0_src_all.tar.gz" +) +MD5="0b5b0c9b0b5dba4129cc67482eb24e58" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rrbsdata/pre-unlink.sh b/recipes/bioconductor-rrbsdata/pre-unlink.sh new file mode 100644 index 0000000000000..4eaac70510516 --- /dev/null +++ b/recipes/bioconductor-rrbsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RRBSdata diff --git a/recipes/bioconductor-rrdp/build.sh b/recipes/bioconductor-rrdp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rrdp/build.sh +++ b/recipes/bioconductor-rrdp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rrdp/meta.yaml b/recipes/bioconductor-rrdp/meta.yaml index e77374e5f46d0..ebb942388e9e0 100644 --- a/recipes/bioconductor-rrdp/meta.yaml +++ b/recipes/bioconductor-rrdp/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "rRDP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 62f7bdf12d3322afb1756b7aa899244baa7b1d83763112bc7894700c6525b228 + md5: 2a7b1489cb060197edd55b4a334d7cc3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: rRDPData +# SystemRequirements: Java requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-2 | file LICENSE' summary: 'Seamlessly interfaces RDP classifier (version 2.9).' extra: identifiers: - biotools:rrdp - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rrdp + path: recipes/bioconductor-rrdp + version: 1.14.0 + diff --git a/recipes/bioconductor-rrdpdata/meta.yaml b/recipes/bioconductor-rrdpdata/meta.yaml new file mode 100644 index 0000000000000..4ba3f44b461e1 --- /dev/null +++ b/recipes/bioconductor-rrdpdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.2.0" %} +{% set name = "rRDPData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 92bc7797510726832537d8aafdcb220d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# SystemRequirements: Java +requirements: + host: + - 'bioconductor-rrdp >=1.16.0,<1.17.0' + - r-base + run: + - 'bioconductor-rrdp >=1.16.0,<1.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Database used by the default RDP Classifier' + diff --git a/recipes/bioconductor-rrdpdata/post-link.sh b/recipes/bioconductor-rrdpdata/post-link.sh new file mode 100644 index 0000000000000..9e281ed4bd9e1 --- /dev/null +++ b/recipes/bioconductor-rrdpdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rRDPData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/rRDPData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/rRDPData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rrdpdata/bioconductor-rrdpdata_1.2.0_src_all.tar.gz" +) +MD5="92bc7797510726832537d8aafdcb220d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rrdpdata/pre-unlink.sh b/recipes/bioconductor-rrdpdata/pre-unlink.sh new file mode 100644 index 0000000000000..653c3b85f7344 --- /dev/null +++ b/recipes/bioconductor-rrdpdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rRDPData diff --git a/recipes/bioconductor-rrho/build.sh b/recipes/bioconductor-rrho/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rrho/build.sh +++ b/recipes/bioconductor-rrho/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rrho/meta.yaml b/recipes/bioconductor-rrho/meta.yaml index a89f77548ab0b..7ea007dc9f375 100644 --- a/recipes/bioconductor-rrho/meta.yaml +++ b/recipes/bioconductor-rrho/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RRHO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6623394bcf317f9ae880fc19635b6d686b398a263841cda3cf61ff0135e8eb16 + md5: 04b3d6a5bda498c229c22855b329bbb8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: lattice requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package is aimed at inference on the amount of agreement in two sorted lists using the Rank-Rank Hypergeometric Overlap test.' extra: identifiers: - biotools:rrho - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rrho + path: recipes/bioconductor-rrho + version: 1.20.0 + diff --git a/recipes/bioconductor-rsamtools/build.sh b/recipes/bioconductor-rsamtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rsamtools/build.sh +++ b/recipes/bioconductor-rsamtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rsamtools/meta.yaml b/recipes/bioconductor-rsamtools/meta.yaml index 4b648ecbdbab7..f84774d757f5f 100644 --- a/recipes/bioconductor-rsamtools/meta.yaml +++ b/recipes/bioconductor-rsamtools/meta.yaml @@ -1,44 +1,45 @@ -{% set version = "1.32.3" %} +{% set version = "1.34.0" %} {% set name = "Rsamtools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 18da1af49cb11008d9c6b55e67f4a1859afd711e486ab09f23ee8e0185c8f2c2 + md5: cf950e0d0ff34e8464ac04a33aa86d9d build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: GenomicAlignments, ShortRead (>= 1.19.10), GenomicFeatures, TxDb.Dmelanogaster.UCSC.dm3.ensGene, KEGG.db, TxDb.Hsapiens.UCSC.hg18.knownGene, RNAseqData.HNRNPC.bam.chr14, BSgenome.Hsapiens.UCSC.hg19, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-bitops run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-bitops build: @@ -49,10 +50,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 | file LICENSE' summary: 'This package provides an interface to the ''samtools'', ''bcftools'', and ''tabix'' utilities (see ''LICENCE'') for manipulating SAM (Sequence Alignment / Map), FASTA, binary variant call (BCF) and compressed indexed tab-delimited (tabix) files.' extra: identifiers: - biotools:rsamtools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rsamtools + path: recipes/bioconductor-rsamtools + version: 1.32.3 + diff --git a/recipes/bioconductor-rsbml/build.sh b/recipes/bioconductor-rsbml/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rsbml/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rsbml/meta.yaml b/recipes/bioconductor-rsbml/meta.yaml new file mode 100644 index 0000000000000..3a02747d2c291 --- /dev/null +++ b/recipes/bioconductor-rsbml/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "2.40.0" %} +{% set name = "rsbml" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c273ebb42e08542258b93904b3e132e4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# SystemRequirements: libsbml (==5.10.2) +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Links R to libsbml for SBML parsing, validating output, provides an S4 SBML DOM, converts SBML to R graph objects. Optionally links to the SBML ODE Solver Library (SOSLib) for simulating models.' + diff --git a/recipes/bioconductor-rseqan/build.sh b/recipes/bioconductor-rseqan/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rseqan/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rseqan/meta.yaml b/recipes/bioconductor-rseqan/meta.yaml new file mode 100644 index 0000000000000..744f144e8a4f6 --- /dev/null +++ b/recipes/bioconductor-rseqan/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "RSeqAn" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3ccf58bab71c87b4df1c300b4766d750 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'BSD_3_clause + file LICENSE' + summary: 'Headers from the SeqAn C++ library for easy of usage in R.' + diff --git a/recipes/bioconductor-rsffreader/build.sh b/recipes/bioconductor-rsffreader/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rsffreader/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rsffreader/meta.yaml b/recipes/bioconductor-rsffreader/meta.yaml new file mode 100644 index 0000000000000..87f77d8ed1dca --- /dev/null +++ b/recipes/bioconductor-rsffreader/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "0.30.0" %} +{% set name = "rSFFreader" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3d8f6fb10462ef51867185257accc61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: xtable +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'rSFFreader reads sequence, qualities and clip point values from sff files generated by Roche 454 and Life Sciences Ion Torrent sequencers into similar classes as are present for fastq files.' + diff --git a/recipes/bioconductor-rsubread/build.sh b/recipes/bioconductor-rsubread/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rsubread/build.sh +++ b/recipes/bioconductor-rsubread/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rsubread/meta.yaml b/recipes/bioconductor-rsubread/meta.yaml index 16e1294e05aab..d83e583e3e849 100644 --- a/recipes/bioconductor-rsubread/meta.yaml +++ b/recipes/bioconductor-rsubread/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.30.9" %} +{% set version = "1.32.2" %} {% set name = "Rsubread" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 57673882455021a2656e56798da722864b2b1e0aaa9ab5783952179e6af7b323 + md5: f88cd9135e0197dcd179ad0bcbc3d3a5 build: number: 0 rpaths: @@ -29,9 +29,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Rsubread is a toolbox developed for the analyses of second and third generation sequencing data. It can be used for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and it is suitable for the analysis of both short and long reads.' + summary: 'Rsubread is a toolbox developed for the analyses of second and third generation sequencing data. It can be used for read mapping, read counting, SNP calling, structural variant detection and gene fusion discovery. It can be applied to all major sequencing techologies and is suitable for the analysis of both short and long reads.' extra: identifiers: - biotools:rsubread + parent_recipe: + name: bioconductor-rsubread + path: recipes/bioconductor-rsubread + version: 1.30.9 + diff --git a/recipes/bioconductor-rsvsim/build.sh b/recipes/bioconductor-rsvsim/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rsvsim/build.sh +++ b/recipes/bioconductor-rsvsim/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rsvsim/meta.yaml b/recipes/bioconductor-rsvsim/meta.yaml index c75a9ae307c4d..5e66c83a5e70b 100644 --- a/recipes/bioconductor-rsvsim/meta.yaml +++ b/recipes/bioconductor-rsvsim/meta.yaml @@ -1,42 +1,49 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "RSVSim" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 354192b279452b0396eacea6e0b1df60326f2f4e165027b252e5dd81b87790dc + md5: 161be094cdccdb551c4e702d1c687b4b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked, MASS, rtracklayer requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'RSVSim is a package for the simulation of deletions, insertions, inversion, tandem-duplications and translocations of various sizes in any genome available as FASTA-file or BSgenome data package. SV breakpoints can be placed uniformly accross the whole genome, with a bias towards repeat regions and regions of high homology (for hg19) or at user-supplied coordinates.' extra: identifiers: - biotools:rsvsim - doi:10.1093/bioinformatics/btt198 + parent_recipe: + name: bioconductor-rsvsim + path: recipes/bioconductor-rsvsim + version: 1.20.0 + diff --git a/recipes/bioconductor-rta10probeset.db/meta.yaml b/recipes/bioconductor-rta10probeset.db/meta.yaml new file mode 100644 index 0000000000000..9b33e6b33e7ed --- /dev/null +++ b/recipes/bioconductor-rta10probeset.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "rta10probeset.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 62d35f5ac75a51c2ac91730fd681d031 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix rta10 annotation data (chip rta10probeset) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rta10probeset.db/post-link.sh b/recipes/bioconductor-rta10probeset.db/post-link.sh new file mode 100644 index 0000000000000..ead626c812a94 --- /dev/null +++ b/recipes/bioconductor-rta10probeset.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rta10probeset.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rta10probeset.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/rta10probeset.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rta10probeset.db/bioconductor-rta10probeset.db_8.7.0_src_all.tar.gz" +) +MD5="62d35f5ac75a51c2ac91730fd681d031" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rta10probeset.db/pre-unlink.sh b/recipes/bioconductor-rta10probeset.db/pre-unlink.sh new file mode 100644 index 0000000000000..958e09f49026a --- /dev/null +++ b/recipes/bioconductor-rta10probeset.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rta10probeset.db diff --git a/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml new file mode 100644 index 0000000000000..b14c2eb5c1b73 --- /dev/null +++ b/recipes/bioconductor-rta10transcriptcluster.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "8.7.0" %} +{% set name = "rta10transcriptcluster.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c6a854395aec7296ffb7d98534b112f7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix rta10 annotation data (chip rta10transcriptcluster) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh b/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh new file mode 100644 index 0000000000000..1f826208f5173 --- /dev/null +++ b/recipes/bioconductor-rta10transcriptcluster.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rta10transcriptcluster.db_8.7.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rta10transcriptcluster.db_8.7.0.tar.gz" + "https://bioarchive.galaxyproject.org/rta10transcriptcluster.db_8.7.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rta10transcriptcluster.db/bioconductor-rta10transcriptcluster.db_8.7.0_src_all.tar.gz" +) +MD5="c6a854395aec7296ffb7d98534b112f7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rta10transcriptcluster.db/pre-unlink.sh b/recipes/bioconductor-rta10transcriptcluster.db/pre-unlink.sh new file mode 100644 index 0000000000000..fe04f0d94753e --- /dev/null +++ b/recipes/bioconductor-rta10transcriptcluster.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rta10transcriptcluster.db diff --git a/recipes/bioconductor-rtandem/build.sh b/recipes/bioconductor-rtandem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rtandem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtandem/meta.yaml b/recipes/bioconductor-rtandem/meta.yaml new file mode 100644 index 0000000000000..61bd907e8bb38 --- /dev/null +++ b/recipes/bioconductor-rtandem/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.22.0" %} +{% set name = "rTANDEM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c75cc2858cf9b87526cc5da50e93180c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: biomaRt +# SystemRequirements: rTANDEM uses expat and pthread libraries. See the README file for details. +requirements: + host: + - r-base + - 'r-data.table >=1.8.8' + - r-rcpp + - r-xml + run: + - r-base + - 'r-data.table >=1.8.8' + - r-rcpp + - r-xml + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Artistic-1.0 | file LICENSE' + summary: 'This package interfaces the tandem protein identification algorithm in R. Identification can be launched in the X!Tandem style, by using as sole parameter the path to a parameter file. But rTANDEM aslo provides extended syntax and functions to streamline launching analyses, as well as function to convert results, parameters and taxonomy to/from R. A related package, shinyTANDEM, provides visualization interface for result objects.' + diff --git a/recipes/bioconductor-rtca/build.sh b/recipes/bioconductor-rtca/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtca/build.sh +++ b/recipes/bioconductor-rtca/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtca/meta.yaml b/recipes/bioconductor-rtca/meta.yaml index 42eafe36fdf63..b8f8036e5ee71 100644 --- a/recipes/bioconductor-rtca/meta.yaml +++ b/recipes/bioconductor-rtca/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.32.0" %} +{% set version = "1.34.0" %} {% set name = "RTCA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e187ce8ce9482b78ae2ba3ec90aee2e5d2c8829111e615c1b6799b50dada3c20 + md5: bbaf16ffc7c5886019fdcd2f79780e4b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-gtools - r-rcolorbrewer @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'Import, analyze and visualize data from Roche(R) xCELLigence RTCA systems. The package imports real-time cell electrical impedance data into R. As an alternative to commercial software shipped along the system, the Bioconductor package RTCA provides several unique transformation (normalization) strategies and various visualization tools.' extra: identifiers: - biotools:rtca - doi:10.1016/j.compbiolchem.2013.12.004 + parent_recipe: + name: bioconductor-rtca + path: recipes/bioconductor-rtca + version: 1.32.0 + diff --git a/recipes/bioconductor-rtcga.clinical/meta.yaml b/recipes/bioconductor-rtcga.clinical/meta.yaml new file mode 100644 index 0000000000000..adc7b2345cd93 --- /dev/null +++ b/recipes/bioconductor-rtcga.clinical/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "20151101.12.0" %} +{% set name = "RTCGA.clinical" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8b41502e323b7992553be6850c754c40 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides clinical datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Clinical data format is explained here https://wiki.nci.nih.gov/display/TCGA/Clinical+Data+Overview. Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.clinical/post-link.sh b/recipes/bioconductor-rtcga.clinical/post-link.sh new file mode 100644 index 0000000000000..561cd22d7d049 --- /dev/null +++ b/recipes/bioconductor-rtcga.clinical/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.clinical_20151101.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.clinical_20151101.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.clinical_20151101.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.clinical/bioconductor-rtcga.clinical_20151101.12.0_src_all.tar.gz" +) +MD5="8b41502e323b7992553be6850c754c40" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.clinical/pre-unlink.sh b/recipes/bioconductor-rtcga.clinical/pre-unlink.sh new file mode 100644 index 0000000000000..a950cbcfecccd --- /dev/null +++ b/recipes/bioconductor-rtcga.clinical/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.clinical diff --git a/recipes/bioconductor-rtcga.cnv/meta.yaml b/recipes/bioconductor-rtcga.cnv/meta.yaml new file mode 100644 index 0000000000000..38959272aced0 --- /dev/null +++ b/recipes/bioconductor-rtcga.cnv/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "RTCGA.CNV" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 136f7ff44b65e7a2034e913694fbec9a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides CNV (based on Merge snp) datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Retrieving +Data+Using+the+Data+Matrix. Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.cnv/post-link.sh b/recipes/bioconductor-rtcga.cnv/post-link.sh new file mode 100644 index 0000000000000..ba68cab617ba6 --- /dev/null +++ b/recipes/bioconductor-rtcga.cnv/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.CNV_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.CNV_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.CNV_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.cnv/bioconductor-rtcga.cnv_1.10.0_src_all.tar.gz" +) +MD5="136f7ff44b65e7a2034e913694fbec9a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.cnv/pre-unlink.sh b/recipes/bioconductor-rtcga.cnv/pre-unlink.sh new file mode 100644 index 0000000000000..0925e9447bd55 --- /dev/null +++ b/recipes/bioconductor-rtcga.cnv/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.CNV diff --git a/recipes/bioconductor-rtcga.methylation/meta.yaml b/recipes/bioconductor-rtcga.methylation/meta.yaml new file mode 100644 index 0000000000000..c0f6dbd5cf0c5 --- /dev/null +++ b/recipes/bioconductor-rtcga.methylation/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "RTCGA.methylation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 769045e7855bdfbafdb6477a419b72fc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides methylation (humanmethylation27) datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/DNA+methylation Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.methylation/post-link.sh b/recipes/bioconductor-rtcga.methylation/post-link.sh new file mode 100644 index 0000000000000..3cf837d8374de --- /dev/null +++ b/recipes/bioconductor-rtcga.methylation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.methylation_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.methylation_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.methylation_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.methylation/bioconductor-rtcga.methylation_1.10.0_src_all.tar.gz" +) +MD5="769045e7855bdfbafdb6477a419b72fc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.methylation/pre-unlink.sh b/recipes/bioconductor-rtcga.methylation/pre-unlink.sh new file mode 100644 index 0000000000000..8073192818d36 --- /dev/null +++ b/recipes/bioconductor-rtcga.methylation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.methylation diff --git a/recipes/bioconductor-rtcga.mirnaseq/meta.yaml b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml new file mode 100644 index 0000000000000..01fd755e899a4 --- /dev/null +++ b/recipes/bioconductor-rtcga.mirnaseq/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "RTCGA.miRNASeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 245f55ab458f95ce93485c2e108a7a81 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides miRNASeq datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/miRNASeq#miRNASeq-DataOverview Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.mirnaseq/post-link.sh b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh new file mode 100644 index 0000000000000..3f5590930ddd7 --- /dev/null +++ b/recipes/bioconductor-rtcga.mirnaseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.miRNASeq_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.miRNASeq_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.miRNASeq_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mirnaseq/bioconductor-rtcga.mirnaseq_1.10.0_src_all.tar.gz" +) +MD5="245f55ab458f95ce93485c2e108a7a81" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.mirnaseq/pre-unlink.sh b/recipes/bioconductor-rtcga.mirnaseq/pre-unlink.sh new file mode 100644 index 0000000000000..74c35db343787 --- /dev/null +++ b/recipes/bioconductor-rtcga.mirnaseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.miRNASeq diff --git a/recipes/bioconductor-rtcga.mrna/meta.yaml b/recipes/bioconductor-rtcga.mrna/meta.yaml index 703dc34713ecf..42d0fbd759e5c 100644 --- a/recipes/bioconductor-rtcga.mrna/meta.yaml +++ b/recipes/bioconductor-rtcga.mrna/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "RTCGA.mRNA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6d4d430ef650985036851f38f3171091c27b15433ec56742c6124a7ff6de56cb + md5: 7b8d58ede359d36512a5c838c23f0ce2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-rtcga >=1.10.0,<1.12.0' + - 'bioconductor-rtcga >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-rtcga >=1.10.0,<1.12.0' + - 'bioconductor-rtcga >=1.12.0,<1.13.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-2 summary: 'Package provides mRNA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Gene+expression+data Data from 2015-11-01 snapshot.' - +extra: + parent_recipe: + name: bioconductor-rtcga.mrna + path: recipes/bioconductor-rtcga.mrna + version: 1.8.0 diff --git a/recipes/bioconductor-rtcga.mrna/post-link.sh b/recipes/bioconductor-rtcga.mrna/post-link.sh index 07dc9fc5b27e4..bc1d5d5536aa6 100644 --- a/recipes/bioconductor-rtcga.mrna/post-link.sh +++ b/recipes/bioconductor-rtcga.mrna/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RTCGA.mRNA_1.8.0.tar.gz" +FN="RTCGA.mRNA_1.10.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RTCGA.mRNA_1.8.0.tar.gz" - "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.8.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.8.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.mRNA_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.mRNA_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mrna/bioconductor-rtcga.mrna_1.10.0_src_all.tar.gz" ) -MD5="1d681a78685d12c2210f80cbb1429314" +MD5="7b8d58ede359d36512a5c838c23f0ce2" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-rtcga.mutations/meta.yaml b/recipes/bioconductor-rtcga.mutations/meta.yaml new file mode 100644 index 0000000000000..9a2a71c63698d --- /dev/null +++ b/recipes/bioconductor-rtcga.mutations/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "20151101.12.0" %} +{% set name = "RTCGA.mutations" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 742f2540bf6458f5b74a670666c5510a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides mutations datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Mutations data format is explained here https://wiki.nci.nih.gov/display/TCGA/Mutation+Annotation+Format+(MAF)+Specification. There is extra one column with patients'' barcodes. Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.mutations/post-link.sh b/recipes/bioconductor-rtcga.mutations/post-link.sh new file mode 100644 index 0000000000000..5f144571d89fc --- /dev/null +++ b/recipes/bioconductor-rtcga.mutations/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.mutations_20151101.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.mutations_20151101.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.mutations_20151101.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.mutations/bioconductor-rtcga.mutations_20151101.12.0_src_all.tar.gz" +) +MD5="742f2540bf6458f5b74a670666c5510a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.mutations/pre-unlink.sh b/recipes/bioconductor-rtcga.mutations/pre-unlink.sh new file mode 100644 index 0000000000000..7b4647a6223c3 --- /dev/null +++ b/recipes/bioconductor-rtcga.mutations/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.mutations diff --git a/recipes/bioconductor-rtcga.pancan12/meta.yaml b/recipes/bioconductor-rtcga.pancan12/meta.yaml new file mode 100644 index 0000000000000..c66b5e2aa1f71 --- /dev/null +++ b/recipes/bioconductor-rtcga.pancan12/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "RTCGA.PANCAN12" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 182d4b50b5b54b364dcec350ee225320 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides clinical, expression, cnv and mutation data from Genome Cancer Browser.' + diff --git a/recipes/bioconductor-rtcga.pancan12/post-link.sh b/recipes/bioconductor-rtcga.pancan12/post-link.sh new file mode 100644 index 0000000000000..41f2eec7a011b --- /dev/null +++ b/recipes/bioconductor-rtcga.pancan12/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.PANCAN12_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.PANCAN12_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.PANCAN12_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.pancan12/bioconductor-rtcga.pancan12_1.10.0_src_all.tar.gz" +) +MD5="182d4b50b5b54b364dcec350ee225320" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.pancan12/pre-unlink.sh b/recipes/bioconductor-rtcga.pancan12/pre-unlink.sh new file mode 100644 index 0000000000000..200e8ea9eb424 --- /dev/null +++ b/recipes/bioconductor-rtcga.pancan12/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.PANCAN12 diff --git a/recipes/bioconductor-rtcga.rnaseq/meta.yaml b/recipes/bioconductor-rtcga.rnaseq/meta.yaml new file mode 100644 index 0000000000000..fad57ca8b8f80 --- /dev/null +++ b/recipes/bioconductor-rtcga.rnaseq/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "20151101.12.0" %} +{% set name = "RTCGA.rnaseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bf1eb3e02b137d9ded0089bd3a2c4f38 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides rna-seq datasets from The Cancer Genome Atlas Project for all cohorts types from http://gdac.broadinstitute.org/. Rna-seq data format is explained here https://wiki.nci.nih.gov/display/TCGA/RNASeq+Version+2. Data source is illumina hiseq Level 3 RSEM normalized expression data. Data from 2015-11-01 snapshot.' + diff --git a/recipes/bioconductor-rtcga.rnaseq/post-link.sh b/recipes/bioconductor-rtcga.rnaseq/post-link.sh new file mode 100644 index 0000000000000..2e7b15fb7b4b0 --- /dev/null +++ b/recipes/bioconductor-rtcga.rnaseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.rnaseq_20151101.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.rnaseq_20151101.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.rnaseq_20151101.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.rnaseq/bioconductor-rtcga.rnaseq_20151101.12.0_src_all.tar.gz" +) +MD5="bf1eb3e02b137d9ded0089bd3a2c4f38" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.rnaseq/pre-unlink.sh b/recipes/bioconductor-rtcga.rnaseq/pre-unlink.sh new file mode 100644 index 0000000000000..b646642ead460 --- /dev/null +++ b/recipes/bioconductor-rtcga.rnaseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.rnaseq diff --git a/recipes/bioconductor-rtcga.rppa/meta.yaml b/recipes/bioconductor-rtcga.rppa/meta.yaml new file mode 100644 index 0000000000000..fe00f410d9928 --- /dev/null +++ b/recipes/bioconductor-rtcga.rppa/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "RTCGA.RPPA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 22570706e120890e3bc21225a910409b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-rtcga >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Package provides RPPA datasets from The Cancer Genome Atlas Project for all available cohorts types from http://gdac.broadinstitute.org/. Data format is explained here https://wiki.nci.nih.gov/display/TCGA/Protein+Array +Data+Format+Specification?src=search' + diff --git a/recipes/bioconductor-rtcga.rppa/post-link.sh b/recipes/bioconductor-rtcga.rppa/post-link.sh new file mode 100644 index 0000000000000..cbb40d5127d95 --- /dev/null +++ b/recipes/bioconductor-rtcga.rppa/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="RTCGA.RPPA_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RTCGA.RPPA_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/RTCGA.RPPA_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtcga.rppa/bioconductor-rtcga.rppa_1.10.0_src_all.tar.gz" +) +MD5="22570706e120890e3bc21225a910409b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtcga.rppa/pre-unlink.sh b/recipes/bioconductor-rtcga.rppa/pre-unlink.sh new file mode 100644 index 0000000000000..ea92b63e2dc41 --- /dev/null +++ b/recipes/bioconductor-rtcga.rppa/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ RTCGA.RPPA diff --git a/recipes/bioconductor-rtcga/build.sh b/recipes/bioconductor-rtcga/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtcga/build.sh +++ b/recipes/bioconductor-rtcga/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtcga/meta.yaml b/recipes/bioconductor-rtcga/meta.yaml index a08438224c210..3b7f2a2f8a2fd 100644 --- a/recipes/bioconductor-rtcga/meta.yaml +++ b/recipes/bioconductor-rtcga/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "RTCGA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b58175428a99bc3b46ec5e5f50d809442c78c6bc9aa0d7bb32bbbc8b15d2a48 + md5: f8fb7bb4b883c84995b2ed4af281b197 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: devtools, testthat, pander, Biobase, GenomicRanges, IRanges, S4Vectors, RTCGA.rnaseq, RTCGA.clinical, RTCGA.mutations, RTCGA.RPPA, RTCGA.mRNA, RTCGA.miRNASeq, RTCGA.methylation, RTCGA.CNV, RTCGA.PANCAN12, magrittr, tidyr requirements: host: - r-assertthat @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The key is to understand genomics to improve cancer care. RTCGA package offers download and integration of the variety and volume of TCGA data using patient barcode key, what enables easier data possession. This may have an benefcial infuence on impact on development of science and improvement of patients'' treatment. Furthermore, RTCGA package transforms TCGA data to tidy form which is convenient to use.' extra: identifiers: - biotools:rtcga - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rtcga + path: recipes/bioconductor-rtcga + version: 1.10.0 + diff --git a/recipes/bioconductor-rtcgatoolbox/build.sh b/recipes/bioconductor-rtcgatoolbox/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtcgatoolbox/build.sh +++ b/recipes/bioconductor-rtcgatoolbox/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtcgatoolbox/meta.yaml b/recipes/bioconductor-rtcgatoolbox/meta.yaml index 51f4951894966..d38fc4a3d4bc5 100644 --- a/recipes/bioconductor-rtcgatoolbox/meta.yaml +++ b/recipes/bioconductor-rtcgatoolbox/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.1" %} {% set name = "RTCGAToolbox" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 34cc165a907c64898dd096234155b946d6ff87a097c1cc0b65eb68856ee573b8 + md5: 9644f99d8dea390f69387baf45f5fb9a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, Homo.sapiens, knitr, readr, rmarkdown requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-raggedexperiment >=1.4.0,<1.6.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgautils >=1.2.0,<1.3.0' - r-base - - 'r-data.table >=1.9.4' - - r-httr - - r-plyr + - r-data.table - r-rcircos - r-rcurl - r-rjsonio @@ -38,19 +39,18 @@ requirements: - r-survival - r-xml run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-raggedexperiment >=1.4.0,<1.6.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgautils >=1.2.0,<1.3.0' - r-base - - 'r-data.table >=1.9.4' - - r-httr - - r-plyr + - r-data.table - r-rcircos - r-rcurl - r-rjsonio @@ -61,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Managing data from large scale projects such as The Cancer Genome Atlas (TCGA) for further analysis is an important and time consuming step for research projects. Several efforts, such as Firehose project, make TCGA pre-processed data publicly available via web services and data portals but it requires managing, downloading and preparing the data for following steps. We developed an open source and extensible R based data client for Firehose pre-processed data and demonstrated its use with sample case studies. Results showed that RTCGAToolbox could improve data management for researchers who are interested with TCGA data. In addition, it can be integrated with other analysis pipelines for following data analysis.' extra: identifiers: - biotools:rtcgatoolbox + parent_recipe: + name: bioconductor-rtcgatoolbox + path: recipes/bioconductor-rtcgatoolbox + version: 2.10.0 + diff --git a/recipes/bioconductor-rtn/build.sh b/recipes/bioconductor-rtn/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rtn/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtn/meta.yaml b/recipes/bioconductor-rtn/meta.yaml new file mode 100644 index 0000000000000..8b99ea90f8e4d --- /dev/null +++ b/recipes/bioconductor-rtn/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "2.6.0" %} +{% set name = "RTN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 363f71df9984003cdbb95eb4fed87053 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-igraph + - r-mixtools + - r-snow + run: + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-minet >=3.40.0,<3.41.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-data.table + - r-igraph + - r-mixtools + - r-snow +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides classes and methods for transcriptional network inference and analysis. Modulators of transcription factor activity are assessed by conditional mutual information, and master regulators are mapped to phenotypes using different strategies, e.g., gene set enrichment, shadow and synergy analyses. Additionally, master regulators can be linked to genetic markers using eQTL/VSE analysis, taking advantage of the haplotype block structure mapped to the human genome in order to explore risk-associated SNPs identified in GWAS studies.' + diff --git a/recipes/bioconductor-rtnduals/build.sh b/recipes/bioconductor-rtnduals/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rtnduals/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtnduals/meta.yaml b/recipes/bioconductor-rtnduals/meta.yaml new file mode 100644 index 0000000000000..183af50df5cea --- /dev/null +++ b/recipes/bioconductor-rtnduals/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.6.0" %} +{% set name = "RTNduals" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 302f0702b4b1e40a1b3128e3b53c1435 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'RTNduals is a tool that searches for possible co-regulatory loops between regulon pairs generated by the RTN package. It compares the shared targets in order to infer ''dual regulons'', a new concept that tests whether regulators can co-operate or compete in influencing targets.' + diff --git a/recipes/bioconductor-rtnsurvival/build.sh b/recipes/bioconductor-rtnsurvival/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rtnsurvival/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtnsurvival/meta.yaml b/recipes/bioconductor-rtnsurvival/meta.yaml new file mode 100644 index 0000000000000..ffc2295550f71 --- /dev/null +++ b/recipes/bioconductor-rtnsurvival/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.6.0" %} +{% set name = "RTNsurvival" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 917fa8f14be19050667e0e5c42c36c75 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Fletcher2013b, pheatmap, knitr, rmarkdown, BiocStyle, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-rtnduals >=1.6.0,<1.7.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-rcolorbrewer + - r-scales + - r-survival + run: + - 'bioconductor-rtn >=2.6.0,<2.7.0' + - 'bioconductor-rtnduals >=1.6.0,<1.7.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-rcolorbrewer + - r-scales + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'RTNsurvival is a tool for integrating regulons generated by the RTN package with survival information. For a given regulon, the 2-tailed GSEA approach computes a differential Enrichment Score (dES) for each individual sample, and the dES distribution of all samples is then used to assess the survival statistics for the cohort. There are two main survival analysis workflows: a Cox Proportional Hazards approach used to model regulons as predictors of survival time, and a Kaplan-Meier analysis assessing the stratification of a cohort based on the regulon activity. All plots can be fine-tuned to the user''s specifications.' + diff --git a/recipes/bioconductor-rtopper/build.sh b/recipes/bioconductor-rtopper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtopper/build.sh +++ b/recipes/bioconductor-rtopper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtopper/meta.yaml b/recipes/bioconductor-rtopper/meta.yaml index 9b187f0cdf969..a3f0c55188fdc 100644 --- a/recipes/bioconductor-rtopper/meta.yaml +++ b/recipes/bioconductor-rtopper/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "RTopper" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b0bc090c0cdd2c717b069b6a86e8b4855929f2c8d1b1835670824d141dcf6869 + md5: 1248ca53c00dd4a687d62632bc75a1c5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma, org.Hs.eg.db, KEGG.db, GO.db requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'the RTopper package is designed to perform and integrate gene set enrichment results across multiple genomic platforms.' extra: identifiers: - biotools:rtopper + parent_recipe: + name: bioconductor-rtopper + path: recipes/bioconductor-rtopper + version: 1.26.0 + diff --git a/recipes/bioconductor-rtracklayer/build.sh b/recipes/bioconductor-rtracklayer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtracklayer/build.sh +++ b/recipes/bioconductor-rtracklayer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtracklayer/meta.yaml b/recipes/bioconductor-rtracklayer/meta.yaml index 1422f107b808a..ceb7647f1f5d4 100644 --- a/recipes/bioconductor-rtracklayer/meta.yaml +++ b/recipes/bioconductor-rtracklayer/meta.yaml @@ -1,47 +1,48 @@ -{% set version = "1.40.6" %} +{% set version = "1.42.1" %} {% set name = "rtracklayer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9470a3d892d7decd97a5fbe53298e6dada3847a595f00be2e02d057d3dedbdf3 + md5: ed9836f8c2d85972edb8a89f0d454c95 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome (>= 1.33.4), humanStemCell, microRNA (>= 1.1.1), genefilter, limma, org.Hs.eg.db, hgu133plus2.db, GenomicFeatures, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-rcurl >=1.4-2' - 'r-xml >=1.98-0' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - 'r-rcurl >=1.4-2' - 'r-xml >=1.98-0' @@ -53,9 +54,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'Extensible framework for interacting with multiple genome browsers (currently UCSC built-in) and manipulating annotation tracks in various formats (currently GFF, BED, bedGraph, BED15, WIG, BigWig and 2bit built-in). The user may export/import tracks to/from the supported browsers, as well as query and modify the browser state, such as the current viewport.' extra: identifiers: - biotools:rtracklayer + parent_recipe: + name: bioconductor-rtracklayer + path: recipes/bioconductor-rtracklayer + version: 1.40.6 + diff --git a/recipes/bioconductor-rtreemix/build.sh b/recipes/bioconductor-rtreemix/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtreemix/build.sh +++ b/recipes/bioconductor-rtreemix/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtreemix/meta.yaml b/recipes/bioconductor-rtreemix/meta.yaml index caa072e1ce1f1..32ffe8b26d82c 100644 --- a/recipes/bioconductor-rtreemix/meta.yaml +++ b/recipes/bioconductor-rtreemix/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.42.0" %} +{% set version = "1.44.0" %} {% set name = "Rtreemix" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 97a16f117b7ab351f3a151b03c4230b180058edf84ab0ec01f9e6bbf48d8c429 + md5: 54dad4f9295a159b1358b3e09ab86f12 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Rgraphviz requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-hmisc run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-hmisc build: @@ -35,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Rtreemix is a package that offers an environment for estimating the mutagenetic trees mixture models from cross-sectional data and using them for various predictions. It includes functions for fitting the trees mixture models, likelihood computations, model comparisons, waiting time estimations, stability analysis, etc.' extra: identifiers: - biotools:rtreemix - doi:10.1093/bioinformatics/btn410 + parent_recipe: + name: bioconductor-rtreemix + path: recipes/bioconductor-rtreemix + version: 1.42.0 + diff --git a/recipes/bioconductor-rtrm/build.sh b/recipes/bioconductor-rtrm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtrm/build.sh +++ b/recipes/bioconductor-rtrm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtrm/meta.yaml b/recipes/bioconductor-rtrm/meta.yaml index b54406e3ac0eb..73d501b1404ac 100644 --- a/recipes/bioconductor-rtrm/meta.yaml +++ b/recipes/bioconductor-rtrm/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "rTRM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cf70b7ce210d04f56a1e844e917d31696360dc55a3090a547b13ebf84025645a + md5: 2f3ca2f454102df0fb6790d11beb14e4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, MotifDb, graph, PWMEnrich, biomaRt, knitr, Biostrings, BSgenome.Mmusculus.UCSC.mm8.masked, org.Hs.eg.db, org.Mm.eg.db, ggplot2 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - 'r-igraph >=1.0' - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - r-dbi - 'r-igraph >=1.0' @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'rTRM identifies transcriptional regulatory modules (TRMs) from protein-protein interaction networks.' extra: identifiers: - biotools:rtrm + parent_recipe: + name: bioconductor-rtrm + path: recipes/bioconductor-rtrm + version: 1.18.0 + diff --git a/recipes/bioconductor-rtrmui/build.sh b/recipes/bioconductor-rtrmui/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-rtrmui/build.sh +++ b/recipes/bioconductor-rtrmui/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rtrmui/meta.yaml b/recipes/bioconductor-rtrmui/meta.yaml index cbab80514bc2c..ac4ae3b9bbf81 100644 --- a/recipes/bioconductor-rtrmui/meta.yaml +++ b/recipes/bioconductor-rtrmui/meta.yaml @@ -1,44 +1,50 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "rTRMui" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3118083703ff70dea3e53e7cd004e8eb9a6560e48eab10c48597d79ef468794b + md5: 1e0da9b0bbe347b9d4557d8dca91360f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-motifdb >=1.22.0,<1.24.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtrm >=1.18.0,<1.20.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtrm >=1.20.0,<1.21.0' - r-base - 'r-shiny >=0.9' run: - - 'bioconductor-motifdb >=1.22.0,<1.24.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rtrm >=1.18.0,<1.20.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rtrm >=1.20.0,<1.21.0' - r-base - 'r-shiny >=0.9' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a web interface to compute transcriptional regulatory modules with rTRM.' extra: identifiers: - biotools:rtrmui - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-rtrmui + path: recipes/bioconductor-rtrmui + version: 1.18.0 + diff --git a/recipes/bioconductor-rtu34.db/meta.yaml b/recipes/bioconductor-rtu34.db/meta.yaml new file mode 100644 index 0000000000000..86dca752a9579 --- /dev/null +++ b/recipes/bioconductor-rtu34.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "rtu34.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c598b5caedc421e104e2e541f396d213 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Rat Toxicology U34 Array annotation data (chip rtu34) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rtu34.db/post-link.sh b/recipes/bioconductor-rtu34.db/post-link.sh new file mode 100644 index 0000000000000..aab924d2deb5c --- /dev/null +++ b/recipes/bioconductor-rtu34.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rtu34.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/rtu34.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34.db/bioconductor-rtu34.db_3.2.3_src_all.tar.gz" +) +MD5="c598b5caedc421e104e2e541f396d213" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtu34.db/pre-unlink.sh b/recipes/bioconductor-rtu34.db/pre-unlink.sh new file mode 100644 index 0000000000000..e573ae206f470 --- /dev/null +++ b/recipes/bioconductor-rtu34.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rtu34.db diff --git a/recipes/bioconductor-rtu34cdf/meta.yaml b/recipes/bioconductor-rtu34cdf/meta.yaml new file mode 100644 index 0000000000000..1cd357917115a --- /dev/null +++ b/recipes/bioconductor-rtu34cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rtu34cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 317abfcca319d01eb14f16efa6d91da1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the RT_U34.cdf file.' + diff --git a/recipes/bioconductor-rtu34cdf/post-link.sh b/recipes/bioconductor-rtu34cdf/post-link.sh new file mode 100644 index 0000000000000..837dbeaa79856 --- /dev/null +++ b/recipes/bioconductor-rtu34cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rtu34cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rtu34cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34cdf/bioconductor-rtu34cdf_2.18.0_src_all.tar.gz" +) +MD5="317abfcca319d01eb14f16efa6d91da1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtu34cdf/pre-unlink.sh b/recipes/bioconductor-rtu34cdf/pre-unlink.sh new file mode 100644 index 0000000000000..b0bdcc6039566 --- /dev/null +++ b/recipes/bioconductor-rtu34cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rtu34cdf diff --git a/recipes/bioconductor-rtu34probe/meta.yaml b/recipes/bioconductor-rtu34probe/meta.yaml new file mode 100644 index 0000000000000..662173d399bdd --- /dev/null +++ b/recipes/bioconductor-rtu34probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "rtu34probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1778d857a61bf181b80b9fcf46ebd2c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was RT-U34\_probe\_tab.' + diff --git a/recipes/bioconductor-rtu34probe/post-link.sh b/recipes/bioconductor-rtu34probe/post-link.sh new file mode 100644 index 0000000000000..4273b022bebc0 --- /dev/null +++ b/recipes/bioconductor-rtu34probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rtu34probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rtu34probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/rtu34probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rtu34probe/bioconductor-rtu34probe_2.18.0_src_all.tar.gz" +) +MD5="1778d857a61bf181b80b9fcf46ebd2c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rtu34probe/pre-unlink.sh b/recipes/bioconductor-rtu34probe/pre-unlink.sh new file mode 100644 index 0000000000000..16f6e9506c227 --- /dev/null +++ b/recipes/bioconductor-rtu34probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rtu34probe diff --git a/recipes/bioconductor-runibic/build.sh b/recipes/bioconductor-runibic/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-runibic/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-runibic/meta.yaml b/recipes/bioconductor-runibic/meta.yaml new file mode 100644 index 0000000000000..d172fd52c267a --- /dev/null +++ b/recipes/bioconductor-runibic/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "runibic" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d0cedd151b4819370ba67bbde690ddf3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, GEOquery, affy, airway, QUBIC +# SystemRequirements: C++11, GNU make +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-biclust + - 'r-rcpp >=0.12.12' + - r-testthat + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-biclust + - 'r-rcpp >=0.12.12' + - r-testthat + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'This package implements UbiBic algorithm in R. This biclustering algorithm for analysis of gene expression data was introduced by Zhenjia Wang et al. in 2016. It is currently considered the most promising biclustering method for identification of meaningful structures in complex and noisy data.' + diff --git a/recipes/bioconductor-ruvcorr/build.sh b/recipes/bioconductor-ruvcorr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ruvcorr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ruvcorr/meta.yaml b/recipes/bioconductor-ruvcorr/meta.yaml new file mode 100644 index 0000000000000..8982f86f1c943 --- /dev/null +++ b/recipes/bioconductor-ruvcorr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.14.0" %} +{% set name = "RUVcorr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 158715467d2a0cb8bc83af04bd6ea3b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, hgu133a2.db +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' + - r-base + - r-corrplot + - r-gridextra + - r-lattice + - r-mass + - r-psych + - r-reshape2 + - r-snowfall + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-bladderbatch >=1.20.0,<1.21.0' + - r-base + - r-corrplot + - r-gridextra + - r-lattice + - r-mass + - r-psych + - r-reshape2 + - r-snowfall +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'RUVcorr allows to apply global removal of unwanted variation (ridged version of RUV) to real and simulated gene expression data.' + diff --git a/recipes/bioconductor-ruvnormalize/build.sh b/recipes/bioconductor-ruvnormalize/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ruvnormalize/build.sh +++ b/recipes/bioconductor-ruvnormalize/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ruvnormalize/meta.yaml b/recipes/bioconductor-ruvnormalize/meta.yaml index 20c61635a6ac4..d6b64d051e2fb 100644 --- a/recipes/bioconductor-ruvnormalize/meta.yaml +++ b/recipes/bioconductor-ruvnormalize/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RUVnormalize" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0d2eb8ee36e315b797d0aa1dc5fb189ca344122105f645352ab118044f882ade + md5: 167b64fcfec25e40893b0170df327ed1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ruvnormalizedata >=0.114.0,<0.116.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ruvnormalizedata >=1.2.0,<1.3.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-ruvnormalizedata >=0.114.0,<0.116.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ruvnormalizedata >=1.2.0,<1.3.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'RUVnormalize is meant to remove unwanted variation from gene expression data when the factor of interest is not defined, e.g., to clean up a dataset for general use or to do any kind of unsupervised analysis.' extra: identifiers: - biotools:ruvnormalize + parent_recipe: + name: bioconductor-ruvnormalize + path: recipes/bioconductor-ruvnormalize + version: 1.14.0 + diff --git a/recipes/bioconductor-ruvnormalizedata/meta.yaml b/recipes/bioconductor-ruvnormalizedata/meta.yaml index bf6fed4bf7c2f..a0267fc9e53b7 100644 --- a/recipes/bioconductor-ruvnormalizedata/meta.yaml +++ b/recipes/bioconductor-ruvnormalizedata/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "0.114.0" %} +{% set version = "1.2.0" %} {% set name = "RUVnormalizeData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6085d3cbf3770b481faee568fc2bf8ed68b869e837a322bee474aedd3736e4b1 + md5: 8c3859b5bf555e74be9d480d3ba9539b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL-3 summary: 'Microarray gene expression data from the study of Vawter et al., 2004.' - +extra: + parent_recipe: + name: bioconductor-ruvnormalizedata + path: recipes/bioconductor-ruvnormalizedata + version: 0.114.0 diff --git a/recipes/bioconductor-ruvnormalizedata/post-link.sh b/recipes/bioconductor-ruvnormalizedata/post-link.sh index 996433b75aaa1..99dda191def72 100644 --- a/recipes/bioconductor-ruvnormalizedata/post-link.sh +++ b/recipes/bioconductor-ruvnormalizedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="RUVnormalizeData_0.114.0.tar.gz" +FN="RUVnormalizeData_1.2.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/RUVnormalizeData_0.114.0.tar.gz" - "https://bioarchive.galaxyproject.org/RUVnormalizeData_0.114.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_0.114.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/RUVnormalizeData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/RUVnormalizeData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ruvnormalizedata/bioconductor-ruvnormalizedata_1.2.0_src_all.tar.gz" ) -MD5="116061e9ddf8357f83e5460ad86da991" +MD5="8c3859b5bf555e74be9d480d3ba9539b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-ruvseq/build.sh b/recipes/bioconductor-ruvseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ruvseq/build.sh +++ b/recipes/bioconductor-ruvseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ruvseq/meta.yaml b/recipes/bioconductor-ruvseq/meta.yaml index bf3a94ccce23e..4cd7ce9eb2b39 100644 --- a/recipes/bioconductor-ruvseq/meta.yaml +++ b/recipes/bioconductor-ruvseq/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "RUVSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b2e3eee8e6072b5a31ee108d621722963e6da744d15dbd3f99c11ca74ad5259a + md5: ca4bcbee94ae08bc71253b2ab4b96253 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RColorBrewer, zebrafishRNASeq, DESeq2 requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements the remove unwanted variation (RUV) methods of Risso et al. (2014) for the normalization of RNA-Seq read counts between samples.' extra: identifiers: - biotools:ruvseq + parent_recipe: + name: bioconductor-ruvseq + path: recipes/bioconductor-ruvseq + version: 1.14.0 + diff --git a/recipes/bioconductor-rvs/build.sh b/recipes/bioconductor-rvs/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rvs/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rvs/meta.yaml b/recipes/bioconductor-rvs/meta.yaml new file mode 100644 index 0000000000000..5ab103063e35e --- /dev/null +++ b/recipes/bioconductor-rvs/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.4.0" %} +{% set name = "RVS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 187862c0e1c2f0e21da5cb0012793d72 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, testthat, rmarkdown, BiocStyle +requirements: + host: + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - r-grain + - r-kinship2 + run: + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - r-base + - r-grain + - r-kinship2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).' + diff --git a/recipes/bioconductor-rwgcod.db/meta.yaml b/recipes/bioconductor-rwgcod.db/meta.yaml new file mode 100644 index 0000000000000..ea63cb8f3147d --- /dev/null +++ b/recipes/bioconductor-rwgcod.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.4.0" %} +{% set name = "rwgcod.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c8d2fa81b6f03c4ee629a0883431e5fd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.rn.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Codelink Rat Whole Genome Bioarray (~34 000 rat gene targets) annotation data (chip rwgcod) assembled using data from public repositories' + diff --git a/recipes/bioconductor-rwgcod.db/post-link.sh b/recipes/bioconductor-rwgcod.db/post-link.sh new file mode 100644 index 0000000000000..425f4a4fc3f44 --- /dev/null +++ b/recipes/bioconductor-rwgcod.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="rwgcod.db_3.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/rwgcod.db_3.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/rwgcod.db_3.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-rwgcod.db/bioconductor-rwgcod.db_3.4.0_src_all.tar.gz" +) +MD5="c8d2fa81b6f03c4ee629a0883431e5fd" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-rwgcod.db/pre-unlink.sh b/recipes/bioconductor-rwgcod.db/pre-unlink.sh new file mode 100644 index 0000000000000..c5ee1a53792ac --- /dev/null +++ b/recipes/bioconductor-rwgcod.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ rwgcod.db diff --git a/recipes/bioconductor-rwikipathways/build.sh b/recipes/bioconductor-rwikipathways/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-rwikipathways/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-rwikipathways/meta.yaml b/recipes/bioconductor-rwikipathways/meta.yaml new file mode 100644 index 0000000000000..92727e87503ac --- /dev/null +++ b/recipes/bioconductor-rwikipathways/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.2.0" %} +{% set name = "rWikiPathways" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c55c4213a1cd8da4a73083fa4f3c1b0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + - r-catools + - r-httr + - r-rjsonio + run: + - r-base + - r-catools + - r-httr + - r-rjsonio +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Use this package to interface with the WikiPathways API.' + diff --git a/recipes/bioconductor-s4vectors/build.sh b/recipes/bioconductor-s4vectors/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-s4vectors/build.sh +++ b/recipes/bioconductor-s4vectors/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-s4vectors/meta.yaml b/recipes/bioconductor-s4vectors/meta.yaml index c123a9068de32..f0370f7b15a2a 100644 --- a/recipes/bioconductor-s4vectors/meta.yaml +++ b/recipes/bioconductor-s4vectors/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "0.18.3" %} +{% set version = "0.20.1" %} {% set name = "S4Vectors" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c8b7f6045f48340a0d342572564cc8efa5c89915a60fdcf9b5a26379b3d07709 + md5: 688d781fb673cfb94e9f1c164be1e24e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: IRanges, GenomicRanges, SummarizedExperiment, Matrix, DelayedArray, ShortRead, graph, data.table, RUnit, BiocStyle requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The S4Vectors package defines the Vector and List virtual classes and a set of generic functions that extend the semantic of ordinary vectors and lists in R. Package developers can easily implement vector-like or list-like objects as concrete subclasses of Vector or List. In addition, a few low-level concrete subclasses of general interest (e.g. DataFrame, Rle, and Hits) are implemented in the S4Vectors package itself (many more are implemented in the IRanges package and in other Bioconductor infrastructure packages).' extra: identifiers: - biotools:s4vectors - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-s4vectors + path: recipes/bioconductor-s4vectors + version: 0.18.3 + diff --git a/recipes/bioconductor-safe/build.sh b/recipes/bioconductor-safe/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-safe/build.sh +++ b/recipes/bioconductor-safe/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-safe/meta.yaml b/recipes/bioconductor-safe/meta.yaml index ed2f33ef4f19a..acfe58db50896 100644 --- a/recipes/bioconductor-safe/meta.yaml +++ b/recipes/bioconductor-safe/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "3.20.0" %} +{% set version = "3.22.0" %} {% set name = "safe" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 06585dbf2589b828b28b0036149903255a8ed0524586f07f41003e8cfb564564 + md5: 130b1a1220cb3703b2fc990ae2059378 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GO.db, PFAM.db, reactome.db, hgu133a.db, breastCancerUPP, survival, foreach, doRNG, Rgraphviz, GOstats requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-sparsem run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-sparsem test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'SAFE is a resampling-based method for testing functional categories in gene expression experiments. SAFE can be applied to 2-sample and multi-class comparisons, or simple linear regressions. Other experimental designs can also be accommodated through user-defined functions.' extra: identifiers: - biotools:safe - doi:10.1093/bioinformatics/bti260 + parent_recipe: + name: bioconductor-safe + path: recipes/bioconductor-safe + version: 3.20.0 + diff --git a/recipes/bioconductor-sagenhaft/build.sh b/recipes/bioconductor-sagenhaft/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sagenhaft/build.sh +++ b/recipes/bioconductor-sagenhaft/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sagenhaft/meta.yaml b/recipes/bioconductor-sagenhaft/meta.yaml index 82737af388317..550b53bbb7ec4 100644 --- a/recipes/bioconductor-sagenhaft/meta.yaml +++ b/recipes/bioconductor-sagenhaft/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "sagenhaft" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 633e1e20461413e77db52cd4f86f5588fae837c99696e64bb0942d6d63311d3a + md5: 582c5897ff5d4d7395a42f4655e33962 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements several functions useful for analysis of gene expression data by sequencing tags as done in SAGE (Serial Analysis of Gene Expressen) data, i.e. extraction of a SAGE library from sequence files, sequence error correction, library comparison. Sequencing error correction is implementing using an Expectation Maximization Algorithm based on a Mixture Model of tag counts.' extra: identifiers: - biotools:sagenhaft - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sagenhaft + path: recipes/bioconductor-sagenhaft + version: 1.50.0 + diff --git a/recipes/bioconductor-sagx/build.sh b/recipes/bioconductor-sagx/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sagx/build.sh +++ b/recipes/bioconductor-sagx/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sagx/meta.yaml b/recipes/bioconductor-sagx/meta.yaml index 18c813df89436..2a6ebb3cdfb54 100644 --- a/recipes/bioconductor-sagx/meta.yaml +++ b/recipes/bioconductor-sagx/meta.yaml @@ -1,29 +1,30 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "SAGx" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a59a6d8e5bc536be0ca046145abba776f0098072cc4c31cacfdabdc8cda61402 + md5: 3b4d03837b6be876bd3969c8f0d2a04f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: KEGG.db, hu6800.db, MASS requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base build: - {{ compiler('c') }} @@ -32,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A package for retrieval, preparation and analysis of data from the Affymetrix GeneChip. In particular the issue of identifying differentially expressed genes is addressed.' extra: identifiers: - biotools:sagx - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sagx + path: recipes/bioconductor-sagx + version: 1.54.0 + diff --git a/recipes/bioconductor-samexplorer/build.sh b/recipes/bioconductor-samexplorer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-samexplorer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-samexplorer/meta.yaml b/recipes/bioconductor-samexplorer/meta.yaml new file mode 100644 index 0000000000000..1477f53c89d29 --- /dev/null +++ b/recipes/bioconductor-samexplorer/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.0" %} +{% set name = "samExploreR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cb0b939e582fc62a1a6aedf71529ffc4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle,RUnit,BiocGenerics,Matrix +requirements: + host: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.20.0,<0.21.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 + run: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-rnaseqdata.hnrnpc.bam.chr14 >=0.20.0,<0.21.0' + - 'bioconductor-rsubread >=1.32.0,<1.33.0' + - r-base + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This R package is designed for subsampling procedure to simulate sequencing experiments with reduced sequencing depth. This package can be used to anlayze data generated from all major sequencing platforms such as Illumina GA, HiSeq, MiSeq, Roche GS-FLX, ABI SOLiD and LifeTech Ion PGM Proton sequencers. It supports multiple operating systems incluidng Linux, Mac OS X, FreeBSD and Solaris. Was developed with usage of Rsubread.' + diff --git a/recipes/bioconductor-sampleclassifier/build.sh b/recipes/bioconductor-sampleclassifier/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sampleclassifier/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sampleclassifier/meta.yaml b/recipes/bioconductor-sampleclassifier/meta.yaml new file mode 100644 index 0000000000000..baedfc96dfb4c --- /dev/null +++ b/recipes/bioconductor-sampleclassifier/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.6.0" %} +{% set name = "sampleClassifier" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 605d9bcc34512ef553d246c2168e79a3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: sampleClassifierData, BiocStyle, hgu133a.db, hgu133plus2.db +requirements: + host: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-mgfm >=1.16.0,<1.17.0' + - 'bioconductor-mgfr >=1.8.0,<1.9.0' + - r-base + - r-e1071 + - r-ggplot2 + run: + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-mgfm >=1.16.0,<1.17.0' + - 'bioconductor-mgfr >=1.8.0,<1.9.0' + - r-base + - r-e1071 + - r-ggplot2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package is designed to classify gene expression profiles.' + diff --git a/recipes/bioconductor-sampleclassifierdata/meta.yaml b/recipes/bioconductor-sampleclassifierdata/meta.yaml new file mode 100644 index 0000000000000..99f2a9d3eec97 --- /dev/null +++ b/recipes/bioconductor-sampleclassifierdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.6.0" %} +{% set name = "sampleClassifierData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 82f2071bfa8b19d3909760e813dfa760 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package contains two microarray and two RNA-seq datasets that have been preprocessed for use with the sampleClassifier package. The RNA-seq data are derived from Fagerberg et al. (2014) and the Illumina Body Map 2.0 data. The microarray data are derived from Roth et al. (2006) and Ge et al. (2005).' + diff --git a/recipes/bioconductor-sampleclassifierdata/post-link.sh b/recipes/bioconductor-sampleclassifierdata/post-link.sh new file mode 100644 index 0000000000000..7ae2155f81e6f --- /dev/null +++ b/recipes/bioconductor-sampleclassifierdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="sampleClassifierData_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/sampleClassifierData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/sampleClassifierData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sampleclassifierdata/bioconductor-sampleclassifierdata_1.6.0_src_all.tar.gz" +) +MD5="82f2071bfa8b19d3909760e813dfa760" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sampleclassifierdata/pre-unlink.sh b/recipes/bioconductor-sampleclassifierdata/pre-unlink.sh new file mode 100644 index 0000000000000..532d0ea4d31a9 --- /dev/null +++ b/recipes/bioconductor-sampleclassifierdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ sampleClassifierData diff --git a/recipes/bioconductor-samspectral/build.sh b/recipes/bioconductor-samspectral/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-samspectral/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-samspectral/meta.yaml b/recipes/bioconductor-samspectral/meta.yaml new file mode 100644 index 0000000000000..f3adfdddf5cc6 --- /dev/null +++ b/recipes/bioconductor-samspectral/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.36.0" %} +{% set name = "SamSPECTRAL" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 669e199f0f3c258d47ed388201cd04d2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting "connected components" estimate biological cell populations in the data. See the vignette for more details on how to use this package, some illustrations, and simple examples.' + diff --git a/recipes/bioconductor-sangerseqr/build.sh b/recipes/bioconductor-sangerseqr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sangerseqr/build.sh +++ b/recipes/bioconductor-sangerseqr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sangerseqr/meta.yaml b/recipes/bioconductor-sangerseqr/meta.yaml index 5c43df3f5d2b9..75744f6956bee 100644 --- a/recipes/bioconductor-sangerseqr/meta.yaml +++ b/recipes/bioconductor-sangerseqr/meta.yaml @@ -1,37 +1,44 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "sangerseqR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 70cf453d88d8b4573fd0c948398a3a7127318c6470b4a5eb9a4787e2d5025d0c + md5: a9087a41aa05c312e686f3b5578f82ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, RUnit, BiocGenerics requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-shiny run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - r-shiny test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package contains several tools for analyzing Sanger Sequencing data files in R, including reading .scf and .ab1 files, making basecalls and plotting chromatograms.' extra: identifiers: - biotools:sangerseqr + parent_recipe: + name: bioconductor-sangerseqr + path: recipes/bioconductor-sangerseqr + version: 1.16.0 + diff --git a/recipes/bioconductor-santa/build.sh b/recipes/bioconductor-santa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-santa/build.sh +++ b/recipes/bioconductor-santa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-santa/meta.yaml b/recipes/bioconductor-santa/meta.yaml index 1fbf01b625bcb..d02582cd6d9eb 100644 --- a/recipes/bioconductor-santa/meta.yaml +++ b/recipes/bioconductor-santa/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.18.0" %} +{% set version = "2.20.0" %} {% set name = "SANTA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0bf040813afe4abf395a4231a539d47b02ebdc51b12a751aa975180477b796b3 + md5: 2d2c95468044819a5b1b41c4a563e636 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics, knitr, knitcitations, formatR, org.Sc.sgd.db, BioNet, DLBCL, msm requirements: host: - r-base @@ -34,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package provides methods for measuring the strength of association between a network and a phenotype. It does this by measuring clustering of the phenotype across the network (Knet). Vertices can also be individually ranked by their strength of association with high-weight vertices (Knode).' extra: identifiers: - biotools:santa + parent_recipe: + name: bioconductor-santa + path: recipes/bioconductor-santa + version: 2.18.0 + diff --git a/recipes/bioconductor-sapfinder/build.sh b/recipes/bioconductor-sapfinder/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sapfinder/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sapfinder/meta.yaml b/recipes/bioconductor-sapfinder/meta.yaml new file mode 100644 index 0000000000000..e51ab9bfb84cc --- /dev/null +++ b/recipes/bioconductor-sapfinder/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.20.0" %} +{% set name = "sapFinder" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 39da7f2c1d2a4832b64cee25d9bdc6b2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocGenerics, BiocStyle +requirements: + host: + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-pheatmap + - 'r-rcpp >=0.10.6' + run: + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-pheatmap + - 'r-rcpp >=0.10.6' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'sapFinder is developed to automate (1) variation-associated database construction, (2) database searching, (3) post-processing, (4) HTML-based report generation in shotgun proteomics.' + diff --git a/recipes/bioconductor-saureuscdf/meta.yaml b/recipes/bioconductor-saureuscdf/meta.yaml new file mode 100644 index 0000000000000..fbaa3990fca91 --- /dev/null +++ b/recipes/bioconductor-saureuscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "saureuscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d01883e4c3dd99f32012e6dbab8cdb8b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the S_aureus.cdf file.' + diff --git a/recipes/bioconductor-saureuscdf/post-link.sh b/recipes/bioconductor-saureuscdf/post-link.sh new file mode 100644 index 0000000000000..fdb9e299da0b0 --- /dev/null +++ b/recipes/bioconductor-saureuscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="saureuscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/saureuscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/saureuscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-saureuscdf/bioconductor-saureuscdf_2.18.0_src_all.tar.gz" +) +MD5="d01883e4c3dd99f32012e6dbab8cdb8b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-saureuscdf/pre-unlink.sh b/recipes/bioconductor-saureuscdf/pre-unlink.sh new file mode 100644 index 0000000000000..b546739d99fd1 --- /dev/null +++ b/recipes/bioconductor-saureuscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ saureuscdf diff --git a/recipes/bioconductor-saureusprobe/meta.yaml b/recipes/bioconductor-saureusprobe/meta.yaml new file mode 100644 index 0000000000000..5e571e26a8ad0 --- /dev/null +++ b/recipes/bioconductor-saureusprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "saureusprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eb4e91b10a536cbde4ecc08951ddf4d3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was S\_aureus\_probe\_tab.' + diff --git a/recipes/bioconductor-saureusprobe/post-link.sh b/recipes/bioconductor-saureusprobe/post-link.sh new file mode 100644 index 0000000000000..2c4eeed869409 --- /dev/null +++ b/recipes/bioconductor-saureusprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="saureusprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/saureusprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/saureusprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-saureusprobe/bioconductor-saureusprobe_2.18.0_src_all.tar.gz" +) +MD5="eb4e91b10a536cbde4ecc08951ddf4d3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-saureusprobe/pre-unlink.sh b/recipes/bioconductor-saureusprobe/pre-unlink.sh new file mode 100644 index 0000000000000..ece5d766812ed --- /dev/null +++ b/recipes/bioconductor-saureusprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ saureusprobe diff --git a/recipes/bioconductor-savr/build.sh b/recipes/bioconductor-savr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-savr/build.sh +++ b/recipes/bioconductor-savr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-savr/meta.yaml b/recipes/bioconductor-savr/meta.yaml index f3d3e4a229a4a..20e83c92f236a 100644 --- a/recipes/bioconductor-savr/meta.yaml +++ b/recipes/bioconductor-savr/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "savR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0bc9de78d8df417bbf01eb78e0a8337a135f52d6ac5fecbf23e3e0b9c1985c9f + md5: 765521fb53c6b8ab25bbd2ff26efe67b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Cairo, testthat requirements: host: - r-base @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'Parse Illumina Sequence Analysis Viewer (SAV) files, access data, and generate QC plots.' extra: identifiers: - biotools:savr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-savr + path: recipes/bioconductor-savr + version: 1.18.0 + diff --git a/recipes/bioconductor-sbmlr/build.sh b/recipes/bioconductor-sbmlr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sbmlr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sbmlr/meta.yaml b/recipes/bioconductor-sbmlr/meta.yaml new file mode 100644 index 0000000000000..dfc6cb4940570 --- /dev/null +++ b/recipes/bioconductor-sbmlr/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.78.0" %} +{% set name = "SBMLR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8263d9957245263681e6349e13058a2c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rsbml +requirements: + host: + - r-base + - r-desolve + - r-xml + run: + - r-base + - r-desolve + - r-xml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package contains a systems biology markup language (SBML) interface to R.' + diff --git a/recipes/bioconductor-sc3/build.sh b/recipes/bioconductor-sc3/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sc3/build.sh +++ b/recipes/bioconductor-sc3/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sc3/conda_build_config.yaml b/recipes/bioconductor-sc3/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-sc3/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-sc3/meta.yaml b/recipes/bioconductor-sc3/meta.yaml index c675756455ffa..a1fef7e14801a 100644 --- a/recipes/bioconductor-sc3/meta.yaml +++ b/recipes/bioconductor-sc3/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SC3" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4865fd2e94a7a2fe26ac9fc9d6b7d0c0b4820eeab8e8b222420e4ae4836f8722 + md5: a8a19e4da4d87fcc989a068aac8811c4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rmarkdown, mclust, scater requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-cluster - r-doparallel @@ -38,10 +39,10 @@ requirements: - r-shiny - r-writexls run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-cluster - r-doparallel @@ -65,9 +66,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'A tool for unsupervised clustering and analysis of single cell RNA-Seq data.' extra: identifiers: - biotools:sc3 + parent_recipe: + name: bioconductor-sc3 + path: recipes/bioconductor-sc3 + version: 1.8.0 + diff --git a/recipes/bioconductor-scale4c/build.sh b/recipes/bioconductor-scale4c/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scale4c/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scale4c/meta.yaml b/recipes/bioconductor-scale4c/meta.yaml new file mode 100644 index 0000000000000..62d102ba3507e --- /dev/null +++ b/recipes/bioconductor-scale4c/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.4.0" %} +{% set name = "Scale4C" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 42129ff892946f7832161ae468afd8cf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-smoothie + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-smoothie +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'Scale4C is an R/Bioconductor package for scale-space transformation and visualization of 4C-seq data. The scale-space transformation is a multi-scale visualization technique to transform a 2D signal (e.g. 4C-seq reads on a genomic interval of choice) into a tesselation in the scale space (2D, genomic position x scale factor) by applying different smoothing kernels (Gauss, with increasing sigma). This transformation allows for explorative analysis and comparisons of the data''s structure with other samples.' + diff --git a/recipes/bioconductor-scan.upc/build.sh b/recipes/bioconductor-scan.upc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scan.upc/build.sh +++ b/recipes/bioconductor-scan.upc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scan.upc/conda_build_config.yaml b/recipes/bioconductor-scan.upc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-scan.upc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-scan.upc/meta.yaml b/recipes/bioconductor-scan.upc/meta.yaml index 46eb80a532853..5b575a60190de 100644 --- a/recipes/bioconductor-scan.upc/meta.yaml +++ b/recipes/bioconductor-scan.upc/meta.yaml @@ -1,43 +1,45 @@ -{% set version = "2.22.0" %} +{% set version = "2.24.0" %} {% set name = "SCAN.UPC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 851c199a54f682a2faad4fe4311eb1c51e27d209ad64358f9afa5fcd193f1b5c + md5: 0ae7d434ffec6c7b14c07d12045bb523 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: pd.hg.u95a requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-foreach - r-mass run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-foreach - r-mass @@ -45,9 +47,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: MIT summary: 'SCAN is a microarray normalization method to facilitate personalized-medicine workflows. Rather than processing microarray samples as groups, which can introduce biases and present logistical challenges, SCAN normalizes each sample individually by modeling and removing probe- and array-specific background noise using only data from within each array. SCAN can be applied to one-channel (e.g., Affymetrix) or two-channel (e.g., Agilent) microarrays. The Universal exPression Codes (UPC) method is an extension of SCAN that estimates whether a given gene/transcript is active above background levels in a given sample. The UPC method can be applied to one-channel or two-channel microarrays as well as to RNA-Seq read counts. Because UPC values are represented on the same scale and have an identical interpretation for each platform, they can be used for cross-platform data integration.' extra: identifiers: - biotools:scan.upc + parent_recipe: + name: bioconductor-scan.upc + path: recipes/bioconductor-scan.upc + version: 2.22.0 + diff --git a/recipes/bioconductor-scater-scripts/conda_build_config.yaml b/recipes/bioconductor-scater-scripts/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-scater-scripts/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-scater/build.sh b/recipes/bioconductor-scater/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scater/build.sh +++ b/recipes/bioconductor-scater/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scater/conda_build_config.yaml b/recipes/bioconductor-scater/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-scater/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-scater/meta.yaml b/recipes/bioconductor-scater/meta.yaml index f7baac2012b38..34c5712bc0301 100644 --- a/recipes/bioconductor-scater/meta.yaml +++ b/recipes/bioconductor-scater/meta.yaml @@ -1,38 +1,35 @@ -{% set version = "1.8.4" %} +{% set version = "1.10.0" %} {% set name = "scater" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 266cef66bf96fc94c94abc46886e612611d2fae40170dd3bb91a3ba1d575749c + md5: 6ceb20c1ef06767efb340edbc6479ca4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, biomaRt, beachmat, cowplot, cluster, destiny, knitr, monocle, mvoutlier, rmarkdown, Rtsne, umap, testthat, magrittr, pheatmap, irlba, tximport, tximportData, tximeta, Biobase, limma +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-tximport >=1.8.0,<1.10.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-data.table - r-dplyr - r-ggbeeswarm - r-ggplot2 @@ -40,26 +37,18 @@ requirements: - r-plyr - 'r-rcpp >=0.12.14' - r-reshape2 - - r-rjson - - r-shiny - - r-shinydashboard - r-viridis run: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhdf5 >=2.24.0,<2.26.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-tximport >=1.8.0,<1.10.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-data.table - r-dplyr - r-ggbeeswarm - r-ggplot2 @@ -67,9 +56,6 @@ requirements: - r-plyr - 'r-rcpp >=0.12.14' - r-reshape2 - - r-rjson - - r-shiny - - r-shinydashboard - r-viridis build: - {{ compiler('c') }} @@ -79,9 +65,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'GPL (>= 2)' - summary: 'A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control.' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A collection of tools for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control and visualization.' extra: identifiers: - biotools:scater + parent_recipe: + name: bioconductor-scater + path: recipes/bioconductor-scater + version: 1.8.4 + diff --git a/recipes/bioconductor-scbn/build.sh b/recipes/bioconductor-scbn/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scbn/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scbn/meta.yaml b/recipes/bioconductor-scbn/meta.yaml new file mode 100644 index 0000000000000..73525c7027996 --- /dev/null +++ b/recipes/bioconductor-scbn/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.0.0" %} +{% set name = "SCBN" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 36f0eef432e32fd3a5aa9c63b0bf2dda +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr,rmarkdown +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package provides a scale based normalization (SCBN) method to identify genes with differential expression between different species. It takes into account the available knowledge of conserved orthologous genes and the hypothesis testing framework to detect differentially expressed orthologous genes. The method on this package are described in the article ''A statistical normalization method and differential expression analysis for RNA-seq data between different species'' by Yan Zhou, Jiadi Zhu, Tiejun Tong, Junhui Wang, Bingqing Lin, Jun Zhang (2018, pending publication).' + diff --git a/recipes/bioconductor-scdd/build.sh b/recipes/bioconductor-scdd/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scdd/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scdd/meta.yaml b/recipes/bioconductor-scdd/meta.yaml new file mode 100644 index 0000000000000..1dc70b6158dad --- /dev/null +++ b/recipes/bioconductor-scdd/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.6.0" %} +{% set name = "scDD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8fe3bae3220b1e02e04e58ba27e97d7a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, gridExtra +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scran >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-arm + - r-base + - r-fields + - r-ggplot2 + - r-mclust + - r-outliers + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-ebseq >=1.22.0,<1.23.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scran >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-arm + - r-base + - r-fields + - r-ggplot2 + - r-mclust + - r-outliers +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'This package implements a method to analyze single-cell RNA- seq Data utilizing flexible Dirichlet Process mixture models. Genes with differential distributions of expression are classified into several interesting patterns of differences between two conditions. The package also includes functions for simulating data with these patterns from negative binomial distributions.' + diff --git a/recipes/bioconductor-scde/build.sh b/recipes/bioconductor-scde/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scde/build.sh +++ b/recipes/bioconductor-scde/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scde/meta.yaml b/recipes/bioconductor-scde/meta.yaml index 7545cdc79ac71..a290eb864143b 100644 --- a/recipes/bioconductor-scde/meta.yaml +++ b/recipes/bioconductor-scde/meta.yaml @@ -1,26 +1,27 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "scde" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 11f1a4b9a343e70023364f92a89ead50bfa0f490c9e4c21174d7b1ac47aab7ad + md5: f856b5990653ffab946edf208040bcb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, cba, fastcluster, WGCNA, GO.db, org.Hs.eg.db, rmarkdown requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - r-base - r-cairo - r-extremes @@ -36,9 +37,9 @@ requirements: - r-rmtstat - r-rook run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' - r-base - r-cairo - r-extremes @@ -61,10 +62,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data. scde fits individual error models for single-cell RNA-seq measurements. These models can then be used for assessment of differential expression between groups of cells, as well as other types of analysis. The scde package also contains the pagoda framework which applies pathway and gene set overdispersion analysis to identify and characterize putative cell subpopulations based on transcriptional signatures. The overall approach to the differential expression analysis is detailed in the following publication: "Bayesian approach to single-cell differential expression analysis" (Kharchenko PV, Silberstein L, Scadden DT, Nature Methods, doi: 10.1038/nmeth.2967). The overall approach to subpopulation identification and characterization is detailed in the following pre-print: "Characterizing transcriptional heterogeneity through pathway and gene set overdispersion analysis" (Fan J, Salathia N, Liu R, Kaeser G, Yung Y, Herman J, Kaper F, Fan JB, Zhang K, Chun J, and Kharchenko PV, Nature Methods, doi:10.1038/nmeth.3734).' extra: identifiers: - biotools:scde - doi:10.1038/nmeth.2967 + parent_recipe: + name: bioconductor-scde + path: recipes/bioconductor-scde + version: 2.8.0 + diff --git a/recipes/bioconductor-scfeaturefilter/build.sh b/recipes/bioconductor-scfeaturefilter/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scfeaturefilter/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scfeaturefilter/meta.yaml b/recipes/bioconductor-scfeaturefilter/meta.yaml new file mode 100644 index 0000000000000..0c25ae7dfa6fc --- /dev/null +++ b/recipes/bioconductor-scfeaturefilter/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.2.0" %} +{% set name = "scFeatureFilter" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2e7bf26332bbf95ac86888a7888e8622 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, SingleCellExperiment, SummarizedExperiment, scRNAseq, cowplot +requirements: + host: + - r-base + - 'r-dplyr >=0.7.3' + - 'r-ggplot2 >=2.1.0' + - 'r-magrittr >=1.5' + - 'r-rlang >=0.1.2' + - 'r-tibble >=1.3.4' + run: + - r-base + - 'r-dplyr >=0.7.3' + - 'r-ggplot2 >=2.1.0' + - 'r-magrittr >=1.5' + - 'r-rlang >=0.1.2' + - 'r-tibble >=1.3.4' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'An R implementation of the correlation-based method developed in the Joshi laboratory to analyse and filter processed single-cell RNAseq data. It returns a filtered version of the data containing only genes expression values unaffected by systematic noise.' + diff --git a/recipes/bioconductor-scfind/build.sh b/recipes/bioconductor-scfind/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scfind/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scfind/meta.yaml b/recipes/bioconductor-scfind/meta.yaml new file mode 100644 index 0000000000000..3f76200dc4c17 --- /dev/null +++ b/recipes/bioconductor-scfind/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.4.0" %} +{% set name = "scfind" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f29ed57914ffdecb38b856bd5ceede22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bit + - r-dplyr + - r-hash + - 'r-rcpp >=0.12.12' + - r-reshape2 + run: + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bit + - r-dplyr + - r-hash + - 'r-rcpp >=0.12.12' + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Recently a very large collection of single-cell RNA-seq (scRNA-seq) datasets has been generated and publicly released. For the collection to be useful, the information must be organized in a way that supports queries that are relevant to researchers. `scfind` builds an index from scRNA-seq datasets which organizes the information in a suitable and compact manner so that the datasets can be very efficiently searched for either cells or cell types in which a given list of genes is expressed.' + diff --git a/recipes/bioconductor-scisi/build.sh b/recipes/bioconductor-scisi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scisi/build.sh +++ b/recipes/bioconductor-scisi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scisi/meta.yaml b/recipes/bioconductor-scisi/meta.yaml index c15b753dea266..0b48389be20e8 100644 --- a/recipes/bioconductor-scisi/meta.yaml +++ b/recipes/bioconductor-scisi/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "ScISI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 52d824983f017feeb7703a091d81256abcc278015a648dfae83649af9c80d145 + md5: 88cc06d0227f9111004afc9da312fed3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ppiData, xtable requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-apcomplex >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-rpsixml >=2.22.0,<2.24.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-apcomplex >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-rpsixml >=2.24.0,<2.25.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-apcomplex >=2.46.0,<2.48.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-org.sc.sgd.db >=3.6.0,<3.8.0' - - 'bioconductor-rpsixml >=2.22.0,<2.24.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-apcomplex >=2.48.0,<2.49.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - 'bioconductor-rpsixml >=2.24.0,<2.25.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Package to create In Silico Interactomes' extra: identifiers: - biotools:scisi - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-scisi + path: recipes/bioconductor-scisi + version: 1.52.0 + diff --git a/recipes/bioconductor-sclcbam/meta.yaml b/recipes/bioconductor-sclcbam/meta.yaml new file mode 100644 index 0000000000000..c2440a9be69d0 --- /dev/null +++ b/recipes/bioconductor-sclcbam/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.14.0" %} +{% set name = "SCLCBam" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c9a6578784fd79568802485be95841f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Whole-exome sequencing data from a murine small-cell lung tumor; only contains data of chromosome 4.' + diff --git a/recipes/bioconductor-sclcbam/post-link.sh b/recipes/bioconductor-sclcbam/post-link.sh new file mode 100644 index 0000000000000..dcd6171ad5cea --- /dev/null +++ b/recipes/bioconductor-sclcbam/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SCLCBam_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SCLCBam_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/SCLCBam_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sclcbam/bioconductor-sclcbam_1.14.0_src_all.tar.gz" +) +MD5="c9a6578784fd79568802485be95841f5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sclcbam/pre-unlink.sh b/recipes/bioconductor-sclcbam/pre-unlink.sh new file mode 100644 index 0000000000000..6f53362a5a06e --- /dev/null +++ b/recipes/bioconductor-sclcbam/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SCLCBam diff --git a/recipes/bioconductor-scmap/build.sh b/recipes/bioconductor-scmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scmap/meta.yaml b/recipes/bioconductor-scmap/meta.yaml new file mode 100644 index 0000000000000..8dbae085e7d5f --- /dev/null +++ b/recipes/bioconductor-scmap/meta.yaml @@ -0,0 +1,66 @@ +{% set version = "1.4.0" %} +{% set name = "scmap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 766eeb1333304b3a0fc8ebac09901d6a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-googlevis + - r-matrixstats + - r-proxy + - r-randomforest + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-reshape2 + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-e1071 + - r-ggplot2 + - r-googlevis + - r-matrixstats + - r-proxy + - r-randomforest + - 'r-rcpp >=0.12.12' + - r-rcpparmadillo + - r-reshape2 + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Single-cell RNA-seq (scRNA-seq) is widely used to investigate the composition of complex tissues since the technology allows researchers to define cell-types using unsupervised clustering of the transcriptome. However, due to differences in experimental methods and computational analyses, it is often challenging to directly compare the cells identified in two different experiments. scmap is a method for projecting cells from a scRNA-seq experiment on to the cell-types or individual cells identified in a different experiment.' + diff --git a/recipes/bioconductor-scmeth/build.sh b/recipes/bioconductor-scmeth/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scmeth/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scmeth/meta.yaml b/recipes/bioconductor-scmeth/meta.yaml new file mode 100644 index 0000000000000..dbac708925cc1 --- /dev/null +++ b/recipes/bioconductor-scmeth/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.1" %} +{% set name = "scmeth" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3d53d9f2895ad6c888811c939e9b0207 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BSgenome.Mmusculus.UCSC.mm10, BSgenome.Hsapiens.NCBI.GRCh38, TxDb.Hsapiens.UCSC.hg38.knownGene, org.Hs.eg.db, Biobase, BiocGenerics, ggplot2, ggthemes +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotatr >=1.8.0,<1.9.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dt + - r-knitr + - r-reshape2 + - r-rmarkdown + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-annotatr >=1.8.0,<1.9.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dt + - r-knitr + - r-reshape2 + - r-rmarkdown +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Functions to analyze methylation data can be found here. Some functions are relevant for single cell methylation data but most other functions can be used for any methylation data. Highlight of this workflow is the comprehensive quality control report.' + diff --git a/recipes/bioconductor-scnorm/build.sh b/recipes/bioconductor-scnorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scnorm/build.sh +++ b/recipes/bioconductor-scnorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scnorm/conda_build_config.yaml b/recipes/bioconductor-scnorm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-scnorm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-scnorm/meta.yaml b/recipes/bioconductor-scnorm/meta.yaml index 0ba12d20c39d8..6181bb73080ad 100644 --- a/recipes/bioconductor-scnorm/meta.yaml +++ b/recipes/bioconductor-scnorm/meta.yaml @@ -1,28 +1,29 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "SCnorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f91e137b6037bbbbd3b5e3ce3fa11a54a3c9e4c1af3583145f88c83f986b8d19 + md5: 3c4497c3288269dfaa13c802b30b00b8 build: number: 0 rpaths: - lib/R/lib/ - lib/ -# note the conda_build_config.yaml + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, devtools requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-cluster - r-data.table @@ -31,10 +32,10 @@ requirements: - r-moments - r-quantreg run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-cluster - r-data.table @@ -46,8 +47,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements SCnorm — a method to normalize single-cell RNA-seq data.' - +extra: + parent_recipe: + name: bioconductor-scnorm + path: recipes/bioconductor-scnorm + version: 1.2.1 diff --git a/recipes/bioconductor-scone/build.sh b/recipes/bioconductor-scone/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scone/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scone/meta.yaml b/recipes/bioconductor-scone/meta.yaml new file mode 100644 index 0000000000000..1820605d80682 --- /dev/null +++ b/recipes/bioconductor-scone/meta.yaml @@ -0,0 +1,71 @@ +{% set version = "1.6.0" %} +{% set name = "scone" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2c49a9a930ad38cc1335593692145794 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, DT, ggplot2, knitr, miniUI, NMF, plotly, reshape2, rmarkdown, scran, scRNAseq, shiny, testthat, visNetwork +requirements: + host: + - 'bioconductor-aroma.light >=3.12.0,<3.13.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-ruvseq >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-boot + - r-class + - r-cluster + - r-compositions + - r-diptest + - r-fpc + - r-gplots + - r-hexbin + - r-matrixstats + - r-mixtools + - r-rarpack + - r-rcolorbrewer + run: + - 'bioconductor-aroma.light >=3.12.0,<3.13.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-ruvseq >=1.16.0,<1.17.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-boot + - r-class + - r-cluster + - r-compositions + - r-diptest + - r-fpc + - r-gplots + - r-hexbin + - r-matrixstats + - r-mixtools + - r-rarpack + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SCONE is an R package for comparing and ranking the performance of different normalization schemes for single-cell RNA-seq and other high-throughput analyses.' + diff --git a/recipes/bioconductor-sconify/build.sh b/recipes/bioconductor-sconify/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sconify/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sconify/meta.yaml b/recipes/bioconductor-sconify/meta.yaml new file mode 100644 index 0000000000000..4662cf0113d4a --- /dev/null +++ b/recipes/bioconductor-sconify/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "Sconify" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7dc1b90821623faf0bf978c1c27d27f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-dplyr + - r-fnn + - r-ggplot2 + - r-magrittr + - r-readr + - r-rtsne + - r-tibble + run: + - 'bioconductor-flowcore >=1.48.0,<1.49.0' + - r-base + - r-dplyr + - r-fnn + - r-ggplot2 + - r-magrittr + - r-readr + - r-rtsne + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package does k-nearest neighbor based statistics and visualizations with flow and mass cytometery data. This gives tSNE maps"fold change" functionality and provides a data quality metric by assessing manifold overlap between fcs files expected to be the same. Other applications using this package include imputation, marker redundancy, and testing the relative information loss of lower dimension embeddings compared to the original manifold.' + diff --git a/recipes/bioconductor-scoreinvhap/build.sh b/recipes/bioconductor-scoreinvhap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scoreinvhap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scoreinvhap/meta.yaml b/recipes/bioconductor-scoreinvhap/meta.yaml new file mode 100644 index 0000000000000..78f2360e767b1 --- /dev/null +++ b/recipes/bioconductor-scoreinvhap/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.4.0" %} +{% set name = "scoreInvHap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2ad194689a37b11ae8e50c00056c2e86 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, BiocStyle, rmarkdown +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-snpstats >=1.32.0,<1.33.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'scoreInvHap can get the samples'' inversion status of known inversions. scoreInvHap uses SNP data as input and requires the following information about the inversion: genotype frequencies in the different haplotypes, R2 between the region SNPs and inversion status and heterozygote genotypes in the reference. The package include this data for two well known inversions (8p23 and 17q21.31) and for two additional regions.' + diff --git a/recipes/bioconductor-scpipe/build.sh b/recipes/bioconductor-scpipe/build.sh index 79225b632eebb..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scpipe/build.sh +++ b/recipes/bioconductor-scpipe/build.sh @@ -1,12 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -# We need gcc >= 4.9 and the Makevars are just getting ignored -if [[ $target_platform =~ linux.* ]] ; then - foo=`which g++` - rm $foo - ln -s $GXX $foo - ln -s ${PREFIX}/lib/libgfortran.so.3 ${PREFIX}/lib/libgfortran.so - export LIBRARY_PATH=${PREFIX}/lib -fi -$R CMD INSTALL --build . +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scpipe/conda_build_config.yaml b/recipes/bioconductor-scpipe/conda_build_config.yaml deleted file mode 100644 index cf49bdd148cd7..0000000000000 --- a/recipes/bioconductor-scpipe/conda_build_config.yaml +++ /dev/null @@ -1,8 +0,0 @@ -r_base: - - 3.5.1 -c_compiler: - - gcc # [linux] - - clang # [osx] -cxx_compiler: - - gxx # [linux] - - clangxx # [osx] diff --git a/recipes/bioconductor-scpipe/meta.yaml b/recipes/bioconductor-scpipe/meta.yaml index cd6c82def0b49..7c0d6c3165148 100644 --- a/recipes/bioconductor-scpipe/meta.yaml +++ b/recipes/bioconductor-scpipe/meta.yaml @@ -1,73 +1,93 @@ -{% set version = "1.2.1" %} +{% set version = "1.4.0" %} {% set name = "scPipe" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ae2c9d2c00b750e95fbf735e031bfc0055568a9c6506db1cbb38083ac0e5d89a + md5: 050e7852900eede423bea2c8090970b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Rsubread, knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-dplyr - r-ggally - r-ggplot2 + - r-glue + - r-hashmap + - r-magrittr - r-mass - r-mclust - 'r-rcpp >=0.11.3' - r-reshape - r-robustbase - r-scales + - r-stringr + - r-testthat run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rhtslib >=1.12.1,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rhtslib >=1.14.0,<1.15.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base + - r-dplyr - r-ggally - r-ggplot2 + - r-glue + - r-hashmap + - r-magrittr - r-mass - r-mclust - 'r-rcpp >=0.11.3' - r-reshape - r-robustbase - r-scales + - r-stringr + - r-testthat build: - {{ compiler('c') }} - {{ compiler('cxx') }} - - {{ compiler('fortran') }} - make test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A preprocessing pipeline for single cell RNA-seq data that starts from the fastq files and produces a gene count matrix with associated quality control information. It can process fastq data generated by CEL-seq, MARS-seq, Drop-seq, Chromium 10x and SMART-seq protocols.' - +extra: + parent_recipe: + name: bioconductor-scpipe + path: recipes/bioconductor-scpipe + version: 1.2.1 diff --git a/recipes/bioconductor-scran/build.sh b/recipes/bioconductor-scran/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-scran/build.sh +++ b/recipes/bioconductor-scran/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scran/conda_build_config.yaml b/recipes/bioconductor-scran/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-scran/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-scran/meta.yaml b/recipes/bioconductor-scran/meta.yaml index 8b6b93b8cb024..ff6ae819c0490 100644 --- a/recipes/bioconductor-scran/meta.yaml +++ b/recipes/bioconductor-scran/meta.yaml @@ -1,70 +1,64 @@ -{% set version = "1.8.4" %} +{% set version = "1.10.1" %} {% set name = "scran" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d288b0413d7235b40a71483e6dfbc97587f4474fd5f28b5925f64c95d64e789f + md5: 9e3d89d750bc401907a7cef02154dea7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: testthat, BiocStyle, knitr, beachmat, HDF5Array, irlba, org.Mm.eg.db, DESeq2, monocle, pracma, Biobase, aroma.light +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-scater >=1.8.4,<1.10.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-dt - r-dynamictreecut - - r-fnn - - r-ggplot2 - r-igraph - r-matrix - 'r-rcpp >=0.12.14' - - r-shiny - r-statmod - - r-viridis run: - - 'bioconductor-beachmat >=1.2.1,<1.4.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-delayedmatrixstats >=1.2.0,<1.4.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rhdf5lib >=1.2.1,<1.4.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-scater >=1.8.4,<1.10.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-beachmat >=1.4.0,<1.5.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocneighbors >=1.0.0,<1.1.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-delayedmatrixstats >=1.4.0,<1.5.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rhdf5lib >=1.4.0,<1.5.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - - r-dt - r-dynamictreecut - - r-fnn - - r-ggplot2 - r-igraph - r-matrix - 'r-rcpp >=0.12.14' - - r-shiny - r-statmod - - r-viridis build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -73,9 +67,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Implements functions for low-level analyses of single-cell RNA-seq data. Methods are provided for normalization of cell-specific biases, assignment of cell cycle phase, detection of highly variable and significantly correlated genes, correction of batch effects, identification of marker genes, and other common tasks in single-cell analysis workflows.' extra: identifiers: - biotools:scran + parent_recipe: + name: bioconductor-scran + path: recipes/bioconductor-scran + version: 1.8.4 + diff --git a/recipes/bioconductor-scrnaseq/meta.yaml b/recipes/bioconductor-scrnaseq/meta.yaml index 4379c1c1ccf31..10ac81ced3700 100644 --- a/recipes/bioconductor-scrnaseq/meta.yaml +++ b/recipes/bioconductor-scrnaseq/meta.yaml @@ -1,33 +1,41 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "scRNAseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c2272f78750ac96df37276483d3d11380d54354dbdcf0aa223b9e7d62ed04b54 + md5: fe0e002e82591d592eefbf687d46dc56 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown requirements: - build: - - bioconductor-summarizedexperiment + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - bioconductor-summarizedexperiment + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: CC0 summary: 'Gene-level read counts of three public scRNA-seq datasets. See vignette for details.' +extra: + parent_recipe: + name: bioconductor-scrnaseq + path: recipes/bioconductor-scrnaseq + version: 1.6.0 + diff --git a/recipes/bioconductor-scrnaseq/post-link.sh b/recipes/bioconductor-scrnaseq/post-link.sh index 39176aa32189f..863ca029ffcbe 100644 --- a/recipes/bioconductor-scrnaseq/post-link.sh +++ b/recipes/bioconductor-scrnaseq/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="scRNAseq_1.6.0.tar.gz" +FN="scRNAseq_1.8.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/scRNAseq_1.6.0.tar.gz" - "https://bioarchive.galaxyproject.org/scRNAseq_1.6.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_1.6.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/scRNAseq_1.8.0.tar.gz" + "https://bioarchive.galaxyproject.org/scRNAseq_1.8.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-scrnaseq/bioconductor-scrnaseq_1.8.0_src_all.tar.gz" ) -MD5="16591406c49256c925cbb666e25d19b5" +MD5="fe0e002e82591d592eefbf687d46dc56" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable @@ -43,4 +43,4 @@ fi # Install and clean up R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL rm $TARBALL -rmdir $STAGING \ No newline at end of file +rmdir $STAGING diff --git a/recipes/bioconductor-scruff/build.sh b/recipes/bioconductor-scruff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scruff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scruff/meta.yaml b/recipes/bioconductor-scruff/meta.yaml new file mode 100644 index 0000000000000..2fff464ccdfe2 --- /dev/null +++ b/recipes/bioconductor-scruff/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.0.1" %} +{% set name = "scruff" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 32fcb7089073e8f44303048a54ac2059 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, Rsubread, testthat +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-ggplot2 + - r-ggthemes + - r-plyr + - r-refgenome + - r-scales + - r-stringdist + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-data.table + - r-ggplot2 + - r-ggthemes + - r-plyr + - r-refgenome + - r-scales + - r-stringdist +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'A pipeline which processes single cell RNA-seq (scRNA-seq) reads from CEL-seq and CEL-seq2 protocols. Demultiplex scRNA-seq FASTQ files, align reads to reference genome using Rsubread, and generate UMI filtered count matrix. Also provide visualizations of read alignments and pre- and post-alignment QC metrics.' + diff --git a/recipes/bioconductor-scsr/build.sh b/recipes/bioconductor-scsr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-scsr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-scsr/meta.yaml b/recipes/bioconductor-scsr/meta.yaml new file mode 100644 index 0000000000000..dc4a8031625c1 --- /dev/null +++ b/recipes/bioconductor-scsr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.18.0" %} +{% set name = "scsR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0f4b6a6a4da4a834cf90834a9d93f83b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-ggplot2 + - r-hash + - r-plyr + - r-rcolorbrewer + - r-sqldf + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-base + - r-ggplot2 + - r-hash + - r-plyr + - r-rcolorbrewer + - r-sqldf +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Corrects genome-wide siRNA screens for seed mediated off-target effect. Suitable functions to identify the effective seeds/miRNAs and to visualize their effect are also provided in the package.' + diff --git a/recipes/bioconductor-sdams/build.sh b/recipes/bioconductor-sdams/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sdams/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sdams/meta.yaml b/recipes/bioconductor-sdams/meta.yaml new file mode 100644 index 0000000000000..634b3c06007ef --- /dev/null +++ b/recipes/bioconductor-sdams/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.2.0" %} +{% set name = "SDAMS" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0eb7021f092abd2f4741bfec7bbe2315 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +requirements: + host: + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-trust + run: + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-trust +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'This Package utilizes a Semi-parametric Differential Abundance analysis (SDA) method for metabolomics and proteomics data from mass spectrometry. SDA is able to robustly handle non-normally distributed data and provides a clear quantification of the effect size.' + diff --git a/recipes/bioconductor-segmentseq/build.sh b/recipes/bioconductor-segmentseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-segmentseq/build.sh +++ b/recipes/bioconductor-segmentseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-segmentseq/meta.yaml b/recipes/bioconductor-segmentseq/meta.yaml index 3b7cda06cbccf..04055a9f22cbe 100644 --- a/recipes/bioconductor-segmentseq/meta.yaml +++ b/recipes/bioconductor-segmentseq/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "segmentSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 28d8d72b03d540e5c5d3edfa6f734e70ef345d353788e0fc41e7265ba57c7c27 + md5: d824a0fa29add988a1ce56eb6fe3dcdb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-abind - r-base run: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' - r-abind - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'High-throughput sequencing technologies allow the production of large volumes of short sequences, which can be aligned to the genome to create a set of matches to the genome. By looking for regions of the genome which to which there are high densities of matches, we can infer a segmentation of the genome into regions of biological significance. The methods in this package allow the simultaneous segmentation of data from multiple samples, taking into account replicate data, in order to create a consensus segmentation. This has obvious applications in a number of classes of sequencing experiments, particularly in the discovery of small RNA loci and novel mRNA transcriptome discovery.' extra: identifiers: - biotools:segmentseq - doi:10.1093/bioinformatics/btr687 + parent_recipe: + name: bioconductor-segmentseq + path: recipes/bioconductor-segmentseq + version: 2.14.0 + diff --git a/recipes/bioconductor-selex/build.sh b/recipes/bioconductor-selex/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-selex/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-selex/meta.yaml b/recipes/bioconductor-selex/meta.yaml new file mode 100644 index 0000000000000..ce54b40e55fd9 --- /dev/null +++ b/recipes/bioconductor-selex/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.14.0" %} +{% set name = "SELEX" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 50fc8dc5e8723d5c1d93f7e1b9140ca8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# SystemRequirements: Java (>= 1.5) +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - 'r-rjava >=0.5-0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - 'r-rjava >=0.5-0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Tools for quantifying DNA binding specificities based on SELEX-seq data' + diff --git a/recipes/bioconductor-semdist/build.sh b/recipes/bioconductor-semdist/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-semdist/build.sh +++ b/recipes/bioconductor-semdist/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-semdist/meta.yaml b/recipes/bioconductor-semdist/meta.yaml index 926d87c2a4e3b..628ce857d7958 100644 --- a/recipes/bioconductor-semdist/meta.yaml +++ b/recipes/bioconductor-semdist/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SemDist" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ef8dd578f134b7161a5d737fe41d4d6c35015f8cb760673a2f072202c1f1c17e + md5: eab03908affcfa4650727b2d59de3a1e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GOSemSim requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package implements methods to calculate information accretion for a given version of the gene ontology and uses this data to calculate remaining uncertainty, misinformation, and semantic similarity for given sets of predicted annotations and true annotations from a protein function predictor.' extra: identifiers: - biotools:semdist - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-semdist + path: recipes/bioconductor-semdist + version: 1.14.0 + diff --git a/recipes/bioconductor-semisup/build.sh b/recipes/bioconductor-semisup/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-semisup/build.sh +++ b/recipes/bioconductor-semisup/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-semisup/meta.yaml b/recipes/bioconductor-semisup/meta.yaml index 6dcbf1d1b427d..f657d25a4bc28 100644 --- a/recipes/bioconductor-semisup/meta.yaml +++ b/recipes/bioconductor-semisup/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "semisup" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 569f50fb9511417bce439881e31cc0c87c45ca514ab98b63ab79f3527f3cc90d + md5: 7de301d6f0da4d2fb6c7b720c33d0801 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat requirements: host: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-vgam run: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-vgam test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'This R packages moves away from testing interaction terms, and move towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in distribution between some individuals in one group and all other individuals, it possibly has an interactive effect. Implicitly, the membership probabilities may suggest potential interacting variables.' - + summary: 'Useful for detecting SNPs with interactive effects on a quantitative trait. This R packages moves away from testing interaction terms, and moves towards testing whether an individual SNP is involved in any interaction. This reduces the multiple testing burden to one test per SNP, and allows for interactions with unobserved factors. Analysing one SNP at a time, it splits the individuals into two groups, based on the number of minor alleles. If the quantitative trait differs in mean between the two groups, the SNP has a main effect. If the quantitative trait differs in distribution between some individuals in one group and all other individuals, it possibly has an interactive effect. Implicitly, the membership probabilities may suggest potential interacting variables.' +extra: + parent_recipe: + name: bioconductor-semisup + path: recipes/bioconductor-semisup + version: 1.4.0 diff --git a/recipes/bioconductor-sepa/build.sh b/recipes/bioconductor-sepa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sepa/build.sh +++ b/recipes/bioconductor-sepa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sepa/meta.yaml b/recipes/bioconductor-sepa/meta.yaml index b2464a2b75eab..d29d1056602d2 100644 --- a/recipes/bioconductor-sepa/meta.yaml +++ b/recipes/bioconductor-sepa/meta.yaml @@ -1,35 +1,37 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SEPA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 827977cece3573fc600d90bfc7cd17f4ebadd02e0dde494ad6dfac1077efc391 + md5: 8e24d376c6932b319c7220271d2ac3d9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 - r-segmented - r-shiny run: - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-org.mm.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-ggplot2 - r-reshape2 @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'Given single-cell RNA-seq data and true experiment time of cells or pseudo-time cell ordering, SEPA provides convenient functions for users to assign genes into different gene expression patterns such as constant, monotone increasing and increasing then decreasing. SEPA then performs GO enrichment analysis to analysis the functional roles of genes with same or similar patterns.' extra: identifiers: - biotools:sepa - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sepa + path: recipes/bioconductor-sepa + version: 1.10.0 + diff --git a/recipes/bioconductor-sepira/build.sh b/recipes/bioconductor-sepira/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sepira/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sepira/meta.yaml b/recipes/bioconductor-sepira/meta.yaml new file mode 100644 index 0000000000000..47c95a16975c8 --- /dev/null +++ b/recipes/bioconductor-sepira/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.2.0" %} +{% set name = "SEPIRA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9c692e31570fd41c696bb62f2f48b45e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, igraph +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-corpcor >=1.6.9' + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-corpcor >=1.6.9' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'SEPIRA (Systems EPigenomics Inference of Regulatory Activity) is an algorithm that infers sample-specific transcription factor activity from the genome-wide expression or DNA methylation profile of the sample.' + diff --git a/recipes/bioconductor-seq2pathway.data/meta.yaml b/recipes/bioconductor-seq2pathway.data/meta.yaml index 7e842531f579b..018f005c1f63e 100644 --- a/recipes/bioconductor-seq2pathway.data/meta.yaml +++ b/recipes/bioconductor-seq2pathway.data/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "seq2pathway.data" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: c54109592ef4eef69c86a2c4491c6f89c21afafc31916db917d13baa360b3a64 + md5: ca93e7796ded3a3f92e56f3539a39291 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Supporting data for the seq2patheway package. Includes modified gene sets from MsigDB and org.Hs.eg.db; gene locus definitions from GENCODE project.' - +extra: + parent_recipe: + name: bioconductor-seq2pathway.data + path: recipes/bioconductor-seq2pathway.data + version: 1.12.0 diff --git a/recipes/bioconductor-seq2pathway.data/post-link.sh b/recipes/bioconductor-seq2pathway.data/post-link.sh index 194d777896700..66950da1c447b 100644 --- a/recipes/bioconductor-seq2pathway.data/post-link.sh +++ b/recipes/bioconductor-seq2pathway.data/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="seq2pathway.data_1.12.0.tar.gz" +FN="seq2pathway.data_1.14.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/seq2pathway.data_1.12.0.tar.gz" - "https://bioarchive.galaxyproject.org/seq2pathway.data_1.12.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.12.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seq2pathway.data_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/seq2pathway.data_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seq2pathway.data/bioconductor-seq2pathway.data_1.14.0_src_all.tar.gz" ) -MD5="b8290b0259648264b2194867c624224f" +MD5="ca93e7796ded3a3f92e56f3539a39291" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-seq2pathway/build.sh b/recipes/bioconductor-seq2pathway/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-seq2pathway/build.sh +++ b/recipes/bioconductor-seq2pathway/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seq2pathway/meta.yaml b/recipes/bioconductor-seq2pathway/meta.yaml index 928575e1981e5..281f67227bf18 100644 --- a/recipes/bioconductor-seq2pathway/meta.yaml +++ b/recipes/bioconductor-seq2pathway/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "seq2pathway" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9edd3eec43f9c9b33cbb04cc52c3ef6af2c32230f8a65a846e41fb227ca37bea + md5: 3902ddfb016b893e874cd6eadc13c1d2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-seq2pathway.data >=1.12.0,<1.14.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-seq2pathway.data >=1.14.0,<1.15.0' - r-base - r-gsa - r-nnet - r-wgcna run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-seq2pathway.data >=1.12.0,<1.14.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-seq2pathway.data >=1.14.0,<1.15.0' - r-base - r-gsa - r-nnet @@ -37,9 +38,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data, consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores, and the gene2pathway summarizes gene scores to pathway-scores for each sample. The seq2gene has the feasibility to assign both coding and non-exon regions to a broader range of neighboring genes than only the nearest one, thus facilitating the study of functional non-coding regions. The gene2pathway takes into account the quantity of significance for gene members within a pathway compared those outside a pathway. The output of seq2pathway is a general structure of quantitative pathway-level scores, thus allowing one to functional interpret such datasets as RNA-seq, ChIP-seq, GWAS, and derived from other next generational sequencing experiments.' extra: identifiers: - biotools:seq2pathway + parent_recipe: + name: bioconductor-seq2pathway + path: recipes/bioconductor-seq2pathway + version: 1.12.0 + diff --git a/recipes/bioconductor-seqarray/build.sh b/recipes/bioconductor-seqarray/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqarray/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqarray/meta.yaml b/recipes/bioconductor-seqarray/meta.yaml new file mode 100644 index 0000000000000..3d5e946905fcd --- /dev/null +++ b/recipes/bioconductor-seqarray/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.22.2" %} +{% set name = "SeqArray" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8466db82f29db889abcaa8d5e2ac89c2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: Biobase, BiocGenerics, BiocParallel, RUnit, Rcpp, SNPRelate, digest, crayon, knitr, Rsamtools, VariantAnnotation +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Big data management of whole-genome sequencing variant calls with thousands of individuals: genotypic data (e.g., SNVs, indels and structural variation calls) and annotations in SeqArray files are stored in an array-oriented and compressed manner, with efficient data access using the R programming language.' + diff --git a/recipes/bioconductor-seqbias/build.sh b/recipes/bioconductor-seqbias/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqbias/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqbias/meta.yaml b/recipes/bioconductor-seqbias/meta.yaml new file mode 100644 index 0000000000000..fad23e53893f3 --- /dev/null +++ b/recipes/bioconductor-seqbias/meta.yaml @@ -0,0 +1,45 @@ +{% set version = "1.30.0" %} +{% set name = "seqbias" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a7246cbe2d95208f29cf3651e25b9688 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: Rsamtools, ggplot2 +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'This package implements a model of per-position sequencing bias in high-throughput sequencing data using a simple Bayesian network, the structure and parameters of which are trained on a set of aligned reads and a reference genome sequence.' + diff --git a/recipes/bioconductor-seqc/meta.yaml b/recipes/bioconductor-seqc/meta.yaml new file mode 100644 index 0000000000000..6f1ab46abeb57 --- /dev/null +++ b/recipes/bioconductor-seqc/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.16.0" %} +{% set name = "seqc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 376dcb3255c528683e1c4be13ee3c5c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'The SEQC/MAQC-III Consortium has produced benchmark RNA-seq data for the assessment of RNA sequencing technologies and data analysis methods (Nat Biotechnol, 2014). Billions of sequence reads have been generated from ten different sequencing sites. This package contains the summarized read count data for ~2000 sequencing libraries. It also includes all the exon-exon junctions discovered from the study. TaqMan RT-PCR data for ~1000 genes and ERCC spike-in sequence data are included in this package as well.' + diff --git a/recipes/bioconductor-seqc/post-link.sh b/recipes/bioconductor-seqc/post-link.sh new file mode 100644 index 0000000000000..eda8c5cce93b2 --- /dev/null +++ b/recipes/bioconductor-seqc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="seqc_1.16.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seqc_1.16.0.tar.gz" + "https://bioarchive.galaxyproject.org/seqc_1.16.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seqc/bioconductor-seqc_1.16.0_src_all.tar.gz" +) +MD5="376dcb3255c528683e1c4be13ee3c5c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-seqc/pre-unlink.sh b/recipes/bioconductor-seqc/pre-unlink.sh new file mode 100644 index 0000000000000..866e61fc24798 --- /dev/null +++ b/recipes/bioconductor-seqc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ seqc diff --git a/recipes/bioconductor-seqcat/build.sh b/recipes/bioconductor-seqcat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqcat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqcat/meta.yaml b/recipes/bioconductor-seqcat/meta.yaml new file mode 100644 index 0000000000000..499f08b72387e --- /dev/null +++ b/recipes/bioconductor-seqcat/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.4.0" %} +{% set name = "seqCAT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 02c71dd7b83aae90fea8c864a286bea1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, rmarkdown, testthat, BiocManager +requirements: + host: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-dplyr >=0.5.0' + - 'r-ggplot2 >=2.2.1' + - 'r-lazyeval >=0.2.0' + - 'r-scales >=0.4.1' + - 'r-tidyr >=0.6.1' + run: + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-dplyr >=0.5.0' + - 'r-ggplot2 >=2.2.1' + - 'r-lazyeval >=0.2.0' + - 'r-scales >=0.4.1' + - 'r-tidyr >=0.6.1' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENCE' + summary: 'The seqCAT package uses variant calling data (in the form of VCF files) from high throughput sequencing technologies to authenticate and validate the source, function and characteristics of biological samples used in scientific endeavours.' + diff --git a/recipes/bioconductor-seqcna.annot/meta.yaml b/recipes/bioconductor-seqcna.annot/meta.yaml new file mode 100644 index 0000000000000..80d2785840518 --- /dev/null +++ b/recipes/bioconductor-seqcna.annot/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "seqCNA.annot" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a83620fb92adae77c4f61769854844a6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Provides annotation on GC content, mappability and genomic features for various genomes' + diff --git a/recipes/bioconductor-seqcna.annot/post-link.sh b/recipes/bioconductor-seqcna.annot/post-link.sh new file mode 100644 index 0000000000000..5d8fffa78ba89 --- /dev/null +++ b/recipes/bioconductor-seqcna.annot/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="seqCNA.annot_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seqCNA.annot_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/seqCNA.annot_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seqcna.annot/bioconductor-seqcna.annot_1.18.0_src_all.tar.gz" +) +MD5="a83620fb92adae77c4f61769854844a6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-seqcna.annot/pre-unlink.sh b/recipes/bioconductor-seqcna.annot/pre-unlink.sh new file mode 100644 index 0000000000000..b9e0c7ca14c2b --- /dev/null +++ b/recipes/bioconductor-seqcna.annot/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ seqCNA.annot diff --git a/recipes/bioconductor-seqcna/build.sh b/recipes/bioconductor-seqcna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqcna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqcna/meta.yaml b/recipes/bioconductor-seqcna/meta.yaml new file mode 100644 index 0000000000000..a75654e303535 --- /dev/null +++ b/recipes/bioconductor-seqcna/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.28.0" %} +{% set name = "seqCNA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0942b2ccaa95004fcf5b5155bede0e76 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# SystemRequirements: samtools +requirements: + host: + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-seqcna.annot >=1.18.0,<1.19.0' + - 'r-adehabitatlt >=0.3.4' + - r-base + - 'r-dosnow >=1.0.5' + run: + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-seqcna.annot >=1.18.0,<1.19.0' + - 'r-adehabitatlt >=0.3.4' + - r-base + - 'r-dosnow >=1.0.5' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Copy number analysis of high-throughput sequencing cancer data with fast summarization, extensive filtering and improved normalization' + diff --git a/recipes/bioconductor-seqcombo/build.sh b/recipes/bioconductor-seqcombo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqcombo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqcombo/meta.yaml b/recipes/bioconductor-seqcombo/meta.yaml new file mode 100644 index 0000000000000..199b7be42a3c5 --- /dev/null +++ b/recipes/bioconductor-seqcombo/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.0" %} +{% set name = "seqcombo" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 11fc14a9982f27f6dee303f81a268f6b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: emojifont, knitr, prettydoc, tibble +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-igraph + - r-magrittr + - r-rvcheck + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - r-base + - r-cowplot + - r-dplyr + - r-ggplot2 + - r-igraph + - r-magrittr + - r-rvcheck +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides useful functions for visualizing sequence recombination and virus reassortment events.' + diff --git a/recipes/bioconductor-seqgsea/build.sh b/recipes/bioconductor-seqgsea/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-seqgsea/build.sh +++ b/recipes/bioconductor-seqgsea/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqgsea/meta.yaml b/recipes/bioconductor-seqgsea/meta.yaml index ab98655ac3229..f12adefff49a1 100644 --- a/recipes/bioconductor-seqgsea/meta.yaml +++ b/recipes/bioconductor-seqgsea/meta.yaml @@ -1,41 +1,48 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SeqGSEA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 72bf104155765f009f1c92d6aba534d8219a20c35de6ea2463c67e889e1ef11c + md5: d9b007488cfb754cb9f146925d1e4bf8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: easyRNASeq, GenomicRanges requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' - r-base - r-doparallel run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' - r-base - r-doparallel test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The package generally provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.' extra: identifiers: - biotools:seqgsea + parent_recipe: + name: bioconductor-seqgsea + path: recipes/bioconductor-seqgsea + version: 1.20.0 + diff --git a/recipes/bioconductor-seqlogo/build.sh b/recipes/bioconductor-seqlogo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-seqlogo/build.sh +++ b/recipes/bioconductor-seqlogo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqlogo/meta.yaml b/recipes/bioconductor-seqlogo/meta.yaml index a27cc278e70d0..ad923c3d42dcf 100644 --- a/recipes/bioconductor-seqlogo/meta.yaml +++ b/recipes/bioconductor-seqlogo/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "seqLogo" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 81459d392504a00a520f501282aa2c246be7ad893de68aaadca9473b1bc3bb9b + md5: 435a5d989d6fcb86466ab7bbd546bf70 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'seqLogo takes the position weight matrix of a DNA sequence motif and plots the corresponding sequence logo as introduced by Schneider and Stephens (1990).' extra: identifiers: - biotools:seqlogo - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-seqlogo + path: recipes/bioconductor-seqlogo + version: 1.46.0 + diff --git a/recipes/bioconductor-seqpattern/build.sh b/recipes/bioconductor-seqpattern/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-seqpattern/build.sh +++ b/recipes/bioconductor-seqpattern/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqpattern/meta.yaml b/recipes/bioconductor-seqpattern/meta.yaml index 8378daf104e40..957643481125c 100644 --- a/recipes/bioconductor-seqpattern/meta.yaml +++ b/recipes/bioconductor-seqpattern/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "seqPattern" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7c5c0e62021cfeafa31682277e88aa343969650cfdd28eef5e1138e61af58037 + md5: eaa324090a3e3aea517439104aff6721 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Drerio.UCSC.danRer7, CAGEr, RUnit, BiocGenerics, BiocStyle requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-kernsmooth - r-plotrix run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-kernsmooth - r-plotrix @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Visualising oligonucleotide patterns and sequence motifs occurrences across a large set of sequences centred at a common reference point and sorted by a user defined feature.' extra: identifiers: - biotools:seqpattern - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-seqpattern + path: recipes/bioconductor-seqpattern + version: 1.12.0 + diff --git a/recipes/bioconductor-seqplots/build.sh b/recipes/bioconductor-seqplots/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqplots/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqplots/meta.yaml b/recipes/bioconductor-seqplots/meta.yaml new file mode 100644 index 0000000000000..8871035b4c27c --- /dev/null +++ b/recipes/bioconductor-seqplots/meta.yaml @@ -0,0 +1,81 @@ +{% set version = "1.20.0" %} +{% set name = "seqplots" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c4103c7256e3428c1877dd6536fc8795 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, covr +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-class + - r-dbi + - r-digest + - 'r-dt >=0.1.0' + - r-fields + - r-ggplot2 + - r-gridextra + - r-jsonlite + - r-kohonen + - r-plotrix + - r-rcolorbrewer + - r-reshape2 + - r-rsqlite + - 'r-shiny >=0.13.0' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-biocmanager + - r-class + - r-dbi + - r-digest + - 'r-dt >=0.1.0' + - r-fields + - r-ggplot2 + - r-gridextra + - r-jsonlite + - r-kohonen + - r-plotrix + - r-rcolorbrewer + - r-reshape2 + - r-rsqlite + - 'r-shiny >=0.13.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'SeqPlots is a tool for plotting next generation sequencing (NGS) based experiments'' signal tracks, e.g. reads coverage from ChIP-seq, RNA-seq and DNA accessibility assays like DNase-seq and MNase-seq, over user specified genomic features, e.g. promoters, gene bodies, etc. It can also calculate sequence motif density profiles from reference genome. The data are visualized as average signal profile plot, with error estimates (standard error and 95% confidence interval) shown as fields, or as series of heatmaps that can be sorted and clustered using hierarchical clustering, k-means algorithm and self organising maps. Plots can be prepared using R programming language or web browser based graphical user interface (GUI) implemented using Shiny framework. The dual-purpose implementation allows running the software locally on desktop or deploying it on server. SeqPlots is useful for both for exploratory data analyses and preparing replicable, publication quality plots. Other features of the software include collaboration and data sharing capabilities, as well as ability to store pre-calculated result matrixes, that combine many sequencing experiments and in-silico generated tracks with multiple different features. These binaries can be further used to generate new combination plots on fly, run automated batch operations or share with colleagues, who can adjust their plotting parameters without loading actual tracks and recalculating numeric values. SeqPlots relays on Bioconductor packages, mainly on rtracklayer for data input and BSgenome packages for reference genome sequence and annotations.' + diff --git a/recipes/bioconductor-seqsetvis/build.sh b/recipes/bioconductor-seqsetvis/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqsetvis/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqsetvis/meta.yaml b/recipes/bioconductor-seqsetvis/meta.yaml new file mode 100644 index 0000000000000..1bd5578331264 --- /dev/null +++ b/recipes/bioconductor-seqsetvis/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "seqsetvis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: be248a791399d770509db66a23438452 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocFileCache, BiocManager, BiocStyle, ChIPpeakAnno, covr, cowplot, knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-eulerr + - r-ggplot2 + - r-png + - r-rcolorbrewer + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-eulerr + - r-ggplot2 + - r-png + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'seqsetvis enables the visualization and analysis of multiple genomic datasets. Although seqsetvis was designed for the comparison of mulitple ChIP-seq datasets, this package is domain-agnostic and allows the processing of multiple genomic coordinate files (bed-like files) and signal files (bigwig files or bam pileups).' + diff --git a/recipes/bioconductor-seqsqc/build.sh b/recipes/bioconductor-seqsqc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqsqc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqsqc/meta.yaml b/recipes/bioconductor-seqsqc/meta.yaml new file mode 100644 index 0000000000000..af0e4b912482a --- /dev/null +++ b/recipes/bioconductor-seqsqc/meta.yaml @@ -0,0 +1,59 @@ +{% set version = "1.4.0" %} +{% set name = "SeqSQC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 567ec0880b33d8207b237e337e17fb98 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base + - r-e1071 + - r-ggally + - r-ggplot2 + - r-rbokeh + - r-rcolorbrewer + - r-reshape2 + - r-rmarkdown + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-snprelate >=1.16.0,<1.17.0' + - r-base + - r-e1071 + - r-ggally + - r-ggplot2 + - r-rbokeh + - r-rcolorbrewer + - r-reshape2 + - r-rmarkdown +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The SeqSQC is designed to identify problematic samples in NGS data, including samples with gender mismatch, contamination, cryptic relatedness, and population outlier.' + diff --git a/recipes/bioconductor-seqtools/build.sh b/recipes/bioconductor-seqtools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-seqtools/build.sh +++ b/recipes/bioconductor-seqtools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqtools/meta.yaml b/recipes/bioconductor-seqtools/meta.yaml index abac7db3f8112..6daed11dbc373 100644 --- a/recipes/bioconductor-seqtools/meta.yaml +++ b/recipes/bioconductor-seqtools/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "seqTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cbc433c0f1c72b7f4bb494b8006d80c56638f843a67c8f9726dc276ea3cd9611 + md5: fb3f61a5e3916be5eb4ab19e44b857d5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Analyze read length, phred scores and alphabet frequency and DNA k-mers on uncompressed and compressed fastq files.' extra: identifiers: - biotools:seqtools - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-seqtools + path: recipes/bioconductor-seqtools + version: 1.14.0 + diff --git a/recipes/bioconductor-seqvartools/build.sh b/recipes/bioconductor-seqvartools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-seqvartools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-seqvartools/meta.yaml b/recipes/bioconductor-seqvartools/meta.yaml new file mode 100644 index 0000000000000..fa1814f7ea22e --- /dev/null +++ b/recipes/bioconductor-seqvartools/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.20.0" %} +{% set name = "SeqVarTools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7543f794ecea97ebbb71eaf8171f0af1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, RUnit, stringr +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - r-base + - r-dplyr + - r-gwasexacthw + - r-logistf + - r-matrix + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqarray >=1.22.0,<1.23.0' + - r-base + - r-dplyr + - r-gwasexacthw + - r-logistf + - r-matrix + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'An interface to the fast-access storage format for VCF data provided in SeqArray, with tools for common operations and analysis.' + diff --git a/recipes/bioconductor-serumstimulation/meta.yaml b/recipes/bioconductor-serumstimulation/meta.yaml new file mode 100644 index 0000000000000..0553b876fd924 --- /dev/null +++ b/recipes/bioconductor-serumstimulation/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "serumStimulation" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 702b8e053465a52491f19961654f3dc0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Contains 13 micro array data results from a serum stimulation experiment' + diff --git a/recipes/bioconductor-serumstimulation/post-link.sh b/recipes/bioconductor-serumstimulation/post-link.sh new file mode 100644 index 0000000000000..f837c5eab6f11 --- /dev/null +++ b/recipes/bioconductor-serumstimulation/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="serumStimulation_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/serumStimulation_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/serumStimulation_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-serumstimulation/bioconductor-serumstimulation_1.18.0_src_all.tar.gz" +) +MD5="702b8e053465a52491f19961654f3dc0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-serumstimulation/pre-unlink.sh b/recipes/bioconductor-serumstimulation/pre-unlink.sh new file mode 100644 index 0000000000000..d7430eecb76cd --- /dev/null +++ b/recipes/bioconductor-serumstimulation/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ serumStimulation diff --git a/recipes/bioconductor-sesame/build.sh b/recipes/bioconductor-sesame/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sesame/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sesame/meta.yaml b/recipes/bioconductor-sesame/meta.yaml new file mode 100644 index 0000000000000..a2b861c258264 --- /dev/null +++ b/recipes/bioconductor-sesame/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.0" %} +{% set name = "sesame" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 39b48bfe5a5aca7b74685fd0a922aed4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: scales, knitr, rmarkdown, testthat, minfi, SummarizedExperiment, FlowSorted.CordBloodNorway.450k +requirements: + host: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sesamedata >=1.0.0,<1.1.0' + - r-base + - r-ggplot2 + - r-mass + - r-r6 + - r-randomforest + - r-wheatmap + run: + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-sesamedata >=1.0.0,<1.1.0' + - r-base + - r-ggplot2 + - r-mass + - r-r6 + - r-randomforest + - r-wheatmap +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Tools For analyzing Illumina Infinium DNA methylation arrays.' + diff --git a/recipes/bioconductor-sesamedata/meta.yaml b/recipes/bioconductor-sesamedata/meta.yaml new file mode 100644 index 0000000000000..2eab1c1af96d5 --- /dev/null +++ b/recipes/bioconductor-sesamedata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.0.0" %} +{% set name = "sesameData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dc24068fe6bdc6ef7e62c89c38b8d949 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicRanges, BiocGenerics, sesame, testthat, knitr +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-curl + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-curl + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides supporting annotation and test data for SeSAMe package.' + diff --git a/recipes/bioconductor-sesamedata/post-link.sh b/recipes/bioconductor-sesamedata/post-link.sh new file mode 100644 index 0000000000000..8aa3e506eb1b4 --- /dev/null +++ b/recipes/bioconductor-sesamedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="sesameData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/sesameData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/sesameData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sesamedata/bioconductor-sesamedata_1.0.0_src_all.tar.gz" +) +MD5="dc24068fe6bdc6ef7e62c89c38b8d949" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sesamedata/pre-unlink.sh b/recipes/bioconductor-sesamedata/pre-unlink.sh new file mode 100644 index 0000000000000..7a29bbe212709 --- /dev/null +++ b/recipes/bioconductor-sesamedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ sesameData diff --git a/recipes/bioconductor-sevenbridges/build.sh b/recipes/bioconductor-sevenbridges/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sevenbridges/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sevenbridges/meta.yaml b/recipes/bioconductor-sevenbridges/meta.yaml new file mode 100644 index 0000000000000..d94940b9f88e8 --- /dev/null +++ b/recipes/bioconductor-sevenbridges/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.12.3" %} +{% set name = "sevenbridges" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 483ec1b5383a56f9806d8f7de4559d14 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, readr +requirements: + host: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-curl + - r-docopt + - r-dplyr + - r-httr + - r-jsonlite + - r-objectproperties + - r-stringr + - r-uuid + - r-yaml + run: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-curl + - r-docopt + - r-dplyr + - r-httr + - r-jsonlite + - r-objectproperties + - r-stringr + - r-uuid + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'Apache License 2.0 | file LICENSE' + summary: 'R client and utilities for Seven Bridges platform API, from Cancer Genomics Cloud to other Seven Bridges supported platforms.' + diff --git a/recipes/bioconductor-sevenc/build.sh b/recipes/bioconductor-sevenc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sevenc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sevenc/meta.yaml b/recipes/bioconductor-sevenc/meta.yaml new file mode 100644 index 0000000000000..0d6af838112e1 --- /dev/null +++ b/recipes/bioconductor-sevenc/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.2.0" %} +{% set name = "sevenC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 276812bfe5e2ed5a8d6e7cd28c4effb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, GenomicInteractions, covr +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-boot >=1.3-20' + - 'r-data.table >=1.10.4' + - 'r-purrr >=0.2.2' + - 'r-readr >=1.1.0' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-boot >=1.3-20' + - 'r-data.table >=1.10.4' + - 'r-purrr >=0.2.2' + - 'r-readr >=1.1.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Chromatin looping is an essential feature of eukaryotic genomes and can bring regulatory sequences, such as enhancers or transcription factor binding sites, in the close physical proximity of regulated target genes. Here, we provide sevenC, an R package that uses protein binding signals from ChIP-seq and sequence motif information to predict chromatin looping events. Cross-linking of proteins that bind close to loop anchors result in ChIP-seq signals at both anchor loci. These signals are used at CTCF motif pairs together with their distance and orientation to each other to predict whether they interact or not. The resulting chromatin loops might be used to associate enhancers or transcription factor binding sites (e.g., ChIP-seq peaks) to regulated target genes.' + diff --git a/recipes/bioconductor-seventygenedata/meta.yaml b/recipes/bioconductor-seventygenedata/meta.yaml new file mode 100644 index 0000000000000..fc80f425fa5c7 --- /dev/null +++ b/recipes/bioconductor-seventygenedata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "seventyGeneData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f5232714137c1bb3d94e058b651ab041 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, gdata, limma, breastCancerNKI +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Gene expression data for the two breast cancer cohorts published by van''t Veer and Van de Vijver in 2002' + diff --git a/recipes/bioconductor-seventygenedata/post-link.sh b/recipes/bioconductor-seventygenedata/post-link.sh new file mode 100644 index 0000000000000..4287fdf2c564b --- /dev/null +++ b/recipes/bioconductor-seventygenedata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="seventyGeneData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/seventyGeneData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/seventyGeneData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-seventygenedata/bioconductor-seventygenedata_1.18.0_src_all.tar.gz" +) +MD5="f5232714137c1bb3d94e058b651ab041" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-seventygenedata/pre-unlink.sh b/recipes/bioconductor-seventygenedata/pre-unlink.sh new file mode 100644 index 0000000000000..af5ae656b5681 --- /dev/null +++ b/recipes/bioconductor-seventygenedata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ seventyGeneData diff --git a/recipes/bioconductor-sgseq/build.sh b/recipes/bioconductor-sgseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sgseq/build.sh +++ b/recipes/bioconductor-sgseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sgseq/meta.yaml b/recipes/bioconductor-sgseq/meta.yaml index 21422e3ce1169..f2e9ecd838585 100644 --- a/recipes/bioconductor-sgseq/meta.yaml +++ b/recipes/bioconductor-sgseq/meta.yaml @@ -1,51 +1,53 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SGSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e61fb11182dcbaf177f882b46ff4df73e58d77e2cfdf94aee5f8ed473179c387 + md5: cad23f2e205a14cb4e84326111b98f9c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, knitr, rmarkdown requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-igraph - r-runit run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-igraph - r-runit @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'SGSeq is a software package for analyzing splice events from RNA-seq data. Input data are RNA-seq reads mapped to a reference genome in BAM format. Genes are represented as a splice graph, which can be obtained from existing annotation or predicted from the mapped sequence reads. Splice events are identified from the graph and are quantified locally using structurally compatible reads at the start or end of each splice variant. The software includes functions for splice event prediction, quantification, visualization and interpretation.' extra: identifiers: - biotools:sgseq + parent_recipe: + name: bioconductor-sgseq + path: recipes/bioconductor-sgseq + version: 1.14.0 + diff --git a/recipes/bioconductor-shdz.db/meta.yaml b/recipes/bioconductor-shdz.db/meta.yaml new file mode 100644 index 0000000000000..23642c3e2f5b1 --- /dev/null +++ b/recipes/bioconductor-shdz.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "SHDZ.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 63c4439a272a5cd0c4746e9e53a7bdc7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SHDZ http://genome-www5.stanford.edu/ Annotation Data (SHDZ) assembled using data from public repositories' + diff --git a/recipes/bioconductor-shdz.db/post-link.sh b/recipes/bioconductor-shdz.db/post-link.sh new file mode 100644 index 0000000000000..574476e938bf5 --- /dev/null +++ b/recipes/bioconductor-shdz.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SHDZ.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SHDZ.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/SHDZ.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-shdz.db/bioconductor-shdz.db_3.2.3_src_all.tar.gz" +) +MD5="63c4439a272a5cd0c4746e9e53a7bdc7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-shdz.db/pre-unlink.sh b/recipes/bioconductor-shdz.db/pre-unlink.sh new file mode 100644 index 0000000000000..25376a9ac03b5 --- /dev/null +++ b/recipes/bioconductor-shdz.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SHDZ.db diff --git a/recipes/bioconductor-shinymethyl/build.sh b/recipes/bioconductor-shinymethyl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-shinymethyl/build.sh +++ b/recipes/bioconductor-shinymethyl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-shinymethyl/meta.yaml b/recipes/bioconductor-shinymethyl/meta.yaml index 7ae3455afe4e0..d51c5c762b657 100644 --- a/recipes/bioconductor-shinymethyl/meta.yaml +++ b/recipes/bioconductor-shinymethyl/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "shinyMethyl" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1ca469110677b1a38683a16fa24c17224853996fe01676e482375dcdc02ce7cd + md5: fb818769476e39badee29c91a49736dc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: shinyMethylData, minfiData, BiocStyle, RUnit, digest, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcolorbrewer - 'r-shiny >=0.13.2' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.6.0' - - 'bioconductor-minfi >=1.26.2,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' - r-base - r-matrixstats - r-rcolorbrewer @@ -37,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Interactive tool for visualizing Illumina methylation array data. Both the 450k and EPIC array are supported.' extra: identifiers: - biotools:shinymethyl + parent_recipe: + name: bioconductor-shinymethyl + path: recipes/bioconductor-shinymethyl + version: 1.16.0 + diff --git a/recipes/bioconductor-shinymethyldata/meta.yaml b/recipes/bioconductor-shinymethyldata/meta.yaml new file mode 100644 index 0000000000000..aefef7b0266ff --- /dev/null +++ b/recipes/bioconductor-shinymethyldata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.2.0" %} +{% set name = "shinyMethylData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c7cfcef8e0c7dff18eb34609812ea3b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extracted data from 369 TCGA Head and Neck Cancer DNA methylation samples. The extracted data serve as an example dataset for the package shinyMethyl. Original samples are from 450k methylation arrays, and were obtained from The Cancer Genome Atlas (TCGA). 310 samples are from tumor, 50 are matched normals and 9 are technical replicates of a control cell line.' + diff --git a/recipes/bioconductor-shinymethyldata/post-link.sh b/recipes/bioconductor-shinymethyldata/post-link.sh new file mode 100644 index 0000000000000..15f332904320b --- /dev/null +++ b/recipes/bioconductor-shinymethyldata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="shinyMethylData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/shinyMethylData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/shinyMethylData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-shinymethyldata/bioconductor-shinymethyldata_1.2.0_src_all.tar.gz" +) +MD5="c7cfcef8e0c7dff18eb34609812ea3b4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-shinymethyldata/pre-unlink.sh b/recipes/bioconductor-shinymethyldata/pre-unlink.sh new file mode 100644 index 0000000000000..b006cdc8c664a --- /dev/null +++ b/recipes/bioconductor-shinymethyldata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ shinyMethylData diff --git a/recipes/bioconductor-shinytandem/build.sh b/recipes/bioconductor-shinytandem/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-shinytandem/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-shinytandem/meta.yaml b/recipes/bioconductor-shinytandem/meta.yaml new file mode 100644 index 0000000000000..5527b0e4c5420 --- /dev/null +++ b/recipes/bioconductor-shinytandem/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.20.0" %} +{% set name = "shinyTANDEM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7ebddfcdaff66bac03d0982c93f572d5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-mixtools + - r-shiny + - r-xtable + run: + - 'bioconductor-rtandem >=1.22.0,<1.23.0' + - r-base + - r-mixtools + - r-shiny + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides a GUI interface for rTANDEM. The GUI is primarily designed to visualize rTANDEM result object or result xml files. But it will also provides an interface for creating parameter objects, launching searches or performing conversions between R objects and xml files.' + diff --git a/recipes/bioconductor-shortread/build.sh b/recipes/bioconductor-shortread/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-shortread/build.sh +++ b/recipes/bioconductor-shortread/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-shortread/meta.yaml b/recipes/bioconductor-shortread/meta.yaml index 962a36d424c53..b1471dc0521ad 100644 --- a/recipes/bioconductor-shortread/meta.yaml +++ b/recipes/bioconductor-shortread/meta.yaml @@ -1,52 +1,53 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "ShortRead" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cb058f83d68937dc1ec1d6662d2597c65bbdfc943a24ffe5bbab7085cf1f1f0d + md5: 455d4397ae013d40ad8f5eb6e215d6b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, RUnit, biomaRt, GenomicFeatures, yeastNagalakshmi requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-hwriter - r-lattice - r-latticeextra run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-hwriter - r-lattice @@ -60,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.' extra: identifiers: - biotools:shortread + parent_recipe: + name: bioconductor-shortread + path: recipes/bioconductor-shortread + version: 1.38.0 + diff --git a/recipes/bioconductor-siamcat/build.sh b/recipes/bioconductor-siamcat/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-siamcat/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-siamcat/meta.yaml b/recipes/bioconductor-siamcat/meta.yaml new file mode 100644 index 0000000000000..4949dc5008e11 --- /dev/null +++ b/recipes/bioconductor-siamcat/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.2.0" %} +{% set name = "SIAMCAT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 06b5bd798aee4515ec2b3a0d79104cd7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, optparse, testthat, knitr, rmarkdown +requirements: + host: + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - r-base + - r-beanplot + - r-corrplot + - r-glmnet + - r-gridbase + - r-gridextra + - r-infotheo + - r-liblinear + - r-matrixstats + - r-mlr + - r-paramhelpers + - r-proc + - r-prroc + - r-rcolorbrewer + - r-scales + - r-stringr + run: + - 'bioconductor-phyloseq >=1.26.0,<1.27.0' + - r-base + - r-beanplot + - r-corrplot + - r-glmnet + - r-gridbase + - r-gridextra + - r-infotheo + - r-liblinear + - r-matrixstats + - r-mlr + - r-paramhelpers + - r-proc + - r-prroc + - r-rcolorbrewer + - r-scales + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Pipeline for Statistical Inference of Associations between Microbial Communities And host phenoTypes (SIAMCAT). A primary goal of analyzing microbiome data is to determine changes in community composition that are associated with environmental factors. In particular, linking human microbiome composition to host phenotypes such as diseases has become an area of intense research. For this, robust statistical modeling and biomarker extraction toolkits are crucially needed. SIAMCAT provides a full pipeline supporting data preprocessing, statistical association testing, statistical modeling (LASSO logistic regression) including tools for evaluation and interpretation of these models (such as cross validation, parameter selection, ROC analysis and diagnostic model plots).' + diff --git a/recipes/bioconductor-sictools/build.sh b/recipes/bioconductor-sictools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sictools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sictools/meta.yaml b/recipes/bioconductor-sictools/meta.yaml new file mode 100644 index 0000000000000..839f15b2727ea --- /dev/null +++ b/recipes/bioconductor-sictools/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.12.0" %} +{% set name = "SICtools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4e9730f2194cfb50c7808bfe43f0c3af +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - 'r-doparallel >=1.0.8' + - 'r-matrixstats >=0.10.0' + - 'r-plyr >=1.8.3' + - 'r-stringr >=0.6.2' + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - 'r-doparallel >=1.0.8' + - 'r-matrixstats >=0.10.0' + - 'r-plyr >=1.8.3' + - 'r-stringr >=0.6.2' + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'This package is to find SNV/Indel differences between two bam files with near relationship in a way of pairwise comparison thourgh each base position across the genome region of interest. The difference is inferred by fisher test and euclidean distance, the input of which is the base count (A,T,G,C) in a given position and read counts for indels that span no less than 2bp on both sides of indel region.' + diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml new file mode 100644 index 0000000000000..44fcf8a40a1af --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.2" %} +{% set name = "SIFT.Hsapiens.dbSNP132" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c374f0bf4c99357cfe99e0b192c00d75 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Database of SIFT predictions for Homo sapiens dbSNP build 132' + diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh b/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh new file mode 100644 index 0000000000000..14dcbf4ad9771 --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" + "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP132_1.0.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp132/bioconductor-sift.hsapiens.dbsnp132_1.0.2_src_all.tar.gz" +) +MD5="c374f0bf4c99357cfe99e0b192c00d75" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp132/pre-unlink.sh b/recipes/bioconductor-sift.hsapiens.dbsnp132/pre-unlink.sh new file mode 100644 index 0000000000000..485cd16b718af --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp132/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SIFT.Hsapiens.dbSNP132 diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml new file mode 100644 index 0000000000000..4289cca0a5ce5 --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "SIFT.Hsapiens.dbSNP137" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c3e73f826399af5ff368d1aab12cfd1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-rsqlite >=0.11.0' + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Database of PROVEAN/SIFT predictions for Homo sapiens dbSNP build 137' + diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh b/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh new file mode 100644 index 0000000000000..fba7b3de0e899 --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/SIFT.Hsapiens.dbSNP137_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sift.hsapiens.dbsnp137/bioconductor-sift.hsapiens.dbsnp137_1.0.0_src_all.tar.gz" +) +MD5="3c3e73f826399af5ff368d1aab12cfd1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sift.hsapiens.dbsnp137/pre-unlink.sh b/recipes/bioconductor-sift.hsapiens.dbsnp137/pre-unlink.sh new file mode 100644 index 0000000000000..99b76c94386dd --- /dev/null +++ b/recipes/bioconductor-sift.hsapiens.dbsnp137/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SIFT.Hsapiens.dbSNP137 diff --git a/recipes/bioconductor-sigar/build.sh b/recipes/bioconductor-sigar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sigar/build.sh +++ b/recipes/bioconductor-sigar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigar/meta.yaml b/recipes/bioconductor-sigar/meta.yaml index fa7335cd03280..b3a895c435633 100644 --- a/recipes/bioconductor-sigar/meta.yaml +++ b/recipes/bioconductor-sigar/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "sigaR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bab613194873b70ba0a6e8cde7e550bad897593bc546667a59f20bf6f7f8d7ce + md5: f27d79fb98bc4327fbc638f140a3f0d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: CGHcall requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph @@ -31,10 +33,10 @@ requirements: - r-quadprog - r-snowfall run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-cghbase >=1.40.0,<1.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-cghbase >=1.42.0,<1.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - 'r-corpcor >=1.6.2' - r-igraph @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Facilitates the joint analysis of high-throughput data from multiple molecular levels. Contains functions for manipulation of objects, various analysis types, and some visualization.' extra: identifiers: - biotools:sigar - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sigar + path: recipes/bioconductor-sigar + version: 1.28.0 + diff --git a/recipes/bioconductor-sigcheck/build.sh b/recipes/bioconductor-sigcheck/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sigcheck/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigcheck/meta.yaml b/recipes/bioconductor-sigcheck/meta.yaml new file mode 100644 index 0000000000000..c268948558dd4 --- /dev/null +++ b/recipes/bioconductor-sigcheck/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "2.14.0" %} +{% set name = "SigCheck" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f63b63b11545697c94145639594dd0bb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, breastCancerNKI, qusage +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - r-base + - r-e1071 + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-mlinterfaces >=1.62.0,<1.63.0' + - r-base + - r-e1071 + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'While gene signatures are frequently used to predict phenotypes (e.g. predict prognosis of cancer patients), it it not always clear how optimal or meaningful they are (cf David Venet, Jacques E. Dumont, and Vincent Detours'' paper "Most Random Gene Expression Signatures Are Significantly Associated with Breast Cancer Outcome"). Based on suggestions in that paper, SigCheck accepts a data set (as an ExpressionSet) and a gene signature, and compares its performance on survival and/or classification tasks against a) random gene signatures of the same length; b) known, related and unrelated gene signatures; and c) permuted data and/or metadata.' + diff --git a/recipes/bioconductor-sigfeature/build.sh b/recipes/bioconductor-sigfeature/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sigfeature/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigfeature/meta.yaml b/recipes/bioconductor-sigfeature/meta.yaml new file mode 100644 index 0000000000000..825b662899333 --- /dev/null +++ b/recipes/bioconductor-sigfeature/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "sigFeature" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5e75e6f3818225a0b8135d9cd4acaaa6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-e1071 + - r-matrix + - r-nlme + - r-openxlsx + - r-pheatmap + - r-rcolorbrewer + - r-sparsem + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocviews >=1.50.0,<1.51.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-e1071 + - r-matrix + - r-nlme + - r-openxlsx + - r-pheatmap + - r-rcolorbrewer + - r-sparsem +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'This package provides a novel feature selection algorithm for binary classification using support vector machine recursive feature elimination SVM-RFE and t-statistic. In this feature selection process, the selected features are differentially significant between the two classes and also they are good classifier with higher degree of classification accuracy.' + diff --git a/recipes/bioconductor-sigfuge/build.sh b/recipes/bioconductor-sigfuge/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sigfuge/build.sh +++ b/recipes/bioconductor-sigfuge/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigfuge/meta.yaml b/recipes/bioconductor-sigfuge/meta.yaml index f38afb479468d..d2e4dede1540f 100644 --- a/recipes/bioconductor-sigfuge/meta.yaml +++ b/recipes/bioconductor-sigfuge/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SigFuge" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1fff662907729e3b68c90232d7443b634b3b371763be5b15a43d6ad508742996 + md5: 617321ada3ea3a85d48d9643d6d64ecc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, prebsdata, Rsamtools (>= 1.17.0), TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matlab - r-reshape - r-sigclust run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-matlab @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Algorithm for testing significance of clustering in RNA-seq data.' extra: identifiers: - biotools:sigfuge - doi:10.1093/nar/gku521 + parent_recipe: + name: bioconductor-sigfuge + path: recipes/bioconductor-sigfuge + version: 1.18.0 + diff --git a/recipes/bioconductor-siggenes/build.sh b/recipes/bioconductor-siggenes/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-siggenes/build.sh +++ b/recipes/bioconductor-siggenes/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-siggenes/meta.yaml b/recipes/bioconductor-siggenes/meta.yaml index dfc816069b8cf..66ebd60bd2322 100644 --- a/recipes/bioconductor-siggenes/meta.yaml +++ b/recipes/bioconductor-siggenes/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "siggenes" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 1e9b945bfdcefbe5357f2d7169af27d4f4d45a90842d623488c1a489909d2f5c + md5: 28a8f05b99d9576b8ace9ea342efe70c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affy, annotate, genefilter, KernSmooth, scrime (>= 1.2.5) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Identification of differentially expressed genes and estimation of the False Discovery Rate (FDR) using both the Significance Analysis of Microarrays (SAM) and the Empirical Bayes Analyses of Microarrays (EBAM).' extra: identifiers: - biotools:siggenes - doi:10.1186/1471-2105-9-144 + parent_recipe: + name: bioconductor-siggenes + path: recipes/bioconductor-siggenes + version: 1.54.0 + diff --git a/recipes/bioconductor-sights/build.sh b/recipes/bioconductor-sights/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sights/build.sh +++ b/recipes/bioconductor-sights/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sights/meta.yaml b/recipes/bioconductor-sights/meta.yaml index b1ea4e4c27bf6..950032a59b187 100644 --- a/recipes/bioconductor-sights/meta.yaml +++ b/recipes/bioconductor-sights/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "sights" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: e40ca2d70559fe57a5fdd6f68aac764a76591964e69c855e3a6d5156bbceb981 + md5: a1d3a465d08ce54a5bfb0d3ff6bbf46e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, ggthemes, gridExtra, xlsx requirements: host: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' - 'r-mass >=7.3' - 'r-reshape2 >=1.4' run: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - 'r-ggplot2 >=2.0' - 'r-lattice >=0.2' @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'SIGHTS is a suite of normalization methods, statistical tests, and diagnostic graphical tools for high throughput screening (HTS) assays. HTS assays use microtitre plates to screen large libraries of compounds for their biological, chemical, or biochemical activity.' extra: identifiers: - biotools:sights - doi:10.1177/1087057114548853 + parent_recipe: + name: bioconductor-sights + path: recipes/bioconductor-sights + version: 1.6.0 + diff --git a/recipes/bioconductor-signer/build.sh b/recipes/bioconductor-signer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-signer/build.sh +++ b/recipes/bioconductor-signer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-signer/meta.yaml b/recipes/bioconductor-signer/meta.yaml index db608430b0b0b..8d757a8cf4327 100644 --- a/recipes/bioconductor-signer/meta.yaml +++ b/recipes/bioconductor-signer/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "signeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 109d1cf32259ea818750d2377a4e8f8711f991b7b87358a857ab4f26f654a630 + md5: 79074171d5f1f9af6f93abcfcc96cbe1 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: knitr, rtracklayer, BSgenome.Hsapiens.UCSC.hg19 +# SystemRequirements: C++11 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-class - r-nloptr @@ -30,10 +32,10 @@ requirements: - r-rcpp - 'r-rcpparmadillo >=0.7.100' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-class - r-nloptr @@ -49,9 +51,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The signeR package provides an empirical Bayesian approach to mutational signature discovery. It is designed to analyze single nucleotide variaton (SNV) counts in cancer genomes, but can also be applied to other features as well. Functionalities to characterize signatures or genome samples according to exposure patterns are also provided.' extra: identifiers: - biotools:signer + parent_recipe: + name: bioconductor-signer + path: recipes/bioconductor-signer + version: 1.6.1 + diff --git a/recipes/bioconductor-signet/build.sh b/recipes/bioconductor-signet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-signet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-signet/meta.yaml b/recipes/bioconductor-signet/meta.yaml new file mode 100644 index 0000000000000..0855f077d79c9 --- /dev/null +++ b/recipes/bioconductor-signet/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.2.2" %} +{% set name = "signet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e4c4ef194cd4a7f22e5a45da76dd3f5b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: graphite, BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-igraph + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - r-base + - r-igraph +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'An R package to detect selection in biological pathways. Using gene selection scores and biological pathways data, one can search for high-scoring subnetworks of genes within pathways and test their significance.' + diff --git a/recipes/bioconductor-sigpathway/build.sh b/recipes/bioconductor-sigpathway/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sigpathway/build.sh +++ b/recipes/bioconductor-sigpathway/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigpathway/meta.yaml b/recipes/bioconductor-sigpathway/meta.yaml index ce3a7f2d33e80..fdb3aa1b0f153 100644 --- a/recipes/bioconductor-sigpathway/meta.yaml +++ b/recipes/bioconductor-sigpathway/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "sigPathway" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 202a3e4d2ea17945fffb67c3bb6ba484dd64c4285ae35656e1da27f84168f5be + md5: b825fbbd08a65e76c61fef39eab3492b build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: hgu133a.db (>= 1.10.0), XML (>= 1.6-3), AnnotationDbi (>= 1.3.12) requirements: host: - r-base @@ -28,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Conducts pathway analysis by calculating the NT_k and NE_k statistics as described in Tian et al. (2005)' extra: identifiers: - biotools:sigpathway - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sigpathway + path: recipes/bioconductor-sigpathway + version: 1.48.0 + diff --git a/recipes/bioconductor-sigsquared/build.sh b/recipes/bioconductor-sigsquared/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sigsquared/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sigsquared/meta.yaml b/recipes/bioconductor-sigsquared/meta.yaml new file mode 100644 index 0000000000000..f9aa26e6d34e5 --- /dev/null +++ b/recipes/bioconductor-sigsquared/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.14.0" %} +{% set name = "sigsquared" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3cc54becc997d3072a3c626a4267462b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-survival +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL version 3' + summary: 'By leveraging statistical properties (log-rank test for survival) of patient cohorts defined by binary thresholds, poor-prognosis patients are identified by the sigsquared package via optimization over a cost function reducing type I and II error.' + diff --git a/recipes/bioconductor-silva128.1mgdb/meta.yaml b/recipes/bioconductor-silva128.1mgdb/meta.yaml new file mode 100644 index 0000000000000..04dff277e7e1e --- /dev/null +++ b/recipes/bioconductor-silva128.1mgdb/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.00.0" %} +{% set name = "silva128.1MgDb" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f73cc038441a0a166c07582eec9a77b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + run: + - 'bioconductor-metagenomefeatures >=2.2.0,<2.3.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Metagenome annotation package with for the SILVA SSR rRNA database release 128.1, Bacterial and Archeal sequences. Contains a MgDb-class object, defined in the metagenomeFeatures package.' + diff --git a/recipes/bioconductor-silva128.1mgdb/post-link.sh b/recipes/bioconductor-silva128.1mgdb/post-link.sh new file mode 100644 index 0000000000000..29dd5a637bd78 --- /dev/null +++ b/recipes/bioconductor-silva128.1mgdb/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="silva128.1MgDb_1.00.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/silva128.1MgDb_1.00.0.tar.gz" + "https://bioarchive.galaxyproject.org/silva128.1MgDb_1.00.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-silva128.1mgdb/bioconductor-silva128.1mgdb_1.00.0_src_all.tar.gz" +) +MD5="f73cc038441a0a166c07582eec9a77b4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-silva128.1mgdb/pre-unlink.sh b/recipes/bioconductor-silva128.1mgdb/pre-unlink.sh new file mode 100644 index 0000000000000..87dc30789282e --- /dev/null +++ b/recipes/bioconductor-silva128.1mgdb/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ silva128.1MgDb diff --git a/recipes/bioconductor-sim/build.sh b/recipes/bioconductor-sim/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sim/build.sh +++ b/recipes/bioconductor-sim/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sim/meta.yaml b/recipes/bioconductor-sim/meta.yaml index 4f00a02f0df17..5849de47031ad 100644 --- a/recipes/bioconductor-sim/meta.yaml +++ b/recipes/bioconductor-sim/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "SIM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ad883a0998f04b9f446c12603f9d6abbe8a502ba6612394ba7a43fd5ba28bc3e + md5: 1c7164bbcfbc8d3dfb2495875c3aa478 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: biomaRt, RColorBrewer requirements: host: - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' - r-base - r-quantreg run: - - 'bioconductor-globaltest >=5.34.1,<5.36.0' - - 'bioconductor-quantsmooth >=1.46.0,<1.48.0' + - 'bioconductor-globaltest >=5.36.0,<5.37.0' + - 'bioconductor-quantsmooth >=1.48.0,<1.49.0' - r-base - r-quantreg build: @@ -34,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Finds associations between two human genomic datasets.' extra: identifiers: - biotools:sim - doi:10.1186/1471-2105-10-203 + parent_recipe: + name: bioconductor-sim + path: recipes/bioconductor-sim + version: 1.50.0 + diff --git a/recipes/bioconductor-simat/build.sh b/recipes/bioconductor-simat/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-simat/build.sh +++ b/recipes/bioconductor-simat/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simat/meta.yaml b/recipes/bioconductor-simat/meta.yaml index ee44840af4264..48dbe8c81eba6 100644 --- a/recipes/bioconductor-simat/meta.yaml +++ b/recipes/bioconductor-simat/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "1.12.1" %} +{% set version = "1.14.0" %} {% set name = "SIMAT" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4ba6cf05252f63457d121e064b0dda6412d3fd93ae1d849469d9e350534f02c3 + md5: a72965e304ff7a6e7b8a499e648aa2d7 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' - r-reshape2 run: - - 'bioconductor-mzr >=2.17.0,<2.19.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' - r-base - r-ggplot2 - 'r-rcpp >=0.11.3' @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a pipeline for analysis of GC-MS data acquired in selected ion monitoring (SIM) mode. The tool also provides a guidance in choosing appropriate fragments for the targets of interest by using an optimization algorithm. This is done by considering overlapping peaks from a provided library by the user.' extra: identifiers: - biotools:simat - doi:10.1186/s12859-015-0681-2 + parent_recipe: + name: bioconductor-simat + path: recipes/bioconductor-simat + version: 1.12.1 + diff --git a/recipes/bioconductor-simbindprofiles/build.sh b/recipes/bioconductor-simbindprofiles/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-simbindprofiles/build.sh +++ b/recipes/bioconductor-simbindprofiles/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simbindprofiles/conda_build_config.yaml b/recipes/bioconductor-simbindprofiles/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-simbindprofiles/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-simbindprofiles/meta.yaml b/recipes/bioconductor-simbindprofiles/meta.yaml index c607ae9e18623..911366bde6865 100644 --- a/recipes/bioconductor-simbindprofiles/meta.yaml +++ b/recipes/bioconductor-simbindprofiles/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SimBindProfiles" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2f3f0ce9098781eb8a6af8134b48a40b610e830212f2328590a430672dab8af4 + md5: 1bebc53f15f0afdd77b7512beaf06c28 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' - r-base - r-mclust run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' - r-base - r-mclust test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'SimBindProfiles identifies common and unique binding regions in genome tiling array data. This package does not rely on peak calling, but directly compares binding profiles processed on the same array platform. It implements a simple threshold approach, thus allowing retrieval of commonly and differentially bound regions between datasets as well as events of compensation and increased binding.' extra: identifiers: - biotools:simbindprofiles - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-simbindprofiles + path: recipes/bioconductor-simbindprofiles + version: 1.18.0 + diff --git a/recipes/bioconductor-simd/build.sh b/recipes/bioconductor-simd/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-simd/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simd/meta.yaml b/recipes/bioconductor-simd/meta.yaml new file mode 100644 index 0000000000000..75a79cbe642a2 --- /dev/null +++ b/recipes/bioconductor-simd/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.0.0" %} +{% set name = "SIMD" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 385e8cbf0131d3ef3707b6ba582948e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, knitr,rmarkdown +requirements: + host: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-methylmnm >=1.20.0,<1.21.0' + - r-base + - r-statmod + run: + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-methylmnm >=1.20.0,<1.21.0' + - r-base + - r-statmod + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package provides a inferential analysis method for detecting differentially expressed CpG sites in MeDIP-seq data. It uses statistical framework and EM algorithm, to identify differentially expressed CpG sites. The methods on this package are described in the article ''Methylation-level Inferences and Detection of Differential Methylation with Medip-seq Data'' by Yan Zhou, Jiadi Zhu, Mingtao Zhao, Baoxue Zhang, Chunfu Jiang and Xiyan Yang (2018, pending publication).' + diff --git a/recipes/bioconductor-similarpeak/build.sh b/recipes/bioconductor-similarpeak/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-similarpeak/build.sh +++ b/recipes/bioconductor-similarpeak/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-similarpeak/meta.yaml b/recipes/bioconductor-similarpeak/meta.yaml index 2bc7afdf3a48d..ad627b701ce47 100644 --- a/recipes/bioconductor-similarpeak/meta.yaml +++ b/recipes/bioconductor-similarpeak/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "similaRpeak" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6a6e60857eaec4a37142a3ddb9cfa0fa112c7e7f55cbd876f4bc8e341e5bac4b + md5: 5131bceb89b919a1df752c9047a55671 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr, Rsamtools, GenomicAlignments, rtracklayer, rmarkdown, BiocStyle requirements: host: - r-base @@ -27,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package calculates metrics which assign a level of similarity between ChIP-Seq profiles.' extra: identifiers: - biotools:similarpeak - doi:10.1371/journal.pcbi.1004751 + parent_recipe: + name: bioconductor-similarpeak + path: recipes/bioconductor-similarpeak + version: 1.12.0 + diff --git a/recipes/bioconductor-simlr/build.sh b/recipes/bioconductor-simlr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-simlr/build.sh +++ b/recipes/bioconductor-simlr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simlr/meta.yaml b/recipes/bioconductor-simlr/meta.yaml index 03cabe1551c15..81727525a1646 100644 --- a/recipes/bioconductor-simlr/meta.yaml +++ b/recipes/bioconductor-simlr/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "SIMLR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 872490b56557dd4752197508c4c995b5c9961c1503fa1f4c7459ccb573266eeb + md5: a8d2108d7606877842718a0a26c6014e build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocGenerics, BiocStyle, testthat, knitr, igraph requirements: host: - r-base @@ -39,10 +40,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' - summary: ' In this package we provide implementations of both SIMLR and CIMLR. These methods were originally applied to single-cell and cancer genomic data, but they are in principle capable of effectively and efficiently learning similarities in all the contexts where diverse and heterogeneous statistical characteristics of the data make the problem harder for standard approaches.' + summary: 'Single-cell RNA-seq technologies enable high throughput gene expression measurement of individual cells, and allow the discovery of heterogeneity within cell populations. Measurement of cell-to-cell gene expression similarity is critical for the identification, visualization and analysis of cell populations. However, single-cell data introduce challenges to conventional measures of gene expression similarity because of the high level of noise, outliers and dropouts. We develop a novel similarity-learning framework, SIMLR (Single-cell Interpretation via Multi-kernel LeaRning), which learns an appropriate distance metric from the data for dimension reduction, clustering and visualization.' extra: identifiers: - biotools:simlr - doi:10.1101/118901 + parent_recipe: + name: bioconductor-simlr + path: recipes/bioconductor-simlr + version: 1.6.0 + diff --git a/recipes/bioconductor-simpintlists/meta.yaml b/recipes/bioconductor-simpintlists/meta.yaml index 53b7e77c9f865..e62148f594c5b 100644 --- a/recipes/bioconductor-simpintlists/meta.yaml +++ b/recipes/bioconductor-simpintlists/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "simpIntLists" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 650cb3b0db9a7c139f5f318e07c2da0c55c274919af2492e37a66245027b2706 + md5: 9276ea6e949af976d59fe3317bb0e208 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains BioGRID interactions for arabidopsis(thale cress), c.elegans, fruit fly, human, mouse, yeast( budding yeast ) and S.pombe (fission yeast) . Entrez ids, official names and unique ids can be used to find proteins. The format of interactions are lists. For each gene/protein, there is an entry in the list with "name" containing name of the gene/protein and "interactors" containing the list of genes/proteins interacting with it.' - +extra: + parent_recipe: + name: bioconductor-simpintlists + path: recipes/bioconductor-simpintlists + version: 1.16.0 diff --git a/recipes/bioconductor-simpintlists/post-link.sh b/recipes/bioconductor-simpintlists/post-link.sh index a8b63176d1126..62006cae2152e 100644 --- a/recipes/bioconductor-simpintlists/post-link.sh +++ b/recipes/bioconductor-simpintlists/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="simpIntLists_1.16.0.tar.gz" +FN="simpIntLists_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/simpIntLists_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/simpIntLists_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/simpIntLists_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/simpIntLists_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-simpintlists/bioconductor-simpintlists_1.18.0_src_all.tar.gz" ) -MD5="7a876bfa3d4e4ae339b90c3f64934a51" +MD5="9276ea6e949af976d59fe3317bb0e208" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-simpleaffy/build.sh b/recipes/bioconductor-simpleaffy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-simpleaffy/build.sh +++ b/recipes/bioconductor-simpleaffy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simpleaffy/conda_build_config.yaml b/recipes/bioconductor-simpleaffy/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-simpleaffy/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-simpleaffy/meta.yaml b/recipes/bioconductor-simpleaffy/meta.yaml index 928eccd768d38..3e16de8309b36 100644 --- a/recipes/bioconductor-simpleaffy/meta.yaml +++ b/recipes/bioconductor-simpleaffy/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "2.56.0" %} +{% set version = "2.58.0" %} {% set name = "simpleaffy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 66370f3b505208b22130c23e7e62aba8fb59e5a0441866536cfd28a5322d8f04 + md5: f6d7cbd0c17d30f74cf54782be74fbba build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' - r-base build: - {{ compiler('c') }} @@ -38,10 +38,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Provides high level functions for reading Affy .CEL files, phenotypic data, and then computing simple things with it, such as t-tests, fold changes and the like. Makes heavy use of the affy library. Also has some basic scatter plot functions and mechanisms for generating high resolution journal figures...' extra: identifiers: - biotools:simpleaffy - doi:10.1093/bioinformatics/bti605 + parent_recipe: + name: bioconductor-simpleaffy + path: recipes/bioconductor-simpleaffy + version: 2.56.0 + diff --git a/recipes/bioconductor-simulatorz/build.sh b/recipes/bioconductor-simulatorz/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-simulatorz/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-simulatorz/meta.yaml b/recipes/bioconductor-simulatorz/meta.yaml new file mode 100644 index 0000000000000..78e2fdbc3a63f --- /dev/null +++ b/recipes/bioconductor-simulatorz/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.16.0" %} +{% set name = "simulatorZ" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 23b14912a86f22445fa0b20ccb9a8769 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: RUnit, BiocStyle, curatedOvarianData, parathyroidSE, superpc +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coxboost + - r-gbm + - r-hmisc + - r-survival + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-coxboost + - r-gbm + - r-hmisc + - r-survival + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'simulatorZ is a package intended primarily to simulate collections of independent genomic data sets, as well as performing training and validation with predicting algorithms. It supports ExpressionSet and RangedSummarizedExperiment objects.' + diff --git a/recipes/bioconductor-sincell/build.sh b/recipes/bioconductor-sincell/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sincell/build.sh +++ b/recipes/bioconductor-sincell/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sincell/meta.yaml b/recipes/bioconductor-sincell/meta.yaml index 17ca23f32c6f2..68af594c92b01 100644 --- a/recipes/bioconductor-sincell/meta.yaml +++ b/recipes/bioconductor-sincell/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "sincell" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 68e2a512cbb5a77cbfa031a55e08310290d1265709c77dff08c3b214cb751bdf + md5: 5d2be7420a6a52d757dc99dcb19b7c69 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, knitr, biomaRt, stringr, monocle requirements: host: - r-base @@ -57,9 +58,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Cell differentiation processes are achieved through a continuum of hierarchical intermediate cell-states that might be captured by single-cell RNA seq. Existing computational approaches for the assessment of cell-state hierarchies from single-cell data might be formalized under a general workflow composed of i) a metric to assess cell-to-cell similarities (combined or not with a dimensionality reduction step), and ii) a graph-building algorithm (optionally making use of a cells-clustering step). Sincell R package implements a methodological toolbox allowing flexible workflows under such framework. Furthermore, Sincell contributes new algorithms to provide cell-state hierarchies with statistical support while accounting for stochastic factors in single-cell RNA seq. Graphical representations and functional association tests are provided to interpret hierarchies.' extra: identifiers: - biotools:sincell + parent_recipe: + name: bioconductor-sincell + path: recipes/bioconductor-sincell + version: 1.12.0 + diff --git a/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml new file mode 100644 index 0000000000000..9e95e63e05d1b --- /dev/null +++ b/recipes/bioconductor-single.mtec.transcriptomes/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "Single.mTEC.Transcriptomes" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b56327144804cf3af178a5750b028707 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DESeq2, GenomicRanges, GenomicFeatures, genefilter, statmod, gdata, RColorBrewer, ggplot2, gplots, cluster, clue, grid, gridExtra, ggbio, Gviz, geneplotter, matrixStats, pheatmap, BiocStyle, knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This data package contains the code used to analyse the single-cell RNA-seq and the bulk ATAC-seq data from the manuscript titled: Single-cell transcriptome analysis reveals coordinated ectopic-gene expression patterns in medullary thymic epithelial cells. This paper was published in Nature Immunology 16,933-941(2015). The data objects provided in this package has been pre-processed: the raw data files can be downloaded from ArrayExpress under the accession identifiers E-MTAB-3346 and E-MTAB-3624. The vignette of this data package provides a documented and reproducible workflow that includes the code that was used to generate each statistic and figure from the manuscript.' + diff --git a/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh new file mode 100644 index 0000000000000..52f6dbc21654d --- /dev/null +++ b/recipes/bioconductor-single.mtec.transcriptomes/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="Single.mTEC.Transcriptomes_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/Single.mTEC.Transcriptomes_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/Single.mTEC.Transcriptomes_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-single.mtec.transcriptomes/bioconductor-single.mtec.transcriptomes_1.10.0_src_all.tar.gz" +) +MD5="b56327144804cf3af178a5750b028707" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-single.mtec.transcriptomes/pre-unlink.sh b/recipes/bioconductor-single.mtec.transcriptomes/pre-unlink.sh new file mode 100644 index 0000000000000..85bc1aa72af1a --- /dev/null +++ b/recipes/bioconductor-single.mtec.transcriptomes/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ Single.mTEC.Transcriptomes diff --git a/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml b/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-singlecellexperiment-scripts/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-singlecellexperiment/build.sh b/recipes/bioconductor-singlecellexperiment/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-singlecellexperiment/build.sh +++ b/recipes/bioconductor-singlecellexperiment/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml b/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-singlecellexperiment/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-singlecellexperiment/meta.yaml b/recipes/bioconductor-singlecellexperiment/meta.yaml index b5e9632f7df0e..15cf632871b26 100644 --- a/recipes/bioconductor-singlecellexperiment/meta.yaml +++ b/recipes/bioconductor-singlecellexperiment/meta.yaml @@ -1,36 +1,44 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "SingleCellExperiment" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6a5ea60b8a9dc442cf1dd9650803677711e6cac6ac6484cd461b14a12264e357 + md5: 42e03af7c4955e1c6fe7afa9d45c7f34 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, scRNAseq, magrittr, Rtsne requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Defines a S4 class for storing data from single-cell experiments. This includes specialized methods to store and retrieve spike-in information, dimensionality reduction coordinates and size factors for each cell, along with the usual metadata for genes and libraries.' +extra: + parent_recipe: + name: bioconductor-singlecellexperiment + path: recipes/bioconductor-singlecellexperiment + version: 1.2.0 + diff --git a/recipes/bioconductor-singlecelltk/build.sh b/recipes/bioconductor-singlecelltk/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-singlecelltk/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-singlecelltk/meta.yaml b/recipes/bioconductor-singlecelltk/meta.yaml new file mode 100644 index 0000000000000..0b4d63e5392c2 --- /dev/null +++ b/recipes/bioconductor-singlecelltk/meta.yaml @@ -0,0 +1,99 @@ +{% set version = "1.2.3" %} +{% set name = "singleCellTK" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 52c4647995b617eba6f157ee2678c058 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, Rsubread, BiocStyle, knitr, bladderbatch, rmarkdown, org.Mm.eg.db, org.Hs.eg.db, scRNAseq, xtable, spelling +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-gsvadata >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mast >=1.8.0,<1.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-ape + - r-base + - r-circlize + - r-cluster + - r-colourpicker + - r-data.table + - r-dt + - r-enrichr + - r-ggplot2 + - r-gridextra + - r-matrixstats + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-rtsne + - r-shiny + - r-shinyalert + - r-shinycssloaders + - r-shinyjs + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' + - 'bioconductor-gsvadata >=1.18.0,<1.19.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mast >=1.8.0,<1.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' + - r-ape + - r-base + - r-circlize + - r-cluster + - r-colourpicker + - r-data.table + - r-dt + - r-enrichr + - r-ggplot2 + - r-gridextra + - r-matrixstats + - r-plotly + - r-rcolorbrewer + - r-reshape2 + - r-rtsne + - r-shiny + - r-shinyalert + - r-shinycssloaders + - r-shinyjs +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Run common single cell analysis directly through your browser including differential expression, downsampling analysis, and clustering.' + diff --git a/recipes/bioconductor-singscore/build.sh b/recipes/bioconductor-singscore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-singscore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-singscore/meta.yaml b/recipes/bioconductor-singscore/meta.yaml new file mode 100644 index 0000000000000..c15565060c5a1 --- /dev/null +++ b/recipes/bioconductor-singscore/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.2.2" %} +{% set name = "singscore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8e278c32b376aafa623be1dd5e33d78b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-magrittr + - r-matrixstats + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggplot2 + - r-ggrepel + - r-ggsci + - r-magrittr + - r-matrixstats + - r-plotly + - r-plyr + - r-rcolorbrewer + - r-reshape + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'A simple single-sample gene signature scoring method that uses rank-based statistics to analyze the sample''s gene expression profile. It scores the expression activities of gene sets at a single-sample level.' + diff --git a/recipes/bioconductor-sispa/build.sh b/recipes/bioconductor-sispa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sispa/build.sh +++ b/recipes/bioconductor-sispa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sispa/meta.yaml b/recipes/bioconductor-sispa/meta.yaml index ceabed2786819..935f14141a6c1 100644 --- a/recipes/bioconductor-sispa/meta.yaml +++ b/recipes/bioconductor-sispa/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SISPA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 950d1bbe7d213f495c19433d33a862b2e1558effebe8e87b29bccfd38552e1fd + md5: 31a2981180fb569f9bceaedf950c2ac0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' - r-base - r-changepoint - r-data.table - r-ggplot2 - r-plyr run: - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-gsva >=1.28.0,<1.30.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-gsva >=1.30.0,<1.31.0' - r-base - r-changepoint - r-data.table @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Sample Integrated Set Profile Analysis (SISPA) is a method designed to define sample groups with similar gene set enrichment profiles.' extra: identifiers: - biotools:sispa - doi:10.1093/nar/gkv1503 + parent_recipe: + name: bioconductor-sispa + path: recipes/bioconductor-sispa + version: 1.10.0 + diff --git a/recipes/bioconductor-sizepower/build.sh b/recipes/bioconductor-sizepower/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sizepower/build.sh +++ b/recipes/bioconductor-sizepower/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sizepower/meta.yaml b/recipes/bioconductor-sizepower/meta.yaml index af8d5ac95ec15..4e0ca181e4303 100644 --- a/recipes/bioconductor-sizepower/meta.yaml +++ b/recipes/bioconductor-sizepower/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.50.0" %} +{% set version = "1.52.0" %} {% set name = "sizepower" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bbd46a7d95922be2e6cff6c257ac8eec1a4cd1f7b577f59fca905747d4bc5fda + md5: bdccb70dcc32782ba50646a7f9e521fe build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'This package has been prepared to assist users in computing either a sample size or power value for a microarray experimental study. The user is referred to the cited references for technical background on the methodology underpinning these calculations. This package provides support for five types of sample size and power calculations. These five types can be adapted in various ways to encompass many of the standard designs encountered in practice.' extra: identifiers: - biotools:sizepower - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sizepower + path: recipes/bioconductor-sizepower + version: 1.50.0 + diff --git a/recipes/bioconductor-skewr/build.sh b/recipes/bioconductor-skewr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-skewr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-skewr/meta.yaml b/recipes/bioconductor-skewr/meta.yaml new file mode 100644 index 0000000000000..d8834233feaa5 --- /dev/null +++ b/recipes/bioconductor-skewr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.14.0" %} +{% set name = "skewr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 96a073b45b0870dedd69129cc678075a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GEOquery, knitr, minfiData +requirements: + host: + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-mixsmsn + - r-rcolorbrewer + run: + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-watermelon >=1.26.0,<1.27.0' + - r-base + - r-mixsmsn + - r-rcolorbrewer +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'The skewr package is a tool for visualizing the output of the Illumina Human Methylation 450k BeadChip to aid in quality control. It creates a panel of nine plots. Six of the plots represent the density of either the methylated intensity or the unmethylated intensity given by one of three subsets of the 485,577 total probes. These subsets include Type I-red, Type I-green, and Type II.The remaining three distributions give the density of the Beta-values for these same three subsets. Each of the nine plots optionally displays the distributions of the "rs" SNP probes and the probes associated with imprinted genes as series of ''tick'' marks located above the x-axis.' + diff --git a/recipes/bioconductor-slalom/build.sh b/recipes/bioconductor-slalom/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-slalom/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-slalom/meta.yaml b/recipes/bioconductor-slalom/meta.yaml new file mode 100644 index 0000000000000..3028e347498a1 --- /dev/null +++ b/recipes/bioconductor-slalom/meta.yaml @@ -0,0 +1,52 @@ +{% set version = "1.4.0" %} +{% set name = "slalom" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2c838537da75daf7cf4b1ad740885da3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rhdf5, scater, testthat +requirements: + host: + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bh + - r-ggplot2 + - 'r-rcpp >=0.12.8' + - r-rcpparmadillo + - r-rsvd + run: + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-bh + - r-ggplot2 + - 'r-rcpp >=0.12.8' + - r-rcpparmadillo + - r-rsvd + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'slalom is a scalable modelling framework for single-cell RNA-seq data that uses gene set annotations to dissect single-cell transcriptome heterogeneity, thereby allowing to identify biological drivers of cell-to-cell variability and model confounding factors.' + diff --git a/recipes/bioconductor-slgi/build.sh b/recipes/bioconductor-slgi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-slgi/build.sh +++ b/recipes/bioconductor-slgi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-slgi/meta.yaml b/recipes/bioconductor-slgi/meta.yaml index 1f982153c5fc5..a714b894b500c 100644 --- a/recipes/bioconductor-slgi/meta.yaml +++ b/recipes/bioconductor-slgi/meta.yaml @@ -1,46 +1,53 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "SLGI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2ec40935be1e95ac7d750a2de571528b7f97a4a07e0c057dce35ab156c53d8e9 + md5: ea0839feb33db33273540c5495db717a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: GO.db, org.Sc.sgd.db requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' - r-base - r-lattice run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-scisi >=1.52.0,<1.54.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-scisi >=1.54.0,<1.55.0' - r-base - r-lattice test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'A variety of data files and functions for the analysis of genetic interactions' extra: identifiers: - biotools:slgi - doi:10.1186/gb-2008-9-9-r135 + parent_recipe: + name: bioconductor-slgi + path: recipes/bioconductor-slgi + version: 1.40.0 + diff --git a/recipes/bioconductor-slingshot/build.sh b/recipes/bioconductor-slingshot/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-slingshot/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-slingshot/meta.yaml b/recipes/bioconductor-slingshot/meta.yaml new file mode 100644 index 0000000000000..81e5a23927226 --- /dev/null +++ b/recipes/bioconductor-slingshot/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "slingshot" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 429308c9bbe073d329feedfe57ae773e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, destiny, gam, knitr, mclust, RColorBrewer, rmarkdown, splatter, testthat, covr +requirements: + host: + - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-igraph + - r-matrixstats + - 'r-princurve >=2.0.4' + - r-rgl + run: + - 'bioconductor-clusterexperiment >=2.2.0,<2.3.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-ape + - r-base + - r-igraph + - r-matrixstats + - 'r-princurve >=2.0.4' + - r-rgl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Provides functions for inferring continuous, branching lineage structures in low-dimensional data. Slingshot was designed to model developmental trajectories in single-cell RNA sequencing data and serve as a component in an analysis pipeline after dimensionality reduction and clustering. It is flexible enough to handle arbitrarily many branching events and allows for the incorporation of prior knowledge through supervised graph construction.' + diff --git a/recipes/bioconductor-slinky/build.sh b/recipes/bioconductor-slinky/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-slinky/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-slinky/meta.yaml b/recipes/bioconductor-slinky/meta.yaml new file mode 100644 index 0000000000000..b9119fae93152 --- /dev/null +++ b/recipes/bioconductor-slinky/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "slinky" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 625f2eaba2348facd2f298f822fe12c8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GeoDE, doParallel, testthat, knitr, rmarkdown, ggplot2, Rtsne, Biobase, BiocStyle +requirements: + host: + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-curl + - r-dplyr + - r-foreach + - r-httr + - r-jsonlite + - r-readr + - r-tidyr + run: + - 'bioconductor-rhdf5 >=2.26.0,<2.27.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-curl + - r-dplyr + - r-foreach + - r-httr + - r-jsonlite + - r-readr + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Wrappers to query the L1000 metadata available via the clue.io REST API as well as helpers for dealing with LINCS gctx files, extracting data sets of interest, converting to SummarizedExperiment objects, and some facilities for performing streamlined differential expression analysis of these data sets.' + diff --git a/recipes/bioconductor-slqpcr/build.sh b/recipes/bioconductor-slqpcr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-slqpcr/build.sh +++ b/recipes/bioconductor-slqpcr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-slqpcr/meta.yaml b/recipes/bioconductor-slqpcr/meta.yaml index b5cb3178ae120..1d0878164f3c3 100644 --- a/recipes/bioconductor-slqpcr/meta.yaml +++ b/recipes/bioconductor-slqpcr/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "SLqPCR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6c1bf37f7be3fa85175cce64752102e0fda6f0f84ddf29a68b1d50315f8ae624 + md5: e1902128c0521f0f1c815fa130cccf05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RColorBrewer requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Functions for analysis of real-time quantitative PCR data at SIRS-Lab GmbH' extra: identifiers: - biotools:slqpcr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-slqpcr + path: recipes/bioconductor-slqpcr + version: 1.46.0 + diff --git a/recipes/bioconductor-smap/build.sh b/recipes/bioconductor-smap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-smap/build.sh +++ b/recipes/bioconductor-smap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-smap/meta.yaml b/recipes/bioconductor-smap/meta.yaml index 304ace1d4174f..2cf845a4ec43f 100644 --- a/recipes/bioconductor-smap/meta.yaml +++ b/recipes/bioconductor-smap/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.44.0" %} +{% set version = "1.46.0" %} {% set name = "SMAP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a1b36f66d00d3d682cfcc1f4878fec0607bb49018664476e7ebe8a7470dc2362 + md5: abf9f359b95a13d9b914fb977ad1b6b7 build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Functions and classes for DNA copy number profiling of array-CGH data' extra: identifiers: - biotools:smap - doi:10.1093/bioinformatics/btn003 + parent_recipe: + name: bioconductor-smap + path: recipes/bioconductor-smap + version: 1.44.0 + diff --git a/recipes/bioconductor-smite/build.sh b/recipes/bioconductor-smite/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-smite/build.sh +++ b/recipes/bioconductor-smite/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-smite/meta.yaml b/recipes/bioconductor-smite/meta.yaml index df3db0fd1bd43..9ef46f3494d7d 100644 --- a/recipes/bioconductor-smite/meta.yaml +++ b/recipes/bioconductor-smite/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "SMITE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8330f34bffd4221b8a60a0ea53604a8cbce6d0451588d324dfa14e2760e88947 + md5: 728be7e8265d62f2288db5acbabc2961 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bionet >=1.40.0,<1.42.0' - - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-reactome.db >=1.64.0,<1.66.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bionet >=1.42.0,<1.43.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-hmisc @@ -36,17 +38,17 @@ requirements: - r-plyr - r-scales run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-bionet >=1.40.0,<1.42.0' - - 'bioconductor-genelendatabase >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-goseq >=1.32.0,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-kegg.db >=3.2.3,<3.4.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-reactome.db >=1.64.0,<1.66.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-bionet >=1.42.0,<1.43.0' + - 'bioconductor-genelendatabase >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-goseq >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-kegg.db >=3.2.0,<3.3.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-reactome.db >=1.66.0,<1.67.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-ggplot2 - r-hmisc @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package builds on the Epimods framework which facilitates finding weighted subnetworks ("modules") on Illumina Infinium 27k arrays using the SpinGlass algorithm, as implemented in the iGraph package. We have created a class of gene centric annotations associated with p-values and effect sizes and scores from any researchers prior statistical results to find functional modules.' extra: identifiers: - biotools:smite - doi:10.1186/s12859-017-1477-3 + parent_recipe: + name: bioconductor-smite + path: recipes/bioconductor-smite + version: 1.8.0 + diff --git a/recipes/bioconductor-snadata/meta.yaml b/recipes/bioconductor-snadata/meta.yaml new file mode 100644 index 0000000000000..60d45164b2785 --- /dev/null +++ b/recipes/bioconductor-snadata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.28.0" %} +{% set name = "SNAData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f7bb6899038f7adb395147bf50e203c2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Rgraphviz +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Data from Wasserman & Faust (1999) "Social Network Analysis"' + diff --git a/recipes/bioconductor-snadata/post-link.sh b/recipes/bioconductor-snadata/post-link.sh new file mode 100644 index 0000000000000..3e3a03a4a6ccf --- /dev/null +++ b/recipes/bioconductor-snadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNAData_1.28.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNAData_1.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNAData_1.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snadata/bioconductor-snadata_1.28.0_src_all.tar.gz" +) +MD5="f7bb6899038f7adb395147bf50e203c2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snadata/pre-unlink.sh b/recipes/bioconductor-snadata/pre-unlink.sh new file mode 100644 index 0000000000000..92f54f304cd65 --- /dev/null +++ b/recipes/bioconductor-snadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNAData diff --git a/recipes/bioconductor-snagee/build.sh b/recipes/bioconductor-snagee/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snagee/build.sh +++ b/recipes/bioconductor-snagee/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snagee/meta.yaml b/recipes/bioconductor-snagee/meta.yaml index 8b63b25f65f3c..93ff26c0f0b91 100644 --- a/recipes/bioconductor-snagee/meta.yaml +++ b/recipes/bioconductor-snagee/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SNAGEE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 49e2489d1a3cbafe8a9896cd81407749ae9048d269acc7e169a8a9543bb6468c + md5: d1587c20f9e38e9a8d85219ff149ce1d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db requirements: host: - - 'bioconductor-snageedata >=1.16.0,<1.18.0' + - 'bioconductor-snageedata >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-snageedata >=1.16.0,<1.18.0' + - 'bioconductor-snageedata >=1.18.0,<1.19.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Signal-to-Noise applied to Gene Expression Experiments. Signal-to-noise ratios can be used as a proxy for quality of gene expression studies and samples. The SNRs can be calculated on any gene expression data set as long as gene IDs are available, no access to the raw data files is necessary. This allows to flag problematic studies and samples in any public data set.' extra: identifiers: - biotools:snagee - doi:10.1371/journal.pone.0051013 + parent_recipe: + name: bioconductor-snagee + path: recipes/bioconductor-snagee + version: 1.20.0 + diff --git a/recipes/bioconductor-snageedata/meta.yaml b/recipes/bioconductor-snageedata/meta.yaml index 26809aa617059..07df1cfa473af 100644 --- a/recipes/bioconductor-snageedata/meta.yaml +++ b/recipes/bioconductor-snageedata/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "SNAGEEdata" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a1fce00836421a20c84b5dc382f5b7b3d23cd1c26c8f82f79e566796a2128f3d + md5: 4b880530c37c0d088386211817f6f07b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db, SNAGEE requirements: host: - r-base @@ -26,8 +28,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'SNAGEE data - gene list and correlation matrix' - +extra: + parent_recipe: + name: bioconductor-snageedata + path: recipes/bioconductor-snageedata + version: 1.16.0 diff --git a/recipes/bioconductor-snageedata/post-link.sh b/recipes/bioconductor-snageedata/post-link.sh index 26e907605f770..8a6536754726b 100644 --- a/recipes/bioconductor-snageedata/post-link.sh +++ b/recipes/bioconductor-snageedata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="SNAGEEdata_1.16.0.tar.gz" +FN="SNAGEEdata_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/SNAGEEdata_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/SNAGEEdata_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNAGEEdata_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNAGEEdata_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snageedata/bioconductor-snageedata_1.18.0_src_all.tar.gz" ) -MD5="a87c42dcdca6e1ea225cf906ceeda44d" +MD5="4b880530c37c0d088386211817f6f07b" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-snapcgh/build.sh b/recipes/bioconductor-snapcgh/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-snapcgh/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snapcgh/meta.yaml b/recipes/bioconductor-snapcgh/meta.yaml new file mode 100644 index 0000000000000..bf834da188b57 --- /dev/null +++ b/recipes/bioconductor-snapcgh/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.52.0" %} +{% set name = "snapCGH" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6aefaf2fe3f35acb952a03488c44ffb9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + - r-cluster + run: + - 'bioconductor-acgh >=1.60.0,<1.61.0' + - 'bioconductor-dnacopy >=1.56.0,<1.57.0' + - 'bioconductor-glad >=2.46.0,<2.47.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-tilingarray >=1.60.0,<1.61.0' + - r-base + - r-cluster + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL + summary: 'Methods for segmenting, normalising and processing aCGH data; including plotting functions for visualising raw and segmented data for individual and multiple arrays.' + diff --git a/recipes/bioconductor-snm/build.sh b/recipes/bioconductor-snm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snm/build.sh +++ b/recipes/bioconductor-snm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snm/meta.yaml b/recipes/bioconductor-snm/meta.yaml index 72a0e8fc39d9d..bdbae809c0804 100644 --- a/recipes/bioconductor-snm/meta.yaml +++ b/recipes/bioconductor-snm/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "snm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 54c5b8e4ae9e7cc567208406e8269173e8b3ff21277bc5a6d3883323770cb50c + md5: c3d4d6770565f32fb9b1b3e1bbaf30ee build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,9 +30,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'SNM is a modeling strategy especially designed for normalizing high-throughput genomic data. The underlying premise of our approach is that your data is a function of what we refer to as study-specific variables. These variables are either biological variables that represent the target of the statistical analysis, or adjustment variables that represent factors arising from the experimental or biological setting the data is drawn from. The SNM approach aims to simultaneously model all study-specific variables in order to more accurately characterize the biological or clinical variables of interest.' extra: identifiers: - biotools:snm + parent_recipe: + name: bioconductor-snm + path: recipes/bioconductor-snm + version: 1.28.0 + diff --git a/recipes/bioconductor-snpchip/build.sh b/recipes/bioconductor-snpchip/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snpchip/build.sh +++ b/recipes/bioconductor-snpchip/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snpchip/conda_build_config.yaml b/recipes/bioconductor-snpchip/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-snpchip/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-snpchip/meta.yaml b/recipes/bioconductor-snpchip/meta.yaml index 0e9602ec9a597..2de4085c8f431 100644 --- a/recipes/bioconductor-snpchip/meta.yaml +++ b/recipes/bioconductor-snpchip/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "SNPchip" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 9b28bd2c43d69308e4bb02714f877614d67e562384f48029b56ad22cf6e3a30a + md5: 6aa3050529ceb3c1500f56d0eb663982 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: crlmm (>= 1.17.14), RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-foreach - r-lattice run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-foreach - r-lattice @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 2)' summary: 'Functions for plotting SNP array data; maintained for historical reasons' extra: identifiers: - biotools:snpchip + parent_recipe: + name: bioconductor-snpchip + path: recipes/bioconductor-snpchip + version: 2.26.0 + diff --git a/recipes/bioconductor-snpediar/build.sh b/recipes/bioconductor-snpediar/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snpediar/build.sh +++ b/recipes/bioconductor-snpediar/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snpediar/meta.yaml b/recipes/bioconductor-snpediar/meta.yaml index 93198cba2dacf..a280f94137447 100644 --- a/recipes/bioconductor-snpediar/meta.yaml +++ b/recipes/bioconductor-snpediar/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "SNPediaR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ffc3328dc2359af63ceca0bfa09d0173babf3c99cc12347255524436d1a442f5 + md5: a1ee826e42e3caa1231e1616d5a0944f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'SNPediaR provides some tools for downloading and parsing data from the SNPedia web site . The implemented functions allow users to import the wiki text available in SNPedia pages and to extract the most relevant information out of them. If some information in the downloaded pages is not automatically processed by the library functions, users can easily implement their own parsers to access it in an efficient way.' extra: identifiers: - biotools:snpediar - doi:10.1007/978-1-4419-9863-7_1039 + parent_recipe: + name: bioconductor-snpediar + path: recipes/bioconductor-snpediar + version: 1.6.0 + diff --git a/recipes/bioconductor-snphood/build.sh b/recipes/bioconductor-snphood/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snphood/build.sh +++ b/recipes/bioconductor-snphood/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snphood/meta.yaml b/recipes/bioconductor-snphood/meta.yaml index c33a948a3294f..c4c313226d84e 100644 --- a/recipes/bioconductor-snphood/meta.yaml +++ b/recipes/bioconductor-snphood/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SNPhood" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6a9e530c54fb6cec5107f81a85490dc596fc6986d546797ba2506d4ec9d2de82 + md5: 7f665ce6a2a88a8df7aee41bd46d4930 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, pryr, rmarkdown, SNPhoodData, corrplot requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-checkmate - r-cluster @@ -40,17 +42,17 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-checkmate - r-cluster @@ -65,10 +67,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>= 3)' summary: 'To date, thousands of single nucleotide polymorphisms (SNPs) have been found to be associated with complex traits and diseases. However, the vast majority of these disease-associated SNPs lie in the non-coding part of the genome, and are likely to affect regulatory elements, such as enhancers and promoters, rather than function of a protein. Thus, to understand the molecular mechanisms underlying genetic traits and diseases, it becomes increasingly important to study the effect of a SNP on nearby molecular traits such as chromatin environment or transcription factor (TF) binding. Towards this aim, we developed SNPhood, a user-friendly *Bioconductor* R package to investigate and visualize the local neighborhood of a set of SNPs of interest for NGS data such as chromatin marks or transcription factor binding sites from ChIP-Seq or RNA- Seq experiments. SNPhood comprises a set of easy-to-use functions to extract, normalize and summarize reads for a genomic region, perform various data quality checks, normalize read counts using additional input files, and to cluster and visualize the regions according to the binding pattern. The regions around each SNP can be binned in a user-defined fashion to allow for analysis of very broad patterns as well as a detailed investigation of specific binding shapes. Furthermore, SNPhood supports the integration with genotype information to investigate and visualize genotype-specific binding patterns. Finally, SNPhood can be employed for determining, investigating, and visualizing allele-specific binding patterns around the SNPs of interest.' extra: identifiers: - biotools:snphood - doi:10.1093/bioinformatics/btw127 + parent_recipe: + name: bioconductor-snphood + path: recipes/bioconductor-snphood + version: 1.10.0 + diff --git a/recipes/bioconductor-snphooddata/meta.yaml b/recipes/bioconductor-snphooddata/meta.yaml new file mode 100644 index 0000000000000..86cb3c80fb78e --- /dev/null +++ b/recipes/bioconductor-snphooddata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.12.0" %} +{% set name = "SNPhoodData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5036868e32ed51fd9ffa32bfeb992051 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle,knitr,rmarkdown +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 3)' + summary: 'This companion package for SNPhood provides some example datasets of a larger size than allowed for the SNPhood package. They include full and real-world examples for performing analyses with the SNPhood package.' + diff --git a/recipes/bioconductor-snphooddata/post-link.sh b/recipes/bioconductor-snphooddata/post-link.sh new file mode 100644 index 0000000000000..dd3e2a505e2e7 --- /dev/null +++ b/recipes/bioconductor-snphooddata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPhoodData_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SNPhoodData_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/SNPhoodData_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snphooddata/bioconductor-snphooddata_1.12.0_src_all.tar.gz" +) +MD5="5036868e32ed51fd9ffa32bfeb992051" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snphooddata/pre-unlink.sh b/recipes/bioconductor-snphooddata/pre-unlink.sh new file mode 100644 index 0000000000000..ac241cbc6685e --- /dev/null +++ b/recipes/bioconductor-snphooddata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPhoodData diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml new file mode 100644 index 0000000000000..8293358f1a3d4 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.99.7" %} +{% set name = "SNPlocs.Hsapiens.dbSNP.20101109" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d18cef7792978f5827025671b1866230 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome (>= 1.16.1), BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 132. The source data files used for this package were created by NCBI on 9 November 2010 and contain SNPs mapped to reference genome GRCh37. WARNING: Note that the GRCh37 genome is the same as the hg19 genome from UCSC except for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 but this injection will exclude chrM (i.e. nothing will be injected in that sequence).' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh new file mode 100644 index 0000000000000..60602e3bcf6a2 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP.20101109_0.99.7.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20101109/bioconductor-snplocs.hsapiens.dbsnp.20101109_0.99.7_src_all.tar.gz" +) +MD5="d18cef7792978f5827025671b1866230" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/pre-unlink.sh new file mode 100644 index 0000000000000..d5d0d0edb2021 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20101109/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP.20101109 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml new file mode 100644 index 0000000000000..eab7d5f6f79a7 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "0.99.11" %} +{% set name = "SNPlocs.Hsapiens.dbSNP.20120608" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6f06b9f619994b2a9b0fd780ead2f0cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 (>= 1.3.19) +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 137. The source data files used for this package were created by NCBI on June 7-8, 2012, and contain SNPs mapped to reference genome GRCh37.p5. WARNING: Note that the GRCh37.p5 genome is a patched version of GRCh37 but the patch doesn''t alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence). IMPORTANT NOTE: This package is deprecated. Please use a SNPlocs data package based on a more recent dbSNP BUILD instead (e.g. BUILD 144 or BUILD 149). You can call BSgenome::available.SNPs() from R to get the list of available SNPlocs data packages.' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh new file mode 100644 index 0000000000000..62604bab32d7e --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP.20120608_0.99.11.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp.20120608/bioconductor-snplocs.hsapiens.dbsnp.20120608_0.99.11_src_all.tar.gz" +) +MD5="6f06b9f619994b2a9b0fd780ead2f0cc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/pre-unlink.sh new file mode 100644 index 0000000000000..b37ae3de7a89b --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp.20120608/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP.20120608 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml new file mode 100644 index 0000000000000..33e135c3d6f72 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.99.11" %} +{% set name = "SNPlocs.Hsapiens.dbSNP141.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 40b55447c33e9d72c2ae8e8fe7f484be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.NCBI.GRCh38 (>= 1.3.19) +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 141. The source data files used for this package were created by NCBI on May 1st, 2014, and contain SNPs mapped to reference genome GRCh38. Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38. IMPORTANT NOTE: This package is deprecated. Please use a SNPlocs data package based on a more recent dbSNP BUILD instead (e.g. BUILD 144 or BUILD 149). You can call BSgenome::available.SNPs() from R to get the list of available SNPlocs data packages.' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh new file mode 100644 index 0000000000000..d321ba423eecd --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.11.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp141.grch38/bioconductor-snplocs.hsapiens.dbsnp141.grch38_0.99.11_src_all.tar.gz" +) +MD5="40b55447c33e9d72c2ae8e8fe7f484be" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..6f3fdab7a7318 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP141.GRCh38 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml new file mode 100644 index 0000000000000..52075d232b155 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "0.99.5" %} +{% set name = "SNPlocs.Hsapiens.dbSNP142.GRCh37" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3038e4f766d3e24f5b7286961a03ba35 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, BSgenome.Hsapiens.UCSC.hg19.masked (>= 1.3.19) +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 142. The source data files used for this package were created by NCBI on October 14, 2014, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37 but the patch doesn''t alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct location but this injection will exclude chrM (i.e. nothing will be injected in that sequence).' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh new file mode 100644 index 0000000000000..ecd54c67f299c --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP142.GRCh37_0.99.5.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp142.grch37/bioconductor-snplocs.hsapiens.dbsnp142.grch37_0.99.5_src_all.tar.gz" +) +MD5="3038e4f766d3e24f5b7286961a03ba35" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/pre-unlink.sh new file mode 100644 index 0000000000000..40abcb8a1abef --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp142.grch37/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP142.GRCh37 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml new file mode 100644 index 0000000000000..cbf0e264941c3 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.20" %} +{% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh37" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bd338bb583cacc18f210e871dac79ebf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13. WARNING: Note that the GRCh37.p13 genome is a patched version of GRCh37. However the patch doesn''t alter chromosomes 1-22, X, Y, MT. GRCh37 itself is the same as the hg19 genome from UCSC *except* for the mitochondrion chromosome. Therefore, the SNPs in this package can be "injected" in BSgenome.Hsapiens.UCSC.hg19 and they will land at the correct position but this injection will exclude chrM (i.e. nothing will be injected in that sequence).' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh new file mode 100644 index 0000000000000..adba749e3d77f --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch37/bioconductor-snplocs.hsapiens.dbsnp144.grch37_0.99.20_src_all.tar.gz" +) +MD5="bd338bb583cacc18f210e871dac79ebf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh new file mode 100644 index 0000000000000..52dbf36ec88d9 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP144.GRCh37 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml index 722cb62101b4c..26b65ce732285 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -1,45 +1,51 @@ {% set version = "0.99.20" %} {% set name = "SNPlocs.Hsapiens.dbSNP144.GRCh38" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b6c6ae8d3a866501146e325d40dc1695b26b522c6f9d063218fc6466bbd5b57b + md5: 128c95e327adf72ae137fb5ae58270fc build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' - +extra: + parent_recipe: + name: bioconductor-snplocs.hsapiens.dbsnp144.grch38 + path: recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38 + version: 0.99.20 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh index 44f757124014d..d376e09e0cb41 100644 --- a/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp144.grch38/post-link.sh @@ -1,7 +1,9 @@ #!/bin/bash FN="SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" URLS=( - "http://bioconductor.org/packages/3.6/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp144.grch38/bioconductor-snplocs.hsapiens.dbsnp144.grch38_0.99.20_src_all.tar.gz" ) MD5="128c95e327adf72ae137fb5ae58270fc" diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml new file mode 100644 index 0000000000000..faeac51916ae9 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.20" %} +{% set name = "SNPlocs.Hsapiens.dbSNP149.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8cf749a8649a53449066b54160a3745c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 149. The source data files used for this package were created by NCBI between November 8-12, 2016, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh new file mode 100644 index 0000000000000..e9c5331abe8b3 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP149.GRCh38_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp149.grch38/bioconductor-snplocs.hsapiens.dbsnp149.grch38_0.99.20_src_all.tar.gz" +) +MD5="8cf749a8649a53449066b54160a3745c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..2a6436d181276 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp149.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP149.GRCh38 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml new file mode 100644 index 0000000000000..dd2a1209ff321 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.20" %} +{% set name = "SNPlocs.Hsapiens.dbSNP150.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 575a7aaa9125d52ca0634b3ac586c9a7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 150. The source data files used for this package were created by NCBI between March 12-14, 2017, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh new file mode 100644 index 0000000000000..99f56d0227806 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP150.GRCh38_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp150.grch38/bioconductor-snplocs.hsapiens.dbsnp150.grch38_0.99.20_src_all.tar.gz" +) +MD5="575a7aaa9125d52ca0634b3ac586c9a7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..65d802c5950d2 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp150.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP150.GRCh38 diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml new file mode 100644 index 0000000000000..7e06571207eed --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.20" %} +{% set name = "SNPlocs.Hsapiens.dbSNP151.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0c1637530d42b10d3e6b8dead09454e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 151. The source data files used for this package were created by NCBI between February 16-22, 2018, and contain SNPs mapped to reference genome GRCh38.p7 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). Note that these SNPs can be "injected" in BSgenome.Hsapiens.NCBI.GRCh38 or in BSgenome.Hsapiens.UCSC.hg38.' + diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh new file mode 100644 index 0000000000000..d0046aad25ddc --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" + "https://bioarchive.galaxyproject.org/SNPlocs.Hsapiens.dbSNP151.GRCh38_0.99.20.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-snplocs.hsapiens.dbsnp151.grch38/bioconductor-snplocs.hsapiens.dbsnp151.grch38_0.99.20_src_all.tar.gz" +) +MD5="0c1637530d42b10d3e6b8dead09454e7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/pre-unlink.sh b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..fb589939e53d6 --- /dev/null +++ b/recipes/bioconductor-snplocs.hsapiens.dbsnp151.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SNPlocs.Hsapiens.dbSNP151.GRCh38 diff --git a/recipes/bioconductor-snprelate/build.sh b/recipes/bioconductor-snprelate/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snprelate/build.sh +++ b/recipes/bioconductor-snprelate/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snprelate/meta.yaml b/recipes/bioconductor-snprelate/meta.yaml index 9e2167869d148..0414e5d38c323 100644 --- a/recipes/bioconductor-snprelate/meta.yaml +++ b/recipes/bioconductor-snprelate/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "SNPRelate" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 994975539df83f04af7fbda4eb0bad506138c755c453016090e545738e100f39 + md5: 9c7ebe9e6249405c2982d1cb812bec74 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: parallel, Matrix, RUnit, knitr, MASS, BiocGenerics requirements: host: - - 'bioconductor-gdsfmt >=1.16.0,<1.18.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - r-base run: - - 'bioconductor-gdsfmt >=1.16.0,<1.18.0' + - 'bioconductor-gdsfmt >=1.18.0,<1.19.0' - r-base build: - {{ compiler('c') }} @@ -31,8 +32,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Genome-wide association studies (GWAS) are widely used to investigate the genetic basis of diseases and traits, but they pose many computational challenges. We developed an R package SNPRelate to provide a binary format for single-nucleotide polymorphism (SNP) data in GWAS utilizing CoreArray Genomic Data Structure (GDS) data files. The GDS format offers the efficient operations specifically designed for integers with two bits, since a SNP could occupy only two bits. SNPRelate is also designed to accelerate two key computations on SNP data using parallel computing for multi-core symmetric multiprocessing computer architectures: Principal Component Analysis (PCA) and relatedness analysis using Identity-By-Descent measures. The SNP GDS format is also used by the GWASTools package with the support of S4 classes and generic functions. The extended GDS format is implemented in the SeqArray package to support the storage of single nucleotide variations (SNVs), insertion/deletion polymorphism (indel) and structural variation calls.' - +extra: + parent_recipe: + name: bioconductor-snprelate + path: recipes/bioconductor-snprelate + version: 1.14.0 diff --git a/recipes/bioconductor-snpstats/build.sh b/recipes/bioconductor-snpstats/build.sh index 32bc29aa16362..c1d13421f5f1e 100644 --- a/recipes/bioconductor-snpstats/build.sh +++ b/recipes/bioconductor-snpstats/build.sh @@ -1,6 +1,11 @@ #!/bin/bash - mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION - -$R CMD INSTALL --build . +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-snpstats/meta.yaml b/recipes/bioconductor-snpstats/meta.yaml index 254d4206a503f..18c27e96ae303 100644 --- a/recipes/bioconductor-snpstats/meta.yaml +++ b/recipes/bioconductor-snpstats/meta.yaml @@ -1,34 +1,32 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "snpStats" %} -{% set bioc = "3.7" %} -{% set sha256 = "7a2d19beee640bba9f48f8c13d9ca69f5be3085c2b280c0ce2711450ad7bcd47" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' - source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: {{ sha256 }} - + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1c1a4fecfb47e7fd1e567eed1dbf2e26 build: number: 0 rpaths: - lib/R/lib/ - lib/ - +# Suggests: hexbin requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-matrix - r-survival run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-matrix - r-survival @@ -39,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Classes and statistical methods for large SNP association studies. This extends the earlier snpMatrix package, allowing for uncertainty in genotypes.' extra: identifiers: - biotools:snpstats - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-snpstats + path: recipes/bioconductor-snpstats + version: 1.30.0 + diff --git a/recipes/bioconductor-soggi/build.sh b/recipes/bioconductor-soggi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-soggi/build.sh +++ b/recipes/bioconductor-soggi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-soggi/meta.yaml b/recipes/bioconductor-soggi/meta.yaml index 6d08f6f42acd6..4106026d13d10 100644 --- a/recipes/bioconductor-soggi/meta.yaml +++ b/recipes/bioconductor-soggi/meta.yaml @@ -1,53 +1,55 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "soGGi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f675d48906f055f72a0665b1dad087d7e500176e2e40c640288a12a6166e949b + md5: e5d0416ddfb35676209c266b0899cbf2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-reshape2 @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The soGGi package provides a toolset to create genomic interval aggregate/summary plots of signal or motif occurence from BAM and bigWig files as well as PWM, rlelist, GRanges and GAlignments Bioconductor objects. soGGi allows for normalisation, transformation and arithmetic operation on and between summary plot objects as well as grouping and subsetting of plots by GRanges objects and user supplied metadata. Plots are created using the GGplot2 libary to allow user defined manipulation of the returned plot object. Coupled together, soGGi features a broad set of methods to visualise genomics data in the context of groups of genomic intervals such as genes, superenhancers and transcription factor binding events.' extra: identifiers: - biotools:soggi - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-soggi + path: recipes/bioconductor-soggi + version: 1.12.0 + diff --git a/recipes/bioconductor-somaticadata/meta.yaml b/recipes/bioconductor-somaticadata/meta.yaml new file mode 100644 index 0000000000000..ce661aa7ccb94 --- /dev/null +++ b/recipes/bioconductor-somaticadata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "SomatiCAData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b0e5b1b155926d58365e3c7daf478a1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'An example cancer whole genome sequencing data for the SomatiCA package' + diff --git a/recipes/bioconductor-somaticadata/post-link.sh b/recipes/bioconductor-somaticadata/post-link.sh new file mode 100644 index 0000000000000..e83e2a95d43aa --- /dev/null +++ b/recipes/bioconductor-somaticadata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SomatiCAData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SomatiCAData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/SomatiCAData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-somaticadata/bioconductor-somaticadata_1.20.0_src_all.tar.gz" +) +MD5="1b0e5b1b155926d58365e3c7daf478a1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-somaticadata/pre-unlink.sh b/recipes/bioconductor-somaticadata/pre-unlink.sh new file mode 100644 index 0000000000000..9fd2e63ebb836 --- /dev/null +++ b/recipes/bioconductor-somaticadata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SomatiCAData diff --git a/recipes/bioconductor-somaticcanceralterations/meta.yaml b/recipes/bioconductor-somaticcanceralterations/meta.yaml new file mode 100644 index 0000000000000..9cf9852f94b5f --- /dev/null +++ b/recipes/bioconductor-somaticcanceralterations/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.18.0" %} +{% set name = "SomaticCancerAlterations" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 75e6cde71f730fa57516677022042573 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, ggbio, ggplot2, knitr +requirements: + host: + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-stringr + run: + - 'bioconductor-exomecopy >=1.28.0,<1.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-stringr + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Collection of somatic cancer alteration datasets' + diff --git a/recipes/bioconductor-somaticcanceralterations/post-link.sh b/recipes/bioconductor-somaticcanceralterations/post-link.sh new file mode 100644 index 0000000000000..a988530f2b9fc --- /dev/null +++ b/recipes/bioconductor-somaticcanceralterations/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SomaticCancerAlterations_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SomaticCancerAlterations_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/SomaticCancerAlterations_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-somaticcanceralterations/bioconductor-somaticcanceralterations_1.18.0_src_all.tar.gz" +) +MD5="75e6cde71f730fa57516677022042573" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-somaticcanceralterations/pre-unlink.sh b/recipes/bioconductor-somaticcanceralterations/pre-unlink.sh new file mode 100644 index 0000000000000..0e4e82d2e7d8a --- /dev/null +++ b/recipes/bioconductor-somaticcanceralterations/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SomaticCancerAlterations diff --git a/recipes/bioconductor-somaticsignatures/build.sh b/recipes/bioconductor-somaticsignatures/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-somaticsignatures/build.sh +++ b/recipes/bioconductor-somaticsignatures/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-somaticsignatures/conda_build_config.yaml b/recipes/bioconductor-somaticsignatures/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-somaticsignatures/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-somaticsignatures/meta.yaml b/recipes/bioconductor-somaticsignatures/meta.yaml index 3f809c2eba1e1..e51714edf2095 100644 --- a/recipes/bioconductor-somaticsignatures/meta.yaml +++ b/recipes/bioconductor-somaticsignatures/meta.yaml @@ -1,47 +1,49 @@ -{% set version = "2.16.0" %} +{% set version = "2.18.0" %} {% set name = "SomaticSignatures" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: dfb8755b115406e213873fae3241c9422a0c15ad17596a9c859177e8f24a8c95 + md5: aecea0dbbe1b16434e7e47466cfea941 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, parallel, BSgenome.Hsapiens.1000genomes.hs37d5, SomaticCancerAlterations, ggdendro, fastICA, sva requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggplot2 - r-nmf - r-proxy - r-reshape2 run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-ggbio >=1.28.5,<1.30.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-pcamethods >=1.72.0,<1.74.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-ggbio >=1.30.0,<1.31.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-pcamethods >=1.74.0,<1.75.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggplot2 - r-nmf @@ -51,9 +53,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'The SomaticSignatures package identifies mutational signatures of single nucleotide variants (SNVs). It provides a infrastructure related to the methodology described in Nik-Zainal (2012, Cell), with flexibility in the matrix decomposition algorithms.' extra: identifiers: - biotools:somaticsignatures + parent_recipe: + name: bioconductor-somaticsignatures + path: recipes/bioconductor-somaticsignatures + version: 2.16.0 + diff --git a/recipes/bioconductor-soybeancdf/meta.yaml b/recipes/bioconductor-soybeancdf/meta.yaml new file mode 100644 index 0000000000000..90dee026bbdac --- /dev/null +++ b/recipes/bioconductor-soybeancdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "soybeancdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a18e0ba5dbcf2291bdec91091dc528e6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Soybean.cdf file.' + diff --git a/recipes/bioconductor-soybeancdf/post-link.sh b/recipes/bioconductor-soybeancdf/post-link.sh new file mode 100644 index 0000000000000..5d3d74add336b --- /dev/null +++ b/recipes/bioconductor-soybeancdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="soybeancdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/soybeancdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/soybeancdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-soybeancdf/bioconductor-soybeancdf_2.18.0_src_all.tar.gz" +) +MD5="a18e0ba5dbcf2291bdec91091dc528e6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-soybeancdf/pre-unlink.sh b/recipes/bioconductor-soybeancdf/pre-unlink.sh new file mode 100644 index 0000000000000..4655de147986e --- /dev/null +++ b/recipes/bioconductor-soybeancdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ soybeancdf diff --git a/recipes/bioconductor-soybeanprobe/meta.yaml b/recipes/bioconductor-soybeanprobe/meta.yaml new file mode 100644 index 0000000000000..3c9345d280830 --- /dev/null +++ b/recipes/bioconductor-soybeanprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "soybeanprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3057a5c387ff35b6c647c4db27041a13 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Soybean\_probe\_tab.' + diff --git a/recipes/bioconductor-soybeanprobe/post-link.sh b/recipes/bioconductor-soybeanprobe/post-link.sh new file mode 100644 index 0000000000000..33023018b68b2 --- /dev/null +++ b/recipes/bioconductor-soybeanprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="soybeanprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/soybeanprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/soybeanprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-soybeanprobe/bioconductor-soybeanprobe_2.18.0_src_all.tar.gz" +) +MD5="3057a5c387ff35b6c647c4db27041a13" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-soybeanprobe/pre-unlink.sh b/recipes/bioconductor-soybeanprobe/pre-unlink.sh new file mode 100644 index 0000000000000..a34e7e157566b --- /dev/null +++ b/recipes/bioconductor-soybeanprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ soybeanprobe diff --git a/recipes/bioconductor-spacepac/build.sh b/recipes/bioconductor-spacepac/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spacepac/build.sh +++ b/recipes/bioconductor-spacepac/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spacepac/meta.yaml b/recipes/bioconductor-spacepac/meta.yaml index 279c23646d8c5..ffcd875dd1616 100644 --- a/recipes/bioconductor-spacepac/meta.yaml +++ b/recipes/bioconductor-spacepac/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.18.3" %} +{% set version = "1.20.0" %} {% set name = "SpacePAC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7a156227d40dc50a8451b2df4b5960b0d3b6cfde00c53c128046ad00819049be + md5: f5a76a8b5ee150030fcaec81b61c6119 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, rgl requirements: host: - - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' - r-base run: - - 'bioconductor-ipac >=1.24.2,<1.26.0' + - 'bioconductor-ipac >=1.26.0,<1.27.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Identifies clustering of somatic mutations in proteins via a simulation approach while considering the protein''s tertiary structure.' extra: identifiers: - biotools:spacepac - doi:10.1186/1471-2105-15-231 + parent_recipe: + name: bioconductor-spacepac + path: recipes/bioconductor-spacepac + version: 1.18.3 + diff --git a/recipes/bioconductor-sparsedossa/build.sh b/recipes/bioconductor-sparsedossa/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sparsedossa/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sparsedossa/meta.yaml b/recipes/bioconductor-sparsedossa/meta.yaml new file mode 100644 index 0000000000000..251393e9d8a5c --- /dev/null +++ b/recipes/bioconductor-sparsedossa/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.0" %} +{% set name = "sparseDOSSA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: afa11ea4a0e219d6ad6c0e2049805e32 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, BiocGenerics, rmarkdown +requirements: + host: + - r-base + - r-mass + - r-mcmcpack + - r-optparse + - 'r-tmvtnorm >=1.4.10' + run: + - r-base + - r-mass + - r-mcmcpack + - r-optparse + - 'r-tmvtnorm >=1.4.10' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'The package is to provide a model based Bayesian method to characterize and simulate microbiome data. sparseDOSSA''s model captures the marginal distribution of each microbial feature as a truncated, zero-inflated log-normal distribution, with parameters distributed as a parent log-normal distribution. The model can be effectively fit to reference microbial datasets in order to parameterize their microbes and communities, or to simulate synthetic datasets of similar population structure. Most importantly, it allows users to include both known feature-feature and feature-metadata correlation structures and thus provides a gold standard to enable benchmarking of statistical methods for metagenomic data analysis.' + diff --git a/recipes/bioconductor-sparsenetgls/build.sh b/recipes/bioconductor-sparsenetgls/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sparsenetgls/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sparsenetgls/meta.yaml b/recipes/bioconductor-sparsenetgls/meta.yaml new file mode 100644 index 0000000000000..f9f8db3b1bda4 --- /dev/null +++ b/recipes/bioconductor-sparsenetgls/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "1.0.0" %} +{% set name = "sparsenetgls" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bac14ecd5a32e5618159719c549b9c1b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, lme4, BiocStyle, knitr, rmarkdown, roxygen2 (>= 5.0.0) +# SystemRequirements: GNU make +requirements: + host: + - r-base + - r-glmnet + - r-huge + - r-mass + - r-matrix + - r-parcor + run: + - r-base + - r-glmnet + - r-huge + - r-mass + - r-matrix + - r-parcor +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The package provides methods of combining the graph structure learning and generalized least squares regression to improve the regression estimation. The main function sparsenetgls() provides solutions for multivariate regression with Gaussian distributed dependant variables and explanatory variables utlizing multiple well-known graph structure learning approaches to estimating the precision matrix, and uses a penalized variance covariance matrix with a distance tuning parameter of the graph structure in deriving the sandwich estimators in generalized least squares (gls) regression. This package also provides functions for assessing a Gaussian graphical model which uses the penalized approach. It uses Receiver Operative Characteristics curve as a visualization tool in the assessment.' + diff --git a/recipes/bioconductor-sparsesignatures/build.sh b/recipes/bioconductor-sparsesignatures/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sparsesignatures/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sparsesignatures/meta.yaml b/recipes/bioconductor-sparsesignatures/meta.yaml new file mode 100644 index 0000000000000..553cefbaff624 --- /dev/null +++ b/recipes/bioconductor-sparsesignatures/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "SparseSignatures" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: dcbc3c8a105ae46137b771ba2ec0735f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, testthat, knitr, +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gridextra + - r-nmf + - r-nnlasso + - r-nnls + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.1000genomes.hs37d5 >=0.99.0,<0.100.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - r-base + - r-data.table + - r-ggplot2 + - r-gridextra + - r-nmf + - r-nnlasso + - r-nnls +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Point mutations occurring in a genome can be divided into 96 categories based on the base being mutated, the base it is mutated into and its two flanking bases. Therefore, for any patient, it is possible to represent all the point mutations occurring in that patient’s tumor as a vector of length 96, where each element represents the count of mutations for a given category in the patient. A mutational signature represents the pattern of mutations produced by a mutagen or mutagenic process inside the cell. Each signature can also be represented by a vector of length 96, where each element represents the probability that this particular mutagenic process generates a mutation of the 96 above mentioned categories. In this R package, we provide a set of functions to extract and visualize the mutational signatures that best explain the mutation counts of a large number of patients.' + diff --git a/recipes/bioconductor-specl/build.sh b/recipes/bioconductor-specl/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-specl/build.sh +++ b/recipes/bioconductor-specl/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-specl/meta.yaml b/recipes/bioconductor-specl/meta.yaml index 5660b9c77d7a6..074033dfdc908 100644 --- a/recipes/bioconductor-specl/meta.yaml +++ b/recipes/bioconductor-specl/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "specL" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e65998f7276f9d1b3680ff60a8c71a00faa1624ffe81138ee75d394d056767fb + md5: 7a519bb898df6985b4ca6e40787c5730 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle (>= 2.2.1), knitr (>= 1.15.1), msqc1 (>= 1.0.0), plotrix (>= 3.6.4), prozor (>= 0.2.2), RUnit (>= 0.4.31) requirements: host: - r-base @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'provides a function for generating spectra libraries which can be used for MRM SRM MS workflows in proteomics. The package provides a BiblioSpec reader, a function which can add the protein information using a FASTA formatted amino acid file, and an export method for using the created library in the Spectronaut software.' extra: identifiers: - biotools:specl + parent_recipe: + name: bioconductor-specl + path: recipes/bioconductor-specl + version: 1.14.0 + diff --git a/recipes/bioconductor-specond/build.sh b/recipes/bioconductor-specond/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-specond/build.sh +++ b/recipes/bioconductor-specond/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-specond/meta.yaml b/recipes/bioconductor-specond/meta.yaml index a476f0f28821c..7e1447a21a26e 100644 --- a/recipes/bioconductor-specond/meta.yaml +++ b/recipes/bioconductor-specond/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "SpeCond" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f5d050e5f6e4a17dcd52277e03d92448285a15350ef4ae2ae366b725d6ea750b + md5: 917e0149bfc0891249d1008f26e5ffb4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fields - 'r-hwriter >=1.1' - 'r-mclust >=3.3.1' - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-fields - 'r-hwriter >=1.1' @@ -35,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'LGPL (>=2)' summary: 'This package performs a gene expression data analysis to detect condition-specific genes. Such genes are significantly up- or down-regulated in a small number of conditions. It does so by fitting a mixture of normal distributions to the expression values. Conditions can be environmental conditions, different tissues, organs or any other sources that you wish to compare in terms of gene expression.' extra: identifiers: - biotools:specond - doi:10.1186/gb-2011-12-12-413 + parent_recipe: + name: bioconductor-specond + path: recipes/bioconductor-specond + version: 1.34.0 + diff --git a/recipes/bioconductor-spem/build.sh b/recipes/bioconductor-spem/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spem/build.sh +++ b/recipes/bioconductor-spem/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spem/meta.yaml b/recipes/bioconductor-spem/meta.yaml index 019cb05cb94d5..5ad0660629491 100644 --- a/recipes/bioconductor-spem/meta.yaml +++ b/recipes/bioconductor-spem/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "SPEM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e8b912777376c86f0cf4de3e6a292a8a4c54cbb70b15b5a5ff46f74779308640 + md5: ef4d7302fe48373c81e008ad7e21a1f6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rsolnp run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-rsolnp test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package can optimize the parameter in S-system models given time series data' extra: identifiers: - biotools:spem - doi:10.1089/cmb.2011.0269 + parent_recipe: + name: bioconductor-spem + path: recipes/bioconductor-spem + version: 1.20.0 + diff --git a/recipes/bioconductor-spia/build.sh b/recipes/bioconductor-spia/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spia/build.sh +++ b/recipes/bioconductor-spia/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spia/meta.yaml b/recipes/bioconductor-spia/meta.yaml index 9eba2082d3379..22ea536c2f046 100644 --- a/recipes/bioconductor-spia/meta.yaml +++ b/recipes/bioconductor-spia/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "SPIA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ad6fbe3f4aa9bb5c10e466f7689f8914d4bcf99a8ad008e0cd1f872ea92dec09 + md5: b78883062aeacd45a6739f7f23e551b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: graph, Rgraphviz, hgu133plus2.db requirements: host: - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - r-base run: - - 'bioconductor-kegggraph >=1.40.0,<1.42.0' + - 'bioconductor-kegggraph >=1.42.0,<1.43.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'This package implements the Signaling Pathway Impact Analysis (SPIA) which uses the information form a list of differentially expressed genes and their log fold changes together with signaling pathways topology, in order to identify the pathways most relevant to the condition under the study.' extra: identifiers: - biotools:spia - doi:10.1093/bioinformatics/btn577 + parent_recipe: + name: bioconductor-spia + path: recipes/bioconductor-spia + version: 2.32.0 + diff --git a/recipes/bioconductor-spidermir/build.sh b/recipes/bioconductor-spidermir/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spidermir/build.sh +++ b/recipes/bioconductor-spidermir/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spidermir/meta.yaml b/recipes/bioconductor-spidermir/meta.yaml index b9f9c572f598b..c06e6db931414 100644 --- a/recipes/bioconductor-spidermir/meta.yaml +++ b/recipes/bioconductor-spidermir/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "SpidermiR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 92b0a36ebdbd3e0224ec23c72788a1db35e7087bc4b9ee30325882f5d12c0b1f + md5: d890b86719a3392cd8daf279d69e0e78 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirnatap >=1.14.0,<1.16.0' - - 'bioconductor-mirnatap.db >=0.99.10,<0.101.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirnatap >=1.16.0,<1.17.0' + - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - r-base - r-gdata - r-ggplot2 @@ -35,11 +37,11 @@ requirements: - r-networkd3 - r-visnetwork run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-mirnatap >=1.14.0,<1.16.0' - - 'bioconductor-mirnatap.db >=0.99.10,<0.101.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-tcgabiolinks >=2.8.4,<2.10.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-mirnatap >=1.16.0,<1.17.0' + - 'bioconductor-mirnatap.db >=0.99.0,<0.100.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' - r-base - r-gdata - r-ggplot2 @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' - summary: 'The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).' + summary: 'The aims of SpidermiR are : i) facilitate the network open-access data retrieval from GeneMania data, ii) prepare the data using the appropriate gene nomenclature, iii) integration of miRNA data in a specific network, iv) provide different standard analyses and v) allow the user to visualize the results. In more detail, the package provides multiple methods for query, prepare and download network data (GeneMania), and the integration with validated and predicted miRNA data (mirWalk, miR2Disease,miRTar, miRTarBase, miRandola,Pharmaco-miR,DIANA, Miranda, PicTar and TargetScan) and the use of standard analysis (igraph) and visualization methods (networkD3).' extra: identifiers: - biotools:spidermir - doi:10.3390/ijms18020274 + parent_recipe: + name: bioconductor-spidermir + path: recipes/bioconductor-spidermir + version: 1.10.0 + diff --git a/recipes/bioconductor-spikein/meta.yaml b/recipes/bioconductor-spikein/meta.yaml new file mode 100644 index 0000000000000..1d8d3ab740701 --- /dev/null +++ b/recipes/bioconductor-spikein/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.24.0" %} +{% set name = "SpikeIn" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c9e1bcb003e2a9789fd4f48e5c98430a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Contains the HGU133 and HGU95 spikein experiment data.' + diff --git a/recipes/bioconductor-spikein/post-link.sh b/recipes/bioconductor-spikein/post-link.sh new file mode 100644 index 0000000000000..3edeaf1046b5b --- /dev/null +++ b/recipes/bioconductor-spikein/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SpikeIn_1.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SpikeIn_1.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/SpikeIn_1.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-spikein/bioconductor-spikein_1.24.0_src_all.tar.gz" +) +MD5="c9e1bcb003e2a9789fd4f48e5c98430a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-spikein/pre-unlink.sh b/recipes/bioconductor-spikein/pre-unlink.sh new file mode 100644 index 0000000000000..1d6956a95b5b8 --- /dev/null +++ b/recipes/bioconductor-spikein/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SpikeIn diff --git a/recipes/bioconductor-spikeinsubset/meta.yaml b/recipes/bioconductor-spikeinsubset/meta.yaml new file mode 100644 index 0000000000000..af8726aef9550 --- /dev/null +++ b/recipes/bioconductor-spikeinsubset/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.22.0" %} +{% set name = "SpikeInSubset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: adc9c4e0f5abe8c9b0c789a3698e5f5a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Includes probe-level and expression data for the HGU133 and HGU95 spike-in experiments' + diff --git a/recipes/bioconductor-spikeinsubset/post-link.sh b/recipes/bioconductor-spikeinsubset/post-link.sh new file mode 100644 index 0000000000000..6bc12e1443bf1 --- /dev/null +++ b/recipes/bioconductor-spikeinsubset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SpikeInSubset_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SpikeInSubset_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/SpikeInSubset_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-spikeinsubset/bioconductor-spikeinsubset_1.22.0_src_all.tar.gz" +) +MD5="adc9c4e0f5abe8c9b0c789a3698e5f5a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-spikeinsubset/pre-unlink.sh b/recipes/bioconductor-spikeinsubset/pre-unlink.sh new file mode 100644 index 0000000000000..2ef8c84fe0889 --- /dev/null +++ b/recipes/bioconductor-spikeinsubset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SpikeInSubset diff --git a/recipes/bioconductor-spikeli/build.sh b/recipes/bioconductor-spikeli/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spikeli/build.sh +++ b/recipes/bioconductor-spikeli/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spikeli/meta.yaml b/recipes/bioconductor-spikeli/meta.yaml index 4dc518da45595..24bde2352f7de 100644 --- a/recipes/bioconductor-spikeli/meta.yaml +++ b/recipes/bioconductor-spikeli/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.40.0" %} +{% set version = "2.42.0" %} {% set name = "spikeLI" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 58d8c8f0d44e49d4970ca194fa389c5c26f832a79e1b92f3e2b5b6b16c96875f + md5: fede6083947ebb7ce4bacafce63b56c6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -25,10 +26,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).' + summary: 'SpikeLI is a package that performs the analysis of the Affymetrix spike-in data using the Langmuir Isotherm. The aim of this package is to show the advantages of a physical-chemistry based analysis of the Affymetrix microarray data compared to the traditional methods. The spike-in (or Latin square) data for the HGU95 and HGU133 chipsets have been downloaded from the Affymetrix web site. The model used in the spikeLI package is described in details in E. Carlon and T. Heim, Physica A 362, 433 (2006).' extra: identifiers: - biotools:spikeli - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-spikeli + path: recipes/bioconductor-spikeli + version: 2.40.0 + diff --git a/recipes/bioconductor-spktools/build.sh b/recipes/bioconductor-spktools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spktools/build.sh +++ b/recipes/bioconductor-spktools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spktools/meta.yaml b/recipes/bioconductor-spktools/meta.yaml index b95e943dc4696..d2b2033138021 100644 --- a/recipes/bioconductor-spktools/meta.yaml +++ b/recipes/bioconductor-spktools/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "spkTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0c82ed79e6abd6f2ff8224e37e9afff7fe98e7b0392ec6a9a94221dc89b791ab + md5: 5a5c7b1b12e15ddcead01e006f4d8294 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: xtable requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-gtools - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-gtools - r-rcolorbrewer @@ -31,10 +33,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package contains functions that can be used to compare expression measures on different array platforms.' extra: identifiers: - biotools:spktools - doi:10.1093/nar/gkn430 + parent_recipe: + name: bioconductor-spktools + path: recipes/bioconductor-spktools + version: 1.36.0 + diff --git a/recipes/bioconductor-splatter/build.sh b/recipes/bioconductor-splatter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splatter/build.sh +++ b/recipes/bioconductor-splatter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splatter/conda_build_config.yaml b/recipes/bioconductor-splatter/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-splatter/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-splatter/meta.yaml b/recipes/bioconductor-splatter/meta.yaml index 23c6dd1df438e..a7d1b2a75be7e 100644 --- a/recipes/bioconductor-splatter/meta.yaml +++ b/recipes/bioconductor-splatter/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.0" %} {% set name = "splatter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5f163d95e7e1e143c7ad453bbe21e04903cc783a87aa1547e35ac9583ee558a2 + md5: 17eddfabe2559761a9c6c9fc730e347c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, covr, cowplot, knitr, limSolve, lme4, progress, pscl, testthat, rmarkdown, S4Vectors, scDD, scran, mfa, phenopath, BASiCS, zinbwave, SparseDC, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-scater >=1.8.4,<1.10.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-akima - r-base - r-checkmate @@ -34,12 +36,12 @@ requirements: - r-matrixstats - r-scales run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-scater >=1.8.4,<1.10.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-scater >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-akima - r-base - r-checkmate @@ -53,8 +55,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 + file LICENSE' summary: 'Splatter is a package for the simulation of single-cell RNA sequencing count data. It provides a simple interface for creating complex simulations that are reproducible and well-documented. Parameters can be estimated from real data and functions are provided for comparing real and simulated datasets.' - +extra: + parent_recipe: + name: bioconductor-splatter + path: recipes/bioconductor-splatter + version: 1.4.3 diff --git a/recipes/bioconductor-splicegear/build.sh b/recipes/bioconductor-splicegear/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splicegear/build.sh +++ b/recipes/bioconductor-splicegear/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splicegear/meta.yaml b/recipes/bioconductor-splicegear/meta.yaml index 8be060082d104..6f9caefb3356a 100644 --- a/recipes/bioconductor-splicegear/meta.yaml +++ b/recipes/bioconductor-splicegear/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "splicegear" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a72f0374a574a265bb22dc66fe9e0c02d316347aaad8d7ba166b6ff57b9cd08d + md5: 16c969a97b03236c8d94b1edf5ba43fd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-xml run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-xml test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'A set of tools to work with alternative splicing' extra: identifiers: - biotools:splicegear - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-splicegear + path: recipes/bioconductor-splicegear + version: 1.52.0 + diff --git a/recipes/bioconductor-splicesites/build.sh b/recipes/bioconductor-splicesites/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-splicesites/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splicesites/meta.yaml b/recipes/bioconductor-splicesites/meta.yaml new file mode 100644 index 0000000000000..fd090b8077c67 --- /dev/null +++ b/recipes/bioconductor-splicesites/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.30.0" %} +{% set name = "spliceSites" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: cfcde22a0fadd95d33faf18e95e1182f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - r-base + - r-doby + - 'r-rbamtools >=2.14.3' + - 'r-refgenome >=1.6.0' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - r-base + - r-doby + - 'r-rbamtools >=2.14.3' + - 'r-refgenome >=1.6.0' + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Performs splice centered analysis on RNA-seq data.' + diff --git a/recipes/bioconductor-splicinggraphs/build.sh b/recipes/bioconductor-splicinggraphs/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splicinggraphs/build.sh +++ b/recipes/bioconductor-splicinggraphs/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splicinggraphs/meta.yaml b/recipes/bioconductor-splicinggraphs/meta.yaml index d8191c6608540..d6a84b321eb14 100644 --- a/recipes/bioconductor-splicinggraphs/meta.yaml +++ b/recipes/bioconductor-splicinggraphs/meta.yaml @@ -1,56 +1,63 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.1" %} {% set name = "SplicingGraphs" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3e530ab3b49b1894739a1ade79535d625d95aa276fa78a69514fbe255be6eb15 + md5: b0a095f5bd1f2ad7309a3ca8bcef3d7c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: igraph, Gviz, TxDb.Hsapiens.UCSC.hg19.knownGene, RNAseqData.HNRNPC.bam.chr14, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-igraph run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-igraph test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This package allows the user to create, manipulate, and visualize splicing graphs and their bubbles based on a gene model for a given organism. Additionally it allows the user to assign RNA-seq reads to the edges of a set of splicing graphs, and to summarize them in different ways.' extra: identifiers: - biotools:splicinggraphs - doi:10.1093/bioinformatics/18.suppl_1.s181 + parent_recipe: + name: bioconductor-splicinggraphs + path: recipes/bioconductor-splicinggraphs + version: 1.20.0 + diff --git a/recipes/bioconductor-splinetimer/build.sh b/recipes/bioconductor-splinetimer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splinetimer/build.sh +++ b/recipes/bioconductor-splinetimer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splinetimer/meta.yaml b/recipes/bioconductor-splinetimer/meta.yaml index 8180d9741c187..f94599e8a617e 100644 --- a/recipes/bioconductor-splinetimer/meta.yaml +++ b/recipes/bioconductor-splinetimer/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "splineTimeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 99cd3c02d5683045e4530a7cdafb75d87a26de1587e018671b96c3fb900d086d + md5: 62d088b9c08349611d18aee11eb7612e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-fis >=1.8.0,<1.10.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fis >=1.10.0,<1.11.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - 'r-genenet >=1.2.13' - r-gtools - r-igraph - 'r-longitudinal >=1.1.12' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-fis >=1.8.0,<1.10.0' - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-fis >=1.10.0,<1.11.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - 'r-genenet >=1.2.13' - r-gtools @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides functions for differential gene expression analysis of gene expression time-course data. Natural cubic spline regression models are used. Identified genes may further be used for pathway enrichment analysis and/or the reconstruction of time dependent gene regulatory association networks.' extra: identifiers: - biotools:splinetimer - doi:10.1371/journal.pone.0160791 + parent_recipe: + name: bioconductor-splinetimer + path: recipes/bioconductor-splinetimer + version: 1.8.0 + diff --git a/recipes/bioconductor-splinter/build.sh b/recipes/bioconductor-splinter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splinter/build.sh +++ b/recipes/bioconductor-splinter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splinter/meta.yaml b/recipes/bioconductor-splinter/meta.yaml index ab98d9950ae06..7b8864b06d79f 100644 --- a/recipes/bioconductor-splinter/meta.yaml +++ b/recipes/bioconductor-splinter/meta.yaml @@ -1,60 +1,71 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "SPLINTER" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5ca730f8563121515a26a6654a67a4c97b3eab20e5f6b664a7fe6104e5e18d4d + md5: afe89b12425d88857eb0177f679efad5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base - r-ggplot2 + - r-googlevis - r-plyr + - r-stringr run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.6.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm9 >=1.4.0,<1.5.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' - r-base - r-ggplot2 + - r-googlevis - r-plyr + - r-stringr test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'SPLINTER provides tools to analyze alternative splicing sites, interpret outcomes based on sequence information, select and design primers for site validiation and give visual representation of the event to guide downstream experiments.' extra: identifiers: - biotools:splinter - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-splinter + path: recipes/bioconductor-splinter + version: 1.6.0 + diff --git a/recipes/bioconductor-splots/build.sh b/recipes/bioconductor-splots/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-splots/build.sh +++ b/recipes/bioconductor-splots/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-splots/meta.yaml b/recipes/bioconductor-splots/meta.yaml index d84a97b861743..c85ea103d779f 100644 --- a/recipes/bioconductor-splots/meta.yaml +++ b/recipes/bioconductor-splots/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "splots" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 840dcb623410683d24adea404f1cfb0285ad6f41c9c653af010d09dbbbc0e204 + md5: 58d6a7e42306390dffe15484f0540ffb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'The splots package provides the plotScreen function for visualising data in microtitre plate or slide format.' extra: identifiers: - biotools:splots - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-splots + path: recipes/bioconductor-splots + version: 1.46.0 + diff --git a/recipes/bioconductor-sponge/build.sh b/recipes/bioconductor-sponge/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-sponge/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sponge/meta.yaml b/recipes/bioconductor-sponge/meta.yaml new file mode 100644 index 0000000000000..c5a9579183ecb --- /dev/null +++ b/recipes/bioconductor-sponge/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.4.0" %} +{% set name = "SPONGE" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6761d96ab04189f01b7bd9260428e22c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, visNetwork, ggplot2, ggrepel, gridExtra, digest, doParallel, bigmemory +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-data.table + - r-dorng + - r-expm + - r-foreach + - r-glmnet + - r-grbase + - r-igraph + - r-iterators + - r-logging + - r-mass + - r-ppcor + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - r-data.table + - r-dorng + - r-expm + - r-foreach + - r-glmnet + - r-grbase + - r-igraph + - r-iterators + - r-logging + - r-mass + - r-ppcor +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=3)' + summary: 'This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input.' + diff --git a/recipes/bioconductor-spotsegmentation/build.sh b/recipes/bioconductor-spotsegmentation/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-spotsegmentation/build.sh +++ b/recipes/bioconductor-spotsegmentation/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-spotsegmentation/meta.yaml b/recipes/bioconductor-spotsegmentation/meta.yaml index 0e641adcf0490..389598b4a4c5b 100644 --- a/recipes/bioconductor-spotsegmentation/meta.yaml +++ b/recipes/bioconductor-spotsegmentation/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "spotSegmentation" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3646b09ff82756759bd871ededbec0888770985df612969b884afbc629eaa0d9 + md5: 1ea2481528bffefd86889ec081f29124 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington.' + summary: 'Spot segmentation via model-based clustering and gridding for blocks within microarray slides, as described in Li et al, Robust Model-Based Segmentation of Microarray Images, Technical Report no. 473, Department of Statistics, University of Washington.' extra: identifiers: - biotools:spotsegmentation - doi:10.1093/bioinformatics/bti447 + parent_recipe: + name: bioconductor-spotsegmentation + path: recipes/bioconductor-spotsegmentation + version: 1.54.0 + diff --git a/recipes/bioconductor-squadd/build.sh b/recipes/bioconductor-squadd/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-squadd/build.sh +++ b/recipes/bioconductor-squadd/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-squadd/meta.yaml b/recipes/bioconductor-squadd/meta.yaml index ba17fc24d9cdd..12a125820042b 100644 --- a/recipes/bioconductor-squadd/meta.yaml +++ b/recipes/bioconductor-squadd/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "SQUADD" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 26ae39028e1b9e5d181377f13b029fbd865a3dfc469c2a75d7534cb04700c58b + md5: 6ec1ec80c00a53aa607426cfa2c15f8b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -27,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package SQUADD is a SQUAD add-on. It permits to generate SQUAD simulation matrix, prediction Heat-Map and Correlation Circle from PCA analysis.' extra: identifiers: - biotools:squadd - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-squadd + path: recipes/bioconductor-squadd + version: 1.30.0 + diff --git a/recipes/bioconductor-sradb/build.sh b/recipes/bioconductor-sradb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sradb/build.sh +++ b/recipes/bioconductor-sradb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sradb/meta.yaml b/recipes/bioconductor-sradb/meta.yaml index 0f402afd60a59..cf7ebe3cd1107 100644 --- a/recipes/bioconductor-sradb/meta.yaml +++ b/recipes/bioconductor-sradb/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.42.2" %} +{% set version = "1.44.0" %} {% set name = "SRAdb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8a2e6401e9df35bc644c2d5e16ba2bc53c6b7fcbd01570939e236c9ceedb3190 + md5: a37d04633f80e87dd7e9a5398712445f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Rgraphviz requirements: host: - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-rcurl - r-rsqlite run: - - 'bioconductor-geoquery >=2.48.0,<2.50.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-geoquery >=2.50.0,<2.51.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-rcurl - r-rsqlite @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The Sequence Read Archive (SRA) is the largest public repository of sequencing data from the next generation of sequencing platforms including Roche 454 GS System, Illumina Genome Analyzer, Applied Biosystems SOLiD System, Helicos Heliscope, and others. However, finding data of interest can be challenging using current tools. SRAdb is an attempt to make access to the metadata associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.' extra: identifiers: - biotools:sradb + parent_recipe: + name: bioconductor-sradb + path: recipes/bioconductor-sradb + version: 1.42.2 + diff --git a/recipes/bioconductor-srap/build.sh b/recipes/bioconductor-srap/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-srap/build.sh +++ b/recipes/bioconductor-srap/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-srap/meta.yaml b/recipes/bioconductor-srap/meta.yaml index fddf335ce2a6d..4224ec04327db 100644 --- a/recipes/bioconductor-srap/meta.yaml +++ b/recipes/bioconductor-srap/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "sRAP" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3dcc600558319df54168bbd97db299ea3f34d17a1d2f0b24b46d6d7405ef7a02 + md5: 5ae1daf3d036da49f0c51a31658604a3 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-gplots - r-pls - r-rocr - r-writexls run: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-gplots - r-pls @@ -35,9 +36,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.' extra: identifiers: - biotools:srap + parent_recipe: + name: bioconductor-srap + path: recipes/bioconductor-srap + version: 1.20.0 + diff --git a/recipes/bioconductor-srgnet/build.sh b/recipes/bioconductor-srgnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-srgnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-srgnet/meta.yaml b/recipes/bioconductor-srgnet/meta.yaml new file mode 100644 index 0000000000000..285afe914c189 --- /dev/null +++ b/recipes/bioconductor-srgnet/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.8.0" %} +{% set name = "SRGnet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ee9c754e6be1b8a5fb9653285327c1fc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-ebcoexpress >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-dmwr >=0.4.1' + - 'r-gbm >=2.1.1' + - r-hmisc + - r-igraph + - r-mass + - r-matrixstats + - 'r-pvclust >=2.0-0' + run: + - 'bioconductor-ebcoexpress >=1.26.0,<1.27.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - 'r-dmwr >=0.4.1' + - 'r-gbm >=2.1.1' + - r-hmisc + - r-igraph + - r-mass + - r-matrixstats + - 'r-pvclust >=2.0-0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'We developed SRGnet to analyze synergistic regulatory mechanisms in transcriptome profiles that act to enhance the overall cell response to combination of mutations, drugs or environmental exposure. This package can be used to identify regulatory modules downstream of synergistic response genes, prioritize synergistic regulatory genes that may be potential intervention targets, and contextualize gene perturbation experiments.' + diff --git a/recipes/bioconductor-srnadiff/build.sh b/recipes/bioconductor-srnadiff/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-srnadiff/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-srnadiff/meta.yaml b/recipes/bioconductor-srnadiff/meta.yaml new file mode 100644 index 0000000000000..481a797bd927e --- /dev/null +++ b/recipes/bioconductor-srnadiff/meta.yaml @@ -0,0 +1,67 @@ +{% set version = "1.2.0" %} +{% set name = "srnadiff" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: edddb2ffd09fabfb744f6a1c42267ca5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, rmarkdown, testthat +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-devtools + - r-ggplot2 + - 'r-rcpp >=0.12.8' + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biocstyle >=2.10.0,<2.11.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-devtools + - r-ggplot2 + - 'r-rcpp >=0.12.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Differential expression of small RNA-seq when reference annotation is not given.' + diff --git a/recipes/bioconductor-sscore/build.sh b/recipes/bioconductor-sscore/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sscore/build.sh +++ b/recipes/bioconductor-sscore/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sscore/conda_build_config.yaml b/recipes/bioconductor-sscore/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-sscore/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-sscore/meta.yaml b/recipes/bioconductor-sscore/meta.yaml index 907bc53922241..5f1c4de66daf6 100644 --- a/recipes/bioconductor-sscore/meta.yaml +++ b/recipes/bioconductor-sscore/meta.yaml @@ -1,38 +1,45 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "sscore" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 54a2d21ec56869fa581999cb2567df7e501f8f132e7005e122822b084a42dc5f + md5: 8d7cc52c819e22d0264a1ca6fff19327 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: affydata requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' - r-base run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-affyio >=1.50.0,<1.52.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-affyio >=1.52.0,<1.53.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'This package contains an implementation of the S-Score algorithm as described by Zhang et al (2002).' extra: identifiers: - biotools:sscore - doi:10.1016/S1046-2023(03)00156-7 + parent_recipe: + name: bioconductor-sscore + path: recipes/bioconductor-sscore + version: 1.52.0 + diff --git a/recipes/bioconductor-sscu/build.sh b/recipes/bioconductor-sscu/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sscu/build.sh +++ b/recipes/bioconductor-sscu/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sscu/meta.yaml b/recipes/bioconductor-sscu/meta.yaml index 2825e28952ffa..5384bd113228d 100644 --- a/recipes/bioconductor-sscu/meta.yaml +++ b/recipes/bioconductor-sscu/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "2.10.0" %} +{% set version = "2.12.0" %} {% set name = "sscu" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d6f279121057630315716894488f8120bcd1f7d2e6811db2079189144bfb0361 + md5: ddbb17a9eb6ef4599fd888772c389faa build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - 'r-seqinr >=3.1-3' run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' - r-base - 'r-seqinr >=3.1-3' test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'The package calculates the indexes for selective stength in codon usage in bacteria species. (1) The package can calculate the strength of selected codon usage bias (sscu, also named as s_index) based on Paul Sharp''s method. The method take into account of background mutation rate, and focus only on four pairs of codons with universal translational advantages in all bacterial species. Thus the sscu index is comparable among different species. (2) The package can detect the strength of translational accuracy selection by Akashi''s test. The test tabulating all codons into four categories with the feature as conserved/variable amino acids and optimal/non-optimal codons. (3) Optimal codon lists (selected codons) can be calculated by either op_highly function (by using the highly expressed genes compared with all genes to identify optimal codons), or op_corre_CodonW/op_corre_NCprime function (by correlative method developed by Hershberg & Petrov). Users will have a list of optimal codons for further analysis, such as input to the Akashi''s test. (4) The detailed codon usage information, such as RSCU value, number of optimal codons in the highly/all gene set, as well as the genomic gc3 value, can be calculate by the optimal_codon_statistics and genomic_gc3 function. (5) Furthermore, we added one test function low_frequency_op in the package. The function try to find the low frequency optimal codons, among all the optimal codons identified by the op_highly function.' extra: identifiers: - biotools:sscu - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-sscu + path: recipes/bioconductor-sscu + version: 2.10.0 + diff --git a/recipes/bioconductor-sseq/build.sh b/recipes/bioconductor-sseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sseq/build.sh +++ b/recipes/bioconductor-sseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sseq/meta.yaml b/recipes/bioconductor-sseq/meta.yaml index c449af14c3bb0..6bacdf48bfe06 100644 --- a/recipes/bioconductor-sseq/meta.yaml +++ b/recipes/bioconductor-sseq/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "sSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2a7f6504753c39258268fe006ef413117e1e75919e924cc432e7bf63189fba8b + md5: 919578bdee1b366adc1b4da3da54f327 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The purpose of this package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments. Gene expression is measured in counts of transcripts and modeled with the Negative Binomial (NB) distribution using a shrinkage approach for dispersion estimation. The method of moment (MM) estimates for dispersion are shrunk towards an estimated target, which minimizes the average squared difference between the shrinkage estimates and the initial estimates. The exact per-gene probability under the NB model is calculated, and used to test the hypothesis that the expected expression of a gene in two conditions identically follow a NB distribution.' extra: identifiers: - biotools:sseq - doi:10.1093/bioinformatics/btt143 + parent_recipe: + name: bioconductor-sseq + path: recipes/bioconductor-sseq + version: 1.18.0 + diff --git a/recipes/bioconductor-ssize/build.sh b/recipes/bioconductor-ssize/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ssize/build.sh +++ b/recipes/bioconductor-ssize/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ssize/meta.yaml b/recipes/bioconductor-ssize/meta.yaml index ba90dc500f9cf..a3425b130145a 100644 --- a/recipes/bioconductor-ssize/meta.yaml +++ b/recipes/bioconductor-ssize/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.54.0" %} +{% set version = "1.56.0" %} {% set name = "ssize" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0645ada9237bfa91449bdeb168e6c3c08b822cdfe5fbe28f6b11b31e58002417 + md5: 0f17e8554718d39959b9edaa732f3c5e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -29,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for computing and displaying sample size information for gene expression arrays.' extra: identifiers: - biotools:ssize - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ssize + path: recipes/bioconductor-ssize + version: 1.54.0 + diff --git a/recipes/bioconductor-sspa/build.sh b/recipes/bioconductor-sspa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sspa/build.sh +++ b/recipes/bioconductor-sspa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sspa/meta.yaml b/recipes/bioconductor-sspa/meta.yaml index 2c0ba527c4efc..66058fa6c6b7a 100644 --- a/recipes/bioconductor-sspa/meta.yaml +++ b/recipes/bioconductor-sspa/meta.yaml @@ -1,30 +1,31 @@ -{% set version = "2.20.0" %} +{% set version = "2.22.0" %} {% set name = "SSPA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c7f1ac6c3727cfe580c91d59fcbace4336332cce7bb86f87961465d9a3af8c06 + md5: a3b1d88d5f8442f6a68205b1ba4ea720 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, genefilter, edgeR, DESeq requirements: host: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-lattice run: - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-lattice build: @@ -34,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'General Sample size and power analysis for microarray and next-generation sequencing data.' extra: identifiers: - biotools:sspa + parent_recipe: + name: bioconductor-sspa + path: recipes/bioconductor-sspa + version: 2.20.0 + diff --git a/recipes/bioconductor-ssviz/build.sh b/recipes/bioconductor-ssviz/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ssviz/build.sh +++ b/recipes/bioconductor-ssviz/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ssviz/meta.yaml b/recipes/bioconductor-ssviz/meta.yaml index 62cc52e8dd8c0..ab3329ff95dd4 100644 --- a/recipes/bioconductor-ssviz/meta.yaml +++ b/recipes/bioconductor-ssviz/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "ssviz" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: bfde64c8c08255da4c4a84b208667a08edd6e472bdd7b585f12944d1bc686eb3 + md5: 325ecbdd8831f8b52db0205cb4d058b0 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-rcolorbrewer - r-reshape run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-ggplot2 - r-rcolorbrewer @@ -35,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Small RNA sequencing viewer' extra: identifiers: - biotools:ssviz - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-ssviz + path: recipes/bioconductor-ssviz + version: 1.14.0 + diff --git a/recipes/bioconductor-stager/build.sh b/recipes/bioconductor-stager/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-stager/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stager/meta.yaml b/recipes/bioconductor-stager/meta.yaml new file mode 100644 index 0000000000000..510c4a4dd6664 --- /dev/null +++ b/recipes/bioconductor-stager/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "stageR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3940cc6f065042cc8dd0c135109ec057 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, methods, Biobase, edgeR, limma, DEXSeq, testthat +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GNU General Public License version 3' + summary: 'The stageR package allows automated stage-wise analysis of high-throughput gene expression data. The method is published in Genome Biology at https://genomebiology.biomedcentral.com/articles/10.1186/s13059-017-1277-0' + diff --git a/recipes/bioconductor-stan/build.sh b/recipes/bioconductor-stan/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-stan/build.sh +++ b/recipes/bioconductor-stan/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stan/meta.yaml b/recipes/bioconductor-stan/meta.yaml index 65c4e1673b180..4cde1e2020b83 100644 --- a/recipes/bioconductor-stan/meta.yaml +++ b/recipes/bioconductor-stan/meta.yaml @@ -1,39 +1,40 @@ -{% set version = "2.8.0" %} +{% set version = "2.10.0" %} {% set name = "STAN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2c148979f22929c741fabc0068c60e2f154d9d3ebaeb47fde168ec22b2b71fed + md5: 02085333ba8cd5929612477801e2683f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, gplots, knitr requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-poilog - r-rsolnp run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-poilog - r-rsolnp @@ -45,9 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' - summary: 'Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of ''genomic states''. The ''genomic states'' may for instance reflect distinct genome-associated protein complexes (e.g. ''transcription states'') or describe recurring patterns of chromatin features (referred to as ''chromatin states''). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA) and non-strand-specific data (e.g. ChIP).' + summary: 'Genome segmentation with hidden Markov models has become a useful tool to annotate genomic elements, such as promoters and enhancers. STAN (genomic STate ANnotation) implements (bidirectional) hidden Markov models (HMMs) using a variety of different probability distributions, which can model a wide range of current genomic data (e.g. continuous, discrete, binary). STAN de novo learns and annotates the genome into a given number of ''genomic states''. The ''genomic states'' may for instance reflect distinct genome-associated protein complexes (e.g. ''transcription states'') or describe recurring patterns of chromatin features (referred to as ''chromatin states''). Unlike other tools, STAN also allows for the integration of strand-specific (e.g. RNA) and non-strand-specific data (e.g. ChIP).' extra: identifiers: - biotools:stan + parent_recipe: + name: bioconductor-stan + path: recipes/bioconductor-stan + version: 2.8.0 + diff --git a/recipes/bioconductor-starank/build.sh b/recipes/bioconductor-starank/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-starank/build.sh +++ b/recipes/bioconductor-starank/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-starank/conda_build_config.yaml b/recipes/bioconductor-starank/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-starank/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-starank/meta.yaml b/recipes/bioconductor-starank/meta.yaml index 136824680ce8b..da55d818a9e4c 100644 --- a/recipes/bioconductor-starank/meta.yaml +++ b/recipes/bioconductor-starank/meta.yaml @@ -1,36 +1,42 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "staRank" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 74c3206b29d28d3ff9e3d1df58db7e4f9449968ac4f851098ae2dd47dfcbb2fa + md5: 88fac0a4fba734ed89056ddab16de7af build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - r-base run: - - 'bioconductor-cellhts2 >=2.44.0,<2.46.0' + - 'bioconductor-cellhts2 >=2.46.0,<2.47.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'Detecting all relevant variables from a data set is challenging, especially when only few samples are available and data is noisy. Stability ranking provides improved variable rankings of increased robustness using resampling or subsampling.' extra: identifiers: - biotools:starank - doi:10.1093/bioinformatics/bts192 + parent_recipe: + name: bioconductor-starank + path: recipes/bioconductor-starank + version: 1.22.0 + diff --git a/recipes/bioconductor-starbiotrek/build.sh b/recipes/bioconductor-starbiotrek/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-starbiotrek/build.sh +++ b/recipes/bioconductor-starbiotrek/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-starbiotrek/meta.yaml b/recipes/bioconductor-starbiotrek/meta.yaml index b39ddd34a254e..e9cf1fc8a5044 100644 --- a/recipes/bioconductor-starbiotrek/meta.yaml +++ b/recipes/bioconductor-starbiotrek/meta.yaml @@ -1,36 +1,38 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "StarBioTrek" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eb4b648ac31d9fbe67f6197360aa1f3b33d37d91be427c3fddd3994524993d0f + md5: 134c8a0dccdc922526b49890f76fecd4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, devtools, roxygen2, qgraph, png, grid requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-spidermir >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-spidermir >=1.12.0,<1.13.0' - r-base - r-e1071 - r-igraph - r-rocr run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-spidermir >=1.10.0,<1.12.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-spidermir >=1.12.0,<1.13.0' - r-base - r-e1071 - r-igraph @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'This tool StarBioTrek presents some methodologies to measure pathway activity and cross-talk among pathways integrating also the information of network data.' extra: identifiers: - biotools:starbiotrek - doi:10.1186/s12918-015-0211-x + parent_recipe: + name: bioconductor-starbiotrek + path: recipes/bioconductor-starbiotrek + version: 1.6.0 + diff --git a/recipes/bioconductor-starr/build.sh b/recipes/bioconductor-starr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-starr/build.sh +++ b/recipes/bioconductor-starr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-starr/conda_build_config.yaml b/recipes/bioconductor-starr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-starr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-starr/meta.yaml b/recipes/bioconductor-starr/meta.yaml index 24007b43c89f6..ee395e002bd74 100644 --- a/recipes/bioconductor-starr/meta.yaml +++ b/recipes/bioconductor-starr/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.36.0" %} +{% set version = "1.38.0" %} {% set name = "Starr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 07cf29e78ad186d057937032b59679424e8032656641cd75992783e205cdb474 + md5: eec8e43bb3dc5d143b06de2f7cda0982 build: number: 0 rpaths: @@ -18,18 +18,18 @@ build: - lib/ requirements: host: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-mass - r-pspline run: - - 'bioconductor-affxparser >=1.52.0,<1.54.0' - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-ringo >=1.44.0,<1.46.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-affxparser >=1.54.0,<1.55.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ringo >=1.46.0,<1.47.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-mass - r-pspline @@ -41,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Starr facilitates the analysis of ChIP-chip data, in particular that of Affymetrix tiling arrays. The package provides functions for data import, quality assessment, data visualization and exploration. Furthermore, it includes high-level analysis features like association of ChIP signals with annotated features, correlation analysis of ChIP signals and other genomic data (e.g. gene expression), peak-finding with the CMARRT algorithm and comparative display of multiple clusters of ChIP-profiles. It uses the basic Bioconductor classes ExpressionSet and probeAnno for maximum compatibility with other software on Bioconductor. All functions from Starr can be used to investigate preprocessed data from the Ringo package, and vice versa. An important novel tool is the the automated generation of correct, up-to-date microarray probe annotation (bpmap) files, which relies on an efficient mapping of short sequences (e.g. the probe sequences on a microarray) to an arbitrary genome.' extra: identifiers: - biotools:starr - doi:10.1186/1471-2105-11-194 + parent_recipe: + name: bioconductor-starr + path: recipes/bioconductor-starr + version: 1.36.0 + diff --git a/recipes/bioconductor-stategra/build.sh b/recipes/bioconductor-stategra/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-stategra/build.sh +++ b/recipes/bioconductor-stategra/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stategra/conda_build_config.yaml b/recipes/bioconductor-stategra/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-stategra/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-stategra/meta.yaml b/recipes/bioconductor-stategra/meta.yaml index b437decc66f9f..5f1dff73540a4 100644 --- a/recipes/bioconductor-stategra/meta.yaml +++ b/recipes/bioconductor-stategra/meta.yaml @@ -1,27 +1,29 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "STATegRa" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a86d2272b62d2a5d1bd50688d3eacbdd53d41a40ec5c19e9a74e6900d070e48a + md5: 12ca7c3e81a4757ca68d7eb69a95e65a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics, knitr (>= 1.6), rmarkdown, BiocStyle (>= 1.3), roxygen2, doSNOW requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-calibrate - r-foreach @@ -30,10 +32,10 @@ requirements: - r-gridextra - r-mass run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-calibrate - r-foreach @@ -45,10 +47,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Classes and tools for multi-omics data integration.' extra: identifiers: - biotools:stategra - doi:10.14806/ej.20.a.768 + parent_recipe: + name: bioconductor-stategra + path: recipes/bioconductor-stategra + version: 1.16.1 + diff --git a/recipes/bioconductor-stattarget/build.sh b/recipes/bioconductor-stattarget/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-stattarget/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stattarget/meta.yaml b/recipes/bioconductor-stattarget/meta.yaml new file mode 100644 index 0000000000000..cadd0d9ce5304 --- /dev/null +++ b/recipes/bioconductor-stattarget/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.12.0" %} +{% set name = "statTarget" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0b804c5355e5971c8cb1a736dcad5f64 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, BiocStyle, knitr, rmarkdown, gWidgets2,gWidgets2RGtk2,RGtk2 +requirements: + host: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' + - r-base + - r-pdist + - r-pls + - r-plyr + - r-randomforest + - r-rrcov + run: + - 'bioconductor-impute >=1.56.0,<1.57.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' + - r-base + - r-pdist + - r-pls + - r-plyr + - r-randomforest + - r-rrcov +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 3)' + summary: 'A streamlined tool provides a graphical user interface for quality control based signal drift correction (QC-RFSC), integration of data from multi-batch MS-based experiments, and the comprehensive statistical analysis in metabolomics and proteomics.' + diff --git a/recipes/bioconductor-stemhypoxia/meta.yaml b/recipes/bioconductor-stemhypoxia/meta.yaml index dfe27af2b3ef6..0af0d7f68d74d 100644 --- a/recipes/bioconductor-stemhypoxia/meta.yaml +++ b/recipes/bioconductor-stemhypoxia/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "stemHypoxia" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5ad7114a399dfbeeee2d5500c515cced17c6953c54cbdb2d682e4a3fa9e66b5c + md5: 1fb8f0225f86414a4c7870ce3c2969bd build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -26,8 +27,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Expression profiling using microarray technology to prove if ''Hypoxia Promotes Efficient Differentiation of Human Embryonic Stem Cells to Functional Endothelium'' by Prado-Lopez et al. (2010) Stem Cells 28:407-418. Full data available at Gene Expression Omnibus series GSE37761.' - +extra: + parent_recipe: + name: bioconductor-stemhypoxia + path: recipes/bioconductor-stemhypoxia + version: 1.16.0 diff --git a/recipes/bioconductor-stemhypoxia/post-link.sh b/recipes/bioconductor-stemhypoxia/post-link.sh index 5d9b756714bf1..8e248bcaa3597 100644 --- a/recipes/bioconductor-stemhypoxia/post-link.sh +++ b/recipes/bioconductor-stemhypoxia/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="stemHypoxia_1.16.0.tar.gz" +FN="stemHypoxia_1.18.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/stemHypoxia_1.16.0.tar.gz" - "https://bioarchive.galaxyproject.org/stemHypoxia_1.16.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.16.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/stemHypoxia_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/stemHypoxia_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stemhypoxia/bioconductor-stemhypoxia_1.18.0_src_all.tar.gz" ) -MD5="b26a9742c2c354c375fb4231b922d439" +MD5="1fb8f0225f86414a4c7870ce3c2969bd" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-stepnorm/build.sh b/recipes/bioconductor-stepnorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-stepnorm/build.sh +++ b/recipes/bioconductor-stepnorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stepnorm/meta.yaml b/recipes/bioconductor-stepnorm/meta.yaml index 5139543063c1b..8588be06a15e6 100644 --- a/recipes/bioconductor-stepnorm/meta.yaml +++ b/recipes/bioconductor-stepnorm/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "stepNorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 62e942c1cd6b34c3f172d383f3db4efc3def651d9b0af7dc68ec8934fcde91fb + md5: 76233358af8236df8f33b593e9699f05 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-mass run: - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Stepwise normalization functions for cDNA microarray data.' extra: identifiers: - biotools:stepnorm - doi:10.1109/IEMBS.2004.1403830 + parent_recipe: + name: bioconductor-stepnorm + path: recipes/bioconductor-stepnorm + version: 1.52.0 + diff --git a/recipes/bioconductor-stjudem/meta.yaml b/recipes/bioconductor-stjudem/meta.yaml new file mode 100644 index 0000000000000..5b49299c7e85f --- /dev/null +++ b/recipes/bioconductor-stjudem/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.22.0" %} +{% set name = "stjudem" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 73c7d2523afdebc972054b62080d37c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'This is a microarray data set on acute lymphoblastic leukemia, published in 2002 (Yeoh et al.Cancer Cell 2002). The experiments were conducted in the St.Jude Children''s Research Hospital, Memphis, Tenessee, USA. The raw data was preprocessed by variance stabilizing normalization (Huber et al.) on probe and subsequent summarization of probe expression values into probe set expression values using median polish.' + diff --git a/recipes/bioconductor-stjudem/post-link.sh b/recipes/bioconductor-stjudem/post-link.sh new file mode 100644 index 0000000000000..72a4fba8f2662 --- /dev/null +++ b/recipes/bioconductor-stjudem/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="stjudem_1.22.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/stjudem_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/stjudem_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-stjudem/bioconductor-stjudem_1.22.0_src_all.tar.gz" +) +MD5="73c7d2523afdebc972054b62080d37c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-stjudem/pre-unlink.sh b/recipes/bioconductor-stjudem/pre-unlink.sh new file mode 100644 index 0000000000000..f9603ff142876 --- /dev/null +++ b/recipes/bioconductor-stjudem/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ stjudem diff --git a/recipes/bioconductor-strandcheckr/build.sh b/recipes/bioconductor-strandcheckr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-strandcheckr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-strandcheckr/meta.yaml b/recipes/bioconductor-strandcheckr/meta.yaml new file mode 100644 index 0000000000000..13a98598a7f9c --- /dev/null +++ b/recipes/bioconductor-strandcheckr/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.0.0" %} +{% set name = "strandCheckR" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3db4172a54f75b10ab4bde8805a76d43 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-reshape2 + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg38.knowngene >=3.4.0,<3.5.0' + - r-base + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-magrittr + - r-reshape2 + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package aims to quantify and remove putative double strand DNA from a strand-specific RNA sample. There are also options and methods to plot the positive/negative proportions of all sliding windows, which allow users to have an idea of how much the sample was contaminated and the appropriate threshold to be used for filtering.' + diff --git a/recipes/bioconductor-streamer/build.sh b/recipes/bioconductor-streamer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-streamer/build.sh +++ b/recipes/bioconductor-streamer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-streamer/meta.yaml b/recipes/bioconductor-streamer/meta.yaml index a357d7ebfc547..2c16cad79ea11 100644 --- a/recipes/bioconductor-streamer/meta.yaml +++ b/recipes/bioconductor-streamer/meta.yaml @@ -1,31 +1,32 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "Streamer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7a5de406c952a62b86152fb5a853a51dfe1248ba84d6815b9a8826166676b201 + md5: a9e80579a4fbeb9963df11b2a97b4e70 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, Rsamtools (>= 1.5.53), GenomicAlignments, Rgraphviz requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' - r-base build: - {{ compiler('c') }} @@ -34,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Large data files can be difficult to work with in R, where data generally resides in memory. This package encourages a style of programming where data is ''streamed'' from disk into R via a `producer'' and through a series of `consumers'' that, typically reduce the original data to a manageable size. The package provides useful Producer and Consumer stream components for operations such as data input, sampling, indexing, and transformation; see package?Streamer for details.' extra: identifiers: - biotools:streamer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-streamer + path: recipes/bioconductor-streamer + version: 1.26.0 + diff --git a/recipes/bioconductor-stringdb/build.sh b/recipes/bioconductor-stringdb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-stringdb/build.sh +++ b/recipes/bioconductor-stringdb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stringdb/meta.yaml b/recipes/bioconductor-stringdb/meta.yaml index 51e651b670956..2da19d15223f6 100644 --- a/recipes/bioconductor-stringdb/meta.yaml +++ b/recipes/bioconductor-stringdb/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "STRINGdb" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 89c2e5c96083c388526f3dd254e3085fe3b9e185965cf67d691b0264b37df05d + md5: bf498d4d580ffc25bca94edcc21934b5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - r-base @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The STRINGdb package provides a R interface to the STRING protein-protein interactions database (http://www.string-db.org).' extra: identifiers: - biotools:stringdb + parent_recipe: + name: bioconductor-stringdb + path: recipes/bioconductor-stringdb + version: 1.20.0 + diff --git a/recipes/bioconductor-stroma4/build.sh b/recipes/bioconductor-stroma4/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-stroma4/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-stroma4/meta.yaml b/recipes/bioconductor-stroma4/meta.yaml new file mode 100644 index 0000000000000..49b88c69c1a9d --- /dev/null +++ b/recipes/bioconductor-stroma4/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.6.0" %} +{% set name = "STROMA4" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 38c0cda4d885fd56e0c424d61fbc7b42 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: breastCancerMAINZ +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - r-cluster + - r-matrixstats + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - r-base + - r-cluster + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This package estimates four stromal properties identified in TNBC patients in each patient of a gene expression datasets. These stromal property assignments can be combined to subtype patients. These four stromal properties were identified in Triple negative breast cancer (TNBC) patients and represent the presence of different cells in the stroma: T-cells (T), B-cells (B), stromal infiltrating epithelial cells (E), and desmoplasia (D). Additionally this package can also be used to estimate generative properties for the Lehmann subtypes, an alternative TNBC subtyping scheme (PMID: 21633166).' + diff --git a/recipes/bioconductor-subseq/build.sh b/recipes/bioconductor-subseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-subseq/build.sh +++ b/recipes/bioconductor-subseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-subseq/meta.yaml b/recipes/bioconductor-subseq/meta.yaml index efdd54ab5bb7c..19db4da53fbdf 100644 --- a/recipes/bioconductor-subseq/meta.yaml +++ b/recipes/bioconductor-subseq/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "subSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d06f05a1dbe1ba52e25dc1a46b2feff337542b632e049108d9488984442525d3 + md5: 83475fe5a158cae0f5b326eb14a6f22d build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: limma, edgeR, DESeq2, DEXSeq (>= 1.9.7), testthat, knitr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-data.table - r-digest @@ -28,8 +30,8 @@ requirements: - r-magrittr - r-tidyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-data.table - r-digest @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'Subsampling of high throughput sequencing count data for use in experiment design and analysis.' extra: identifiers: - biotools:subseq - doi:10.1093/bioinformatics/btu552 + parent_recipe: + name: bioconductor-subseq + path: recipes/bioconductor-subseq + version: 1.10.0 + diff --git a/recipes/bioconductor-sugarcanecdf/meta.yaml b/recipes/bioconductor-sugarcanecdf/meta.yaml new file mode 100644 index 0000000000000..ec5aac9c23ce5 --- /dev/null +++ b/recipes/bioconductor-sugarcanecdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "sugarcanecdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f66d51868068f83d3693d3cb05be418a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Sugar_Cane.cdf file.' + diff --git a/recipes/bioconductor-sugarcanecdf/post-link.sh b/recipes/bioconductor-sugarcanecdf/post-link.sh new file mode 100644 index 0000000000000..d5843f2a22de7 --- /dev/null +++ b/recipes/bioconductor-sugarcanecdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="sugarcanecdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/sugarcanecdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/sugarcanecdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sugarcanecdf/bioconductor-sugarcanecdf_2.18.0_src_all.tar.gz" +) +MD5="f66d51868068f83d3693d3cb05be418a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sugarcanecdf/pre-unlink.sh b/recipes/bioconductor-sugarcanecdf/pre-unlink.sh new file mode 100644 index 0000000000000..81f08888e3900 --- /dev/null +++ b/recipes/bioconductor-sugarcanecdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ sugarcanecdf diff --git a/recipes/bioconductor-sugarcaneprobe/meta.yaml b/recipes/bioconductor-sugarcaneprobe/meta.yaml new file mode 100644 index 0000000000000..e7fe415077b1c --- /dev/null +++ b/recipes/bioconductor-sugarcaneprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "sugarcaneprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 66c101ac73e9235d258b9f996c42778e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Sugar\_Cane\_probe\_tab.' + diff --git a/recipes/bioconductor-sugarcaneprobe/post-link.sh b/recipes/bioconductor-sugarcaneprobe/post-link.sh new file mode 100644 index 0000000000000..5b1924c29523c --- /dev/null +++ b/recipes/bioconductor-sugarcaneprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="sugarcaneprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/sugarcaneprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/sugarcaneprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-sugarcaneprobe/bioconductor-sugarcaneprobe_2.18.0_src_all.tar.gz" +) +MD5="66c101ac73e9235d258b9f996c42778e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-sugarcaneprobe/pre-unlink.sh b/recipes/bioconductor-sugarcaneprobe/pre-unlink.sh new file mode 100644 index 0000000000000..b50ba493c5c04 --- /dev/null +++ b/recipes/bioconductor-sugarcaneprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ sugarcaneprobe diff --git a/recipes/bioconductor-summarizedbenchmark/build.sh b/recipes/bioconductor-summarizedbenchmark/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-summarizedbenchmark/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-summarizedbenchmark/meta.yaml b/recipes/bioconductor-summarizedbenchmark/meta.yaml new file mode 100644 index 0000000000000..2db901e41ef8c --- /dev/null +++ b/recipes/bioconductor-summarizedbenchmark/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "2.0.0" %} +{% set name = "SummarizedBenchmark" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 292d21d10c1ede88ed9c6be5f2d704fb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: iCOBRA, BiocStyle, knitr, magrittr, IHW, qvalue, testthat, DESeq2, edgeR, limma, tximport, readr, scRNAseq, splatter, scater, rnaseqcomp, biomaRt +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-crayon + - r-digest + - r-dplyr + - r-ggplot2 + - r-mclust + - r-rlang + - r-sessioninfo + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-crayon + - r-digest + - r-dplyr + - r-ggplot2 + - r-mclust + - r-rlang + - r-sessioninfo + - r-stringr + - r-tibble + - r-tidyr + - r-upsetr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package defines the BenchDesign and SummarizedBenchmark classes for building, executing, and evaluating benchmark experiments of computational methods. The SummarizedBenchmark class extends the RangedSummarizedExperiment object, and is designed to provide infrastructure to store and compare the results of applying different methods to a shared data set. This class provides an integrated interface to store metadata such as method parameters and software versions as well as ground truths (when these are available) and evaluation metrics.' + diff --git a/recipes/bioconductor-summarizedexperiment/build.sh b/recipes/bioconductor-summarizedexperiment/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-summarizedexperiment/build.sh +++ b/recipes/bioconductor-summarizedexperiment/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-summarizedexperiment/meta.yaml b/recipes/bioconductor-summarizedexperiment/meta.yaml index abe39b1aeeec0..2e3ea4c154ba3 100644 --- a/recipes/bioconductor-summarizedexperiment/meta.yaml +++ b/recipes/bioconductor-summarizedexperiment/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.10.1" %} +{% set version = "1.12.0" %} {% set name = "SummarizedExperiment" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 81dacf10280d5f6e79a5eed84c1ccaac7cf536a47f5b569e4a676bcc12ed7f6c + md5: 5738caa020eb8f8c7f399d9e799500ad build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: annotate, AnnotationDbi, hgu95av2.db, GenomicFeatures, TxDb.Hsapiens.UCSC.hg19.knownGene, BiocStyle, knitr, rmarkdown, digest, jsonlite, rhdf5, HDF5Array (>= 1.7.5), airway, RUnit, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-delayedarray >=0.6.6,<0.8.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-delayedarray >=0.8.0,<0.9.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-matrix test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The SummarizedExperiment container contains one or more assays, each represented by a matrix-like object of numeric or other mode. The rows typically represent genomic ranges of interest and the columns represent samples.' extra: identifiers: - biotools:summarizedexperiment - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-summarizedexperiment + path: recipes/bioconductor-summarizedexperiment + version: 1.10.1 + diff --git a/recipes/bioconductor-suprahex/build.sh b/recipes/bioconductor-suprahex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-suprahex/build.sh +++ b/recipes/bioconductor-suprahex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-suprahex/meta.yaml b/recipes/bioconductor-suprahex/meta.yaml index 1e444251f9a83..6671a4baf46ea 100644 --- a/recipes/bioconductor-suprahex/meta.yaml +++ b/recipes/bioconductor-suprahex/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "supraHex" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3f02f75500f78197af715e1be91a0ce0d3c3748ee2d5ef9ee769ee086a12dde7 + md5: 6a9ce3e5a00dca2709dfbb1569546767 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-ape @@ -31,9 +32,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'A supra-hexagonal map is a giant hexagon on a 2-dimensional grid seamlessly consisting of smaller hexagons. It is supposed to train, analyse and visualise a high-dimensional omics input data. The supraHex is able to carry out gene clustering/meta-clustering and sample correlation, plus intuitive visualisations to facilitate exploratory analysis. More importantly, it allows for overlaying additional data onto the trained map to explore relations between input and additional data. So with supraHex, it is also possible to carry out multilayer omics data comparisons. Newly added utilities are advanced heatmap visualisation and tree-based analysis of sample relationships. Uniquely to this package, users can ultrafastly understand any tabular omics data, both scientifically and artistically, especially in a sample-specific fashion but without loss of information on large genes.' extra: identifiers: - biotools:suprahex + parent_recipe: + name: bioconductor-suprahex + path: recipes/bioconductor-suprahex + version: 1.18.0 + diff --git a/recipes/bioconductor-survcomp/build.sh b/recipes/bioconductor-survcomp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-survcomp/build.sh +++ b/recipes/bioconductor-survcomp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-survcomp/meta.yaml b/recipes/bioconductor-survcomp/meta.yaml index 55e6313a11b0e..1fd32e4594eb0 100644 --- a/recipes/bioconductor-survcomp/meta.yaml +++ b/recipes/bioconductor-survcomp/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "survcomp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 12915ec5ca42bd2fcc7f019b0282c0d64624bc1aaffd1eacba2e598b23af1691 + md5: 9deb430d0aa94bc4738bbed9828cbf08 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Hmisc, CPE, clinfun, xtable, Biobase, BiocManager requirements: host: - r-base @@ -45,9 +46,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Assessment and Comparison for Performance of Risk Prediction (Survival) Models.' extra: identifiers: - biotools:survcomp + parent_recipe: + name: bioconductor-survcomp + path: recipes/bioconductor-survcomp + version: 1.30.0 + diff --git a/recipes/bioconductor-sushi/build.sh b/recipes/bioconductor-sushi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sushi/build.sh +++ b/recipes/bioconductor-sushi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sushi/meta.yaml b/recipes/bioconductor-sushi/meta.yaml index c689e09d1b3d7..406d8193bb07f 100644 --- a/recipes/bioconductor-sushi/meta.yaml +++ b/recipes/bioconductor-sushi/meta.yaml @@ -1,38 +1,44 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "Sushi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8150007890d74ca563a7e070dc27706af5d36191ae17633dd41083495e8525d4 + md5: 1dd42cecf0f9fcc2ce3e5da994e42c4a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base - r-zoo run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base - r-zoo test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Flexible, quantitative, and integrative genomic visualizations for publication-quality multi-panel figures' extra: identifiers: - biotools:sushi - doi:10.1093/bioinformatics/btu379 + parent_recipe: + name: bioconductor-sushi + path: recipes/bioconductor-sushi + version: 1.18.0 + diff --git a/recipes/bioconductor-sva/build.sh b/recipes/bioconductor-sva/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-sva/build.sh +++ b/recipes/bioconductor-sva/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-sva/meta.yaml b/recipes/bioconductor-sva/meta.yaml index 3e1f6ce761d32..cc95b516d49e6 100644 --- a/recipes/bioconductor-sva/meta.yaml +++ b/recipes/bioconductor-sva/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "3.28.0" %} +{% set version = "3.30.0" %} {% set name = "sva" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 5a142ac9faa2ffbf1030b4e5db7963d8038214abd7e1296dee325c09fec27228 + md5: 7bcab6570ee783620cf0a3243e3291eb build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: pamr, bladderbatch, BiocStyle, zebrafishRNASeq, testthat requirements: host: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-matrixstats - r-mgcv run: - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-matrixstats - r-mgcv @@ -38,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The sva package contains functions for removing batch effects and other unwanted variation in high-throughput experiment. Specifically, the sva package contains functions for the identifying and building surrogate variables for high-dimensional data sets. Surrogate variables are covariates constructed directly from high-dimensional data (like gene expression/RNA sequencing/methylation/brain imaging data) that can be used in subsequent analyses to adjust for unknown, unmodeled, or latent sources of noise. The sva package can be used to remove artifacts in three ways: (1) identifying and estimating surrogate variables for unknown sources of variation in high-throughput experiments (Leek and Storey 2007 PLoS Genetics,2008 PNAS), (2) directly removing known batch effects using ComBat (Johnson et al. 2007 Biostatistics) and (3) removing batch effects with known control probes (Leek 2014 biorXiv). Removing batch effects and using surrogate variables in differential expression analysis have been shown to reduce dependence, stabilize error rate estimates, and improve reproducibility, see (Leek and Storey 2007 PLoS Genetics, 2008 PNAS or Leek et al. 2011 Nat. Reviews Genetics).' extra: identifiers: - biotools:sva - doi:10.1371/journal.pgen.0030161 + parent_recipe: + name: bioconductor-sva + path: recipes/bioconductor-sva + version: 3.28.0 + diff --git a/recipes/bioconductor-svaplsseq/build.sh b/recipes/bioconductor-svaplsseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-svaplsseq/build.sh +++ b/recipes/bioconductor-svaplsseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-svaplsseq/meta.yaml b/recipes/bioconductor-svaplsseq/meta.yaml index 313c2634fd00f..045718d9c3616 100644 --- a/recipes/bioconductor-svaplsseq/meta.yaml +++ b/recipes/bioconductor-svaplsseq/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "SVAPLSseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 79005f67f72335851a4ac1f711b3ef0dc7175b6c44d0d184bcfad525ad06034c + md5: fe423b3bc72adcc5ff8aea6256b67c54 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle requirements: host: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-lmtest - r-pls run: - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-ggplot2 - r-lmtest @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The package contains functions that are intended for extracting the signatures of latent variation in RNAseq data and using them to perform an improved differential expression analysis for a set of features (genes, transcripts) between two specified biological groups.' extra: identifiers: - biotools:svaplsseq - doi:10.1101/062125 + parent_recipe: + name: bioconductor-svaplsseq + path: recipes/bioconductor-svaplsseq + version: 1.6.0 + diff --git a/recipes/bioconductor-svm2crm/build.sh b/recipes/bioconductor-svm2crm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-svm2crm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-svm2crm/meta.yaml b/recipes/bioconductor-svm2crm/meta.yaml new file mode 100644 index 0000000000000..9cc6156d51ea9 --- /dev/null +++ b/recipes/bioconductor-svm2crm/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.14.0" %} +{% set name = "SVM2CRM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 406904f28e8238f547ecc79b2d562ffd +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-svm2crmdata >=1.14.0,<1.15.0' + - r-base + - r-liblinear + - r-mclust + - r-pls + - r-rocr + - r-squash + - r-verification + - r-zoo + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-svm2crmdata >=1.14.0,<1.15.0' + - r-base + - r-liblinear + - r-mclust + - r-pls + - r-rocr + - r-squash + - r-verification + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Detection of cis-regulatory elements using svm implemented in LiblineaR.' + diff --git a/recipes/bioconductor-svm2crmdata/meta.yaml b/recipes/bioconductor-svm2crmdata/meta.yaml new file mode 100644 index 0000000000000..94c82d909df79 --- /dev/null +++ b/recipes/bioconductor-svm2crmdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.14.0" %} +{% set name = "SVM2CRMdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 67239ac74ee3b881f2070be62472e43b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'LGPL (>= 2)' + summary: 'An example dataset for use with the SVM2CRM package.' + diff --git a/recipes/bioconductor-svm2crmdata/post-link.sh b/recipes/bioconductor-svm2crmdata/post-link.sh new file mode 100644 index 0000000000000..9dd18cc9985ff --- /dev/null +++ b/recipes/bioconductor-svm2crmdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="SVM2CRMdata_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/SVM2CRMdata_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/SVM2CRMdata_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-svm2crmdata/bioconductor-svm2crmdata_1.14.0_src_all.tar.gz" +) +MD5="67239ac74ee3b881f2070be62472e43b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-svm2crmdata/pre-unlink.sh b/recipes/bioconductor-svm2crmdata/pre-unlink.sh new file mode 100644 index 0000000000000..30a70f6edfd76 --- /dev/null +++ b/recipes/bioconductor-svm2crmdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ SVM2CRMdata diff --git a/recipes/bioconductor-swath2stats/build.sh b/recipes/bioconductor-swath2stats/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-swath2stats/build.sh +++ b/recipes/bioconductor-swath2stats/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-swath2stats/meta.yaml b/recipes/bioconductor-swath2stats/meta.yaml index 70c2cb33e1263..7fa06bdd6b865 100644 --- a/recipes/bioconductor-swath2stats/meta.yaml +++ b/recipes/bioconductor-swath2stats/meta.yaml @@ -1,28 +1,32 @@ -{% set version = "1.10.2" %} +{% set version = "1.12.1" %} {% set name = "SWATH2stats" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 333f5e0deaefb3fcd69d696eed715a05580cccc0e154b645b7d08cd5860623b6 + md5: b9a0757b467c76b415777e94fd0e2da9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, aLFQ, knitr, PECA requirements: host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base - r-data.table - r-ggplot2 - r-reshape2 run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' - r-base - r-data.table - r-ggplot2 @@ -31,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.' extra: identifiers: - biotools:swath2stats + parent_recipe: + name: bioconductor-swath2stats + path: recipes/bioconductor-swath2stats + version: 1.10.2 + diff --git a/recipes/bioconductor-swathxtend/build.sh b/recipes/bioconductor-swathxtend/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-swathxtend/build.sh +++ b/recipes/bioconductor-swathxtend/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-swathxtend/meta.yaml b/recipes/bioconductor-swathxtend/meta.yaml index 209e4f329d0d4..8e36a6de36ba5 100644 --- a/recipes/bioconductor-swathxtend/meta.yaml +++ b/recipes/bioconductor-swathxtend/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "2.2.0" %} +{% set version = "2.4.0" %} {% set name = "SwathXtend" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0ad178da7a9f9a1d043a87dbfe72595c42bedcdcf85e945a46cbe96dc644a93e + md5: 4be2d18fb48add8b1212d8c1e906ecec build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Contains utility functions for integrating spectral libraries for SWATH and statistical data analysis for SWATH generated data.' extra: identifiers: - biotools:swathxtend - doi:10.1074/mcp.M115.055558 + parent_recipe: + name: bioconductor-swathxtend + path: recipes/bioconductor-swathxtend + version: 2.2.0 + diff --git a/recipes/bioconductor-swfdr/build.sh b/recipes/bioconductor-swfdr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-swfdr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-swfdr/meta.yaml b/recipes/bioconductor-swfdr/meta.yaml new file mode 100644 index 0000000000000..7b53c64209038 --- /dev/null +++ b/recipes/bioconductor-swfdr/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.8.0" %} +{% set name = "swfdr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: edaa6e7aa6de877fd3b61d4c03daa5fe +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - r-base + - r-dplyr + - r-ggplot2 + - r-reshape2 + run: + - r-base + - r-dplyr + - r-ggplot2 + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'This package allows users to estimate the science-wise false discovery rate from Jager and Leek, "Empirical estimates suggest most published medical research is true," 2013, Biostatistics, using an EM approach due to the presence of rounding and censoring. It also allows users to estimate the proportion of true null hypotheses in the presence of covariates, using a regression framework, as per Boca and Leek, "A regression framework for the proportion of true null hypotheses," 2015, bioRxiv preprint.' + diff --git a/recipes/bioconductor-swimr/build.sh b/recipes/bioconductor-swimr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-swimr/build.sh +++ b/recipes/bioconductor-swimr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-swimr/meta.yaml b/recipes/bioconductor-swimr/meta.yaml index 135b5bdb2f166..c833ef2acee94 100644 --- a/recipes/bioconductor-swimr/meta.yaml +++ b/recipes/bioconductor-swimr/meta.yaml @@ -1,21 +1,22 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "SwimR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ff895a68334d1787be3a24797f395d0ca67d46cb64e0d159df436807e5ccfe64 + md5: 98716966952df5504255e41de4e57055 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - r-base @@ -33,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'SwimR is an R-based suite that calculates, analyses, and plots the frequency of C. elegans swimming behavior over time. It places a particular emphasis on identifying paralysis and quantifying the kinetic elements of paralysis during swimming. Data is input to SwipR from a custom built program that fits a 5 point morphometric spine to videos of single worms swimming in a buffer called Worm Tracker.' extra: identifiers: - biotools:swimr - doi:10.1016/j.jneumeth.2014.04.024 + parent_recipe: + name: bioconductor-swimr + path: recipes/bioconductor-swimr + version: 1.18.0 + diff --git a/recipes/bioconductor-switchbox/build.sh b/recipes/bioconductor-switchbox/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-switchbox/build.sh +++ b/recipes/bioconductor-switchbox/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-switchbox/meta.yaml b/recipes/bioconductor-switchbox/meta.yaml index c84d1645e3f1e..caa9acdf86753 100644 --- a/recipes/bioconductor-switchbox/meta.yaml +++ b/recipes/bioconductor-switchbox/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "switchBox" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: cb6b004c77d7064b43f836e1ee7eccb44b80a1b75022815917c1def0c3778ed2 + md5: 383194e52f750c3c3ef7764ca66bcdb3 build: number: 0 rpaths: @@ -33,9 +33,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package offer different classifiers based on comparisons of pair of features (TSP), using various decision rules (e.g., majority wins principle).' extra: identifiers: - biotools:switchbox + parent_recipe: + name: bioconductor-switchbox + path: recipes/bioconductor-switchbox + version: 1.16.0 + diff --git a/recipes/bioconductor-switchde/build.sh b/recipes/bioconductor-switchde/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-switchde/build.sh +++ b/recipes/bioconductor-switchde/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-switchde/conda_build_config.yaml b/recipes/bioconductor-switchde/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-switchde/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-switchde/meta.yaml b/recipes/bioconductor-switchde/meta.yaml index d78ef5dcda6de..4305a241b4b33 100644 --- a/recipes/bioconductor-switchde/meta.yaml +++ b/recipes/bioconductor-switchde/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "switchde" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 87142bb58a4816a104bfd7067b971b3ad31eb571230ff0dbc48d02d3f61c2449 + md5: 14868aa05edbb0a7fdf44d890bef9144 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, testthat, numDeriv, tidyr requirements: host: - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dplyr - r-ggplot2 run: - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-dplyr - r-ggplot2 @@ -33,10 +35,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Inference and detection of switch-like differential expression across single-cell RNA-seq trajectories.' extra: identifiers: - biotools:switchde - doi:10.1093/bioinformatics/btw798 + parent_recipe: + name: bioconductor-switchde + path: recipes/bioconductor-switchde + version: 1.6.0 + diff --git a/recipes/bioconductor-synapter/build.sh b/recipes/bioconductor-synapter/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-synapter/build.sh +++ b/recipes/bioconductor-synapter/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-synapter/meta.yaml b/recipes/bioconductor-synapter/meta.yaml index 59070bbe143ce..81a7ec82727b1 100644 --- a/recipes/bioconductor-synapter/meta.yaml +++ b/recipes/bioconductor-synapter/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "2.4.1" %} +{% set version = "2.6.0" %} {% set name = "synapter" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 34650a2b53e157ef1fb2a488fdbd73b80117369a07817c02771b77e8a0404479 + md5: 9e91d29bf1c884a63741647fce9a9866 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: synapterdata (>= 1.13.2), xtable, testthat (>= 0.8), BRAIN, BiocStyle requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-cleaver >=1.18.0,<1.20.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-cleaver >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-knitr - r-lattice @@ -31,12 +33,12 @@ requirements: - 'r-readr >=0.2' - 'r-rmarkdown >=1.0' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-cleaver >=1.18.0,<1.20.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-cleaver >=1.20.0,<1.21.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' - r-base - r-knitr - r-lattice @@ -47,9 +49,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The synapter package provides functionality to reanalyse label-free proteomics data acquired on a Synapt G2 mass spectrometer. One or several runs, possibly processed with additional ion mobility separation to increase identification accuracy can be combined to other quantitation files to maximise identification and quantitation accuracy.' extra: identifiers: - biotools:synapter + parent_recipe: + name: bioconductor-synapter + path: recipes/bioconductor-synapter + version: 2.4.1 + diff --git a/recipes/bioconductor-synapterdata/meta.yaml b/recipes/bioconductor-synapterdata/meta.yaml new file mode 100644 index 0000000000000..6ac073476601d --- /dev/null +++ b/recipes/bioconductor-synapterdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "synapterdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a13fa15f1bcbfa6495cce58c3d439a0e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-synapter >=2.6.0,<2.7.0' + - r-base + run: + - 'bioconductor-synapter >=2.6.0,<2.7.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Data independant acquisition of UPS1 protein mix in an E. coli background obtained on a Waters Synapt G2 instrument.' + diff --git a/recipes/bioconductor-synapterdata/post-link.sh b/recipes/bioconductor-synapterdata/post-link.sh new file mode 100644 index 0000000000000..b8388e8adf2e0 --- /dev/null +++ b/recipes/bioconductor-synapterdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="synapterdata_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/synapterdata_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/synapterdata_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-synapterdata/bioconductor-synapterdata_1.20.0_src_all.tar.gz" +) +MD5="a13fa15f1bcbfa6495cce58c3d439a0e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-synapterdata/pre-unlink.sh b/recipes/bioconductor-synapterdata/pre-unlink.sh new file mode 100644 index 0000000000000..8d103481bafbe --- /dev/null +++ b/recipes/bioconductor-synapterdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ synapterdata diff --git a/recipes/bioconductor-synergyfinder/build.sh b/recipes/bioconductor-synergyfinder/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-synergyfinder/build.sh +++ b/recipes/bioconductor-synergyfinder/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-synergyfinder/meta.yaml b/recipes/bioconductor-synergyfinder/meta.yaml index 3165ccbbe8bab..144c32db44b37 100644 --- a/recipes/bioconductor-synergyfinder/meta.yaml +++ b/recipes/bioconductor-synergyfinder/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.6.1" %} +{% set version = "1.8.0" %} {% set name = "synergyfinder" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ecc6b18511a9204ffb34b425fd8292c44fb072612278829c9e1791e69960e1af + md5: e3f9aa7ba027416ec0644f9bf85f5376 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown requirements: host: - r-base @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Mozilla Public License 2.0 + file LICENSE' summary: 'Efficient implementations for all the popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of the synergy scores as either a two-dimensional or a three-dimensional interaction surface over the dose matrix.' extra: identifiers: - biotools:synergyfinder - doi:10.1093/bioinformatics/btx162 + parent_recipe: + name: bioconductor-synergyfinder + path: recipes/bioconductor-synergyfinder + version: 1.6.1 + diff --git a/recipes/bioconductor-synlet/build.sh b/recipes/bioconductor-synlet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-synlet/build.sh +++ b/recipes/bioconductor-synlet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-synlet/meta.yaml b/recipes/bioconductor-synlet/meta.yaml index b27115cfb8716..58be2bd79c578 100644 --- a/recipes/bioconductor-synlet/meta.yaml +++ b/recipes/bioconductor-synlet/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "synlet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 91ee2e3059dc637f5bb1da82ae5ac62d5503d3ffc6f725fb36d1ab30b2a1198c + md5: 9fd6ecefbc1c02d2473a8bed49a16c49 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, testthat requirements: host: - - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' - r-base - r-doby - r-dplyr @@ -27,7 +29,7 @@ requirements: - r-rcolorbrewer - r-reshape2 run: - - 'bioconductor-rankprod >=3.6.0,<3.8.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' - r-base - r-doby - r-dplyr @@ -39,10 +41,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Select hits from synthetic lethal RNAi screen data. For example, there are two identical celllines except one gene is knocked-down in one cellline. The interest is to find genes that lead to stronger lethal effect when they are knocked-down further by siRNA. Quality control and various visualisation tools are implemented. Four different algorithms could be used to pick up the interesting hits. This package is designed based on 384 wells plates, but may apply to other platforms with proper configuration.' extra: identifiers: - biotools:synlet - doi:10.1101/043570 + parent_recipe: + name: bioconductor-synlet + path: recipes/bioconductor-synlet + version: 1.10.0 + diff --git a/recipes/bioconductor-systempiper/build.sh b/recipes/bioconductor-systempiper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-systempiper/build.sh +++ b/recipes/bioconductor-systempiper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-systempiper/meta.yaml b/recipes/bioconductor-systempiper/meta.yaml index 5d6a4cdeb2fad..905d43595aecc 100644 --- a/recipes/bioconductor-systempiper/meta.yaml +++ b/recipes/bioconductor-systempiper/meta.yaml @@ -1,57 +1,60 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "systemPipeR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 95963a20ac6c26c195b3c36c1ec8091f4f12dc3fd1de3adf067ed63a4cbba094 + md5: a11f46fe7541f5ab67ddba04144771b7 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ape, RUnit, BiocStyle, knitr, rmarkdown, biomaRt, BiocParallel, BiocManager +# SystemRequirements: systemPipeR can be used to run external command-line software (e.g. short read aligners), but the corresponding tool needs to be installed on a system. requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-batchjobs - r-ggplot2 - r-pheatmap - r-rjson run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-gostats >=2.46.0,<2.48.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-shortread >=1.38.0,<1.40.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-gostats >=2.48.0,<2.49.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-shortread >=1.40.0,<1.41.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-batchjobs - r-ggplot2 @@ -61,9 +64,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'R package for building and running automated end-to-end analysis workflows for a wide range of next generation sequence (NGS) applications such as RNA-Seq, ChIP-Seq, VAR-Seq and Ribo-Seq. Important features include a uniform workflow interface across different NGS applications, automated report generation, and support for running both R and command-line software, such as NGS aligners or peak/variant callers, on local computers or compute clusters. Efficient handling of complex sample sets and experimental designs is facilitated by a consistently implemented sample annotation infrastructure. Instructions for using systemPipeR are given in the Overview Vignette (HTML). The remaining Vignettes, linked below, are workflow templates for common NGS use cases.' extra: identifiers: - biotools:systempiper + parent_recipe: + name: bioconductor-systempiper + path: recipes/bioconductor-systempiper + version: 1.14.0 + diff --git a/recipes/bioconductor-systempiperdata/meta.yaml b/recipes/bioconductor-systempiperdata/meta.yaml new file mode 100644 index 0000000000000..e7696b2150ab6 --- /dev/null +++ b/recipes/bioconductor-systempiperdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.10.0" %} +{% set name = "systemPipeRdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ba76fafb811f95cbaba27ef3953e55b3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, BiocStyle, knitr, rmarkdown, systemPipeR +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'systemPipeRdata is a helper package to generate with a single command NGS workflow templates that are intended to be used by its parent package systemPipeR. The latter is an environment for building end-to-end analysis pipelines with automated report generation for next generation sequence (NGS) applications such as RNA-Seq, RIBO-Seq, ChIP-Seq, VAR-Seq and many others. Detailed examples for using systemPipeRdata are given in systemPipeR''s overview vignette.' + diff --git a/recipes/bioconductor-systempiperdata/post-link.sh b/recipes/bioconductor-systempiperdata/post-link.sh new file mode 100644 index 0000000000000..9227607e5f871 --- /dev/null +++ b/recipes/bioconductor-systempiperdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="systemPipeRdata_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/systemPipeRdata_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/systemPipeRdata_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-systempiperdata/bioconductor-systempiperdata_1.10.0_src_all.tar.gz" +) +MD5="ba76fafb811f95cbaba27ef3953e55b3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-systempiperdata/pre-unlink.sh b/recipes/bioconductor-systempiperdata/pre-unlink.sh new file mode 100644 index 0000000000000..2117a1a7bce70 --- /dev/null +++ b/recipes/bioconductor-systempiperdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ systemPipeRdata diff --git a/recipes/bioconductor-tabulamurisdata/meta.yaml b/recipes/bioconductor-tabulamurisdata/meta.yaml new file mode 100644 index 0000000000000..6d8c8c380d46d --- /dev/null +++ b/recipes/bioconductor-tabulamurisdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.0.0" %} +{% set name = "TabulaMurisData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1b4f8f16754586ce5866ac90de5ac0a4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, BiocStyle, SingleCellExperiment, scran, scater, iSEE, testthat +requirements: + host: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + run: + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'Access to processed 10x (droplet) and SmartSeq2 (on FACS-sorted cells) single-cell RNA-seq data from the Tabula Muris consortium (http://tabula-muris.ds.czbiohub.org/).' + diff --git a/recipes/bioconductor-tabulamurisdata/post-link.sh b/recipes/bioconductor-tabulamurisdata/post-link.sh new file mode 100644 index 0000000000000..ce1904f6ae2c1 --- /dev/null +++ b/recipes/bioconductor-tabulamurisdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TabulaMurisData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TabulaMurisData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/TabulaMurisData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tabulamurisdata/bioconductor-tabulamurisdata_1.0.0_src_all.tar.gz" +) +MD5="1b4f8f16754586ce5866ac90de5ac0a4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tabulamurisdata/pre-unlink.sh b/recipes/bioconductor-tabulamurisdata/pre-unlink.sh new file mode 100644 index 0000000000000..e5b08c9ddfbd5 --- /dev/null +++ b/recipes/bioconductor-tabulamurisdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TabulaMurisData diff --git a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml index 945663410a614..a95325a2a1951 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml +++ b/recipes/bioconductor-targetscan.hs.eg.db/meta.yaml @@ -1,35 +1,40 @@ {% set version = "0.6.1" %} {% set name = "targetscan.Hs.eg.db" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c4f55d11e7e95e437ef40f1fe7b2cd0cbd6184494befc4f93455b460a19724dc + md5: d10569315400f6c1b95ad2688632b6de build: - number: 0 + number: 1 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: 'file LICENSE' summary: 'TargetScan miRNA target predictions for human assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3'' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.' - +extra: + parent_recipe: + name: bioconductor-targetscan.hs.eg.db + path: recipes/bioconductor-targetscan.hs.eg.db + version: 0.6.1 diff --git a/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh index d52c0fb2a2121..b3ddb56af4488 100644 --- a/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh +++ b/recipes/bioconductor-targetscan.hs.eg.db/post-link.sh @@ -1,9 +1,10 @@ #!/bin/bash FN="targetscan.Hs.eg.db_0.6.1.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/targetscan.Hs.eg.db_0.6.1.tar.gz" "https://bioarchive.galaxyproject.org/targetscan.Hs.eg.db_0.6.1.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscan.hs.eg.db/bioconductor-targetscan.hs.eg.db_0.6.1_src_all.tar.gz" ) MD5="d10569315400f6c1b95ad2688632b6de" diff --git a/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml new file mode 100644 index 0000000000000..c38332d64a0a1 --- /dev/null +++ b/recipes/bioconductor-targetscan.mm.eg.db/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "0.6.1" %} +{% set name = "targetscan.Mm.eg.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1830815c9d1383739f1ff152da0508c5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'TargetScan miRNA target predictions for mouse assembled using data from the TargetScan website. TargetScan predicts biological targets of miRNAs by searching for the presence of conserved 8mer and 7mer sites that match the seed region of each miRNA. Also identified are sites with mismatches in the seed region that are compensated by conserved 3'' pairing. In mammals, predictions are ranked based on the predicted efficacy of targeting as calculated using the context scores of the sites.' + diff --git a/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh b/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh new file mode 100644 index 0000000000000..f4772f6e6e648 --- /dev/null +++ b/recipes/bioconductor-targetscan.mm.eg.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="targetscan.Mm.eg.db_0.6.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/targetscan.Mm.eg.db_0.6.1.tar.gz" + "https://bioarchive.galaxyproject.org/targetscan.Mm.eg.db_0.6.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscan.mm.eg.db/bioconductor-targetscan.mm.eg.db_0.6.1_src_all.tar.gz" +) +MD5="1830815c9d1383739f1ff152da0508c5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-targetscan.mm.eg.db/pre-unlink.sh b/recipes/bioconductor-targetscan.mm.eg.db/pre-unlink.sh new file mode 100644 index 0000000000000..871ec69c4d1de --- /dev/null +++ b/recipes/bioconductor-targetscan.mm.eg.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ targetscan.Mm.eg.db diff --git a/recipes/bioconductor-targetscore/build.sh b/recipes/bioconductor-targetscore/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-targetscore/build.sh +++ b/recipes/bioconductor-targetscore/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-targetscore/meta.yaml b/recipes/bioconductor-targetscore/meta.yaml index 978883618388a..833d0030e5409 100644 --- a/recipes/bioconductor-targetscore/meta.yaml +++ b/recipes/bioconductor-targetscore/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TargetScore" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ea8824a908c345ee7b92c5a1ddd3619832c69b05fa78a2f8e6c6ef1aa95935e2 + md5: 4334b96fdaf7f911bc922ba9d7d1c1a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: TargetScoreData, gplots, Biobase, GEOquery requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Infer the posterior distributions of microRNA targets by probabilistically modelling the likelihood microRNA-overexpression fold-changes and sequence-based scores. Variaitonal Bayesian Gaussian mixture model (VB-GMM) is applied to log fold-changes and sequence scores to obtain the posteriors of latent variable being the miRNA targets. The final targetScore is computed as the sigmoid-transformed fold-change weighted by the averaged posteriors of target components over all of the features.' extra: identifiers: - biotools:targetscore - doi:10.1093/bioinformatics/btt599 + parent_recipe: + name: bioconductor-targetscore + path: recipes/bioconductor-targetscore + version: 1.18.0 + diff --git a/recipes/bioconductor-targetscoredata/meta.yaml b/recipes/bioconductor-targetscoredata/meta.yaml new file mode 100644 index 0000000000000..2d6df33fa8796 --- /dev/null +++ b/recipes/bioconductor-targetscoredata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.18.0" %} +{% set name = "TargetScoreData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fd759e7712396b9f33e3ad26502a7762 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: TargetScore, gplots +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Precompiled and processed miRNA-overexpression fold-changes from 84 Gene Expression Omnibus (GEO) series corresponding to 6 platforms, 77 human cells or tissues, and 113 distinct miRNAs. Accompanied with the data, we also included in this package the sequence feature scores from TargetScanHuman 6.1 including the context+ score and the probabilities of conserved targeting for each miRNA-mRNA interaction. Thus, the user can use these static sequence-based scores together with user-supplied tissue/cell-specific fold-change due to miRNA overexpression to predict miRNA targets using the package TargetScore (download separately)' + diff --git a/recipes/bioconductor-targetscoredata/post-link.sh b/recipes/bioconductor-targetscoredata/post-link.sh new file mode 100644 index 0000000000000..3a019bc3a630a --- /dev/null +++ b/recipes/bioconductor-targetscoredata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TargetScoreData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TargetScoreData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/TargetScoreData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetscoredata/bioconductor-targetscoredata_1.18.0_src_all.tar.gz" +) +MD5="fd759e7712396b9f33e3ad26502a7762" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-targetscoredata/pre-unlink.sh b/recipes/bioconductor-targetscoredata/pre-unlink.sh new file mode 100644 index 0000000000000..f974bf036b1e4 --- /dev/null +++ b/recipes/bioconductor-targetscoredata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TargetScoreData diff --git a/recipes/bioconductor-targetsearch/build.sh b/recipes/bioconductor-targetsearch/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-targetsearch/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-targetsearch/meta.yaml b/recipes/bioconductor-targetsearch/meta.yaml new file mode 100644 index 0000000000000..7af08e96471e3 --- /dev/null +++ b/recipes/bioconductor-targetsearch/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.38.1" %} +{% set name = "TargetSearch" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 037931da176f5fd0a40ae3a80209e3d7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: TargetSearchData, BiocStyle, knitr +requirements: + host: + - r-base + - r-ncdf4 + run: + - r-base + - r-ncdf4 + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This packages provides a targeted pre-processing method for GC-MS data.' + diff --git a/recipes/bioconductor-targetsearchdata/meta.yaml b/recipes/bioconductor-targetsearchdata/meta.yaml new file mode 100644 index 0000000000000..02ab3c3be28b2 --- /dev/null +++ b/recipes/bioconductor-targetsearchdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "TargetSearchData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f22282a97204579a09ebe055434811b6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides example GC-MS data for TargetSearch Package.' + diff --git a/recipes/bioconductor-targetsearchdata/post-link.sh b/recipes/bioconductor-targetsearchdata/post-link.sh new file mode 100644 index 0000000000000..e235183dc8f56 --- /dev/null +++ b/recipes/bioconductor-targetsearchdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TargetSearchData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TargetSearchData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/TargetSearchData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-targetsearchdata/bioconductor-targetsearchdata_1.20.0_src_all.tar.gz" +) +MD5="f22282a97204579a09ebe055434811b6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-targetsearchdata/pre-unlink.sh b/recipes/bioconductor-targetsearchdata/pre-unlink.sh new file mode 100644 index 0000000000000..70838f33ecb9b --- /dev/null +++ b/recipes/bioconductor-targetsearchdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TargetSearchData diff --git a/recipes/bioconductor-tarseqqc/build.sh b/recipes/bioconductor-tarseqqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tarseqqc/build.sh +++ b/recipes/bioconductor-tarseqqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tarseqqc/meta.yaml b/recipes/bioconductor-tarseqqc/meta.yaml index 762b6645a094c..8caae23b4d2a6 100644 --- a/recipes/bioconductor-tarseqqc/meta.yaml +++ b/recipes/bioconductor-tarseqqc/meta.yaml @@ -1,32 +1,34 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "TarSeqQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e2d70634d99666fec6b80209bb8cfdef7a35f76ddfbfd806751d70e74aad9047 + md5: d63b65c61556d88e875ac624b4142756 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocManager, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-cowplot - r-ggplot2 @@ -35,15 +37,15 @@ requirements: - r-plyr - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-cowplot - r-ggplot2 @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'The package allows the representation of targeted experiment in R. This is based on current packages and incorporates functions to do a quality control over this kind of experiments and a fast exploration of the sequenced regions. An xlsx file is generated as output.' extra: identifiers: - biotools:tarseqqc + parent_recipe: + name: bioconductor-tarseqqc + path: recipes/bioconductor-tarseqqc + version: 1.10.0 + diff --git a/recipes/bioconductor-tbx20bamsubset/meta.yaml b/recipes/bioconductor-tbx20bamsubset/meta.yaml new file mode 100644 index 0000000000000..b572a6ee964cb --- /dev/null +++ b/recipes/bioconductor-tbx20bamsubset/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.18.0" %} +{% set name = "TBX20BamSubset" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6b04fa46c1d81b4965a59ac7a3cbde37 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-xtable + run: + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - r-base + - r-xtable + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'Dual transcriptional activator and repressor roles of TBX20 regulate adult cardiac structure and function. A subset of the RNA-Seq data.' + diff --git a/recipes/bioconductor-tbx20bamsubset/post-link.sh b/recipes/bioconductor-tbx20bamsubset/post-link.sh new file mode 100644 index 0000000000000..b610888040e66 --- /dev/null +++ b/recipes/bioconductor-tbx20bamsubset/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TBX20BamSubset_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TBX20BamSubset_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/TBX20BamSubset_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tbx20bamsubset/bioconductor-tbx20bamsubset_1.18.0_src_all.tar.gz" +) +MD5="6b04fa46c1d81b4965a59ac7a3cbde37" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tbx20bamsubset/pre-unlink.sh b/recipes/bioconductor-tbx20bamsubset/pre-unlink.sh new file mode 100644 index 0000000000000..af5b7c78dbbfb --- /dev/null +++ b/recipes/bioconductor-tbx20bamsubset/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TBX20BamSubset diff --git a/recipes/bioconductor-tcc/build.sh b/recipes/bioconductor-tcc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tcc/build.sh +++ b/recipes/bioconductor-tcc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcc/meta.yaml b/recipes/bioconductor-tcc/meta.yaml index 943ba7aaaaee4..241fd04f9dfd4 100644 --- a/recipes/bioconductor-tcc/meta.yaml +++ b/recipes/bioconductor-tcc/meta.yaml @@ -1,43 +1,50 @@ -{% set version = "1.20.1" %} +{% set version = "1.22.0" %} {% set name = "TCC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 8915a72bf5c1c05c9e2c0c01d653851c516c2e1121a02c02c2d3a498ad8bbe30 + md5: 029f04706733a7472728b005b8591b43 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, BiocGenerics requirements: host: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base run: - - 'bioconductor-bayseq >=2.14.0,<2.16.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-bayseq >=2.16.0,<2.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES). The basic idea of DEGES is that potential differentially expressed genes or transcripts (DEGs) among compared samples should be removed before data normalization to obtain a well-ranked gene list where true DEGs are top-ranked and non-DEGs are bottom ranked. This can be done by performing a multi-step normalization strategy (called DEGES for DEG elimination strategy). A major characteristic of TCC is to provide the robust normalization methods for several kinds of count data (two-group with or without replicates, multi-group/multi-factor, and so on) by virtue of the use of combinations of functions in depended packages.' extra: identifiers: - biotools:tcc + parent_recipe: + name: bioconductor-tcc + path: recipes/bioconductor-tcc + version: 1.20.1 + diff --git a/recipes/bioconductor-tcgabiolinks/build.sh b/recipes/bioconductor-tcgabiolinks/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tcgabiolinks/build.sh +++ b/recipes/bioconductor-tcgabiolinks/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcgabiolinks/meta.yaml b/recipes/bioconductor-tcgabiolinks/meta.yaml index ebd252fd3ea85..632d0e553e2e5 100644 --- a/recipes/bioconductor-tcgabiolinks/meta.yaml +++ b/recipes/bioconductor-tcgabiolinks/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "2.8.4" %} +{% set version = "2.10.0" %} {% set name = "TCGAbiolinks" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fbe2b4bf27934055452be731c42c1a21f77f2702eb1b341a89eb77757d8cb8fe + md5: 226a9f591c6778490b31ccc92c207ee1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: png, BiocStyle, rmarkdown, devtools, maftools, parmigene, c3net, minet, dnet, Biobase, affy, testthat, pathview, clusterProfiler, igraph, supraHex requirements: host: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-circlize - r-data.table @@ -60,20 +62,20 @@ requirements: - 'r-xml >=3.98.0' - r-xml2 run: - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-consensusclusterplus >=1.44.0,<1.46.0' - - 'bioconductor-edaseq >=2.14.1,<2.16.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-consensusclusterplus >=1.46.0,<1.47.0' + - 'bioconductor-edaseq >=2.16.0,<2.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-circlize - r-data.table @@ -105,10 +107,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'The aim of TCGAbiolinks is : i) facilitate the GDC open-access data retrieval, ii) prepare the data using the appropriate pre-processing strategies, iii) provide the means to carry out different standard analyses and iv) to easily reproduce earlier research results. In more detail, the package provides multiple methods for analysis (e.g., differential expression analysis, identifying differentially methylated regions) and methods for visualization (e.g., survival plots, volcano plots, starburst plots) in order to easily develop complete analysis pipelines.' extra: identifiers: - biotools:tcgabiolinks - doi:10.1093/nar/gkv1507 + parent_recipe: + name: bioconductor-tcgabiolinks + path: recipes/bioconductor-tcgabiolinks + version: 2.8.4 + diff --git a/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml new file mode 100644 index 0000000000000..cc8a6de07d61f --- /dev/null +++ b/recipes/bioconductor-tcgabiolinksgui.data/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "TCGAbiolinksGUI.data" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b3eeb50a569df22c6434bd7ff06fa460 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, readr, readxl, dplyr, caret, randomForest, doMC, e1071, DT +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'Supporting data for the TCGAbiolinksGUI package. It includes the following objects: glioma.gcimp.model, glioma.idhwt.model glioma.idhmut.model,glioma.idh.mode, probes2rm, maf.tumor,GDCdisease.' + diff --git a/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh new file mode 100644 index 0000000000000..7c1525baf9af5 --- /dev/null +++ b/recipes/bioconductor-tcgabiolinksgui.data/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TCGAbiolinksGUI.data_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAbiolinksGUI.data_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAbiolinksGUI.data_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgabiolinksgui.data/bioconductor-tcgabiolinksgui.data_1.2.0_src_all.tar.gz" +) +MD5="b3eeb50a569df22c6434bd7ff06fa460" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgabiolinksgui.data/pre-unlink.sh b/recipes/bioconductor-tcgabiolinksgui.data/pre-unlink.sh new file mode 100644 index 0000000000000..67941690543d6 --- /dev/null +++ b/recipes/bioconductor-tcgabiolinksgui.data/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TCGAbiolinksGUI.data diff --git a/recipes/bioconductor-tcgabiolinksgui/build.sh b/recipes/bioconductor-tcgabiolinksgui/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tcgabiolinksgui/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcgabiolinksgui/meta.yaml b/recipes/bioconductor-tcgabiolinksgui/meta.yaml new file mode 100644 index 0000000000000..becb4f78b11bf --- /dev/null +++ b/recipes/bioconductor-tcgabiolinksgui/meta.yaml @@ -0,0 +1,91 @@ +{% set version = "1.8.0" %} +{% set name = "TCGAbiolinksGUI" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2304d156949603d34060268a2b5fa0b4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat, dplyr, knitr, roxygen2, devtools, rvest, xml2, BiocStyle, animation, pander +requirements: + host: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-elmer >=2.6.0,<2.7.0' + - 'bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation27kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-maftools >=1.8.0,<1.9.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-tcgabiolinksgui.data >=1.2.0,<1.3.0' + - r-base + - r-caret + - r-colourpicker + - r-data.table + - 'r-downloader >=0.4' + - r-dt + - 'r-ggplot2 >=2.1.0' + - r-ggrepel + - r-plotly + - r-readr + - 'r-shiny >=0.14.1' + - 'r-shinybs >=0.61' + - 'r-shinydashboard >=0.5.3' + - 'r-shinyfiles >=0.6.2' + - 'r-shinyjs >=0.7' + - 'r-stringr >=1.1.0' + run: + - 'bioconductor-clusterprofiler >=3.10.0,<3.11.0' + - 'bioconductor-elmer >=2.6.0,<2.7.0' + - 'bioconductor-illuminahumanmethylation27kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation27kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylation450kmanifest >=0.4.0,<0.5.0' + - 'bioconductor-illuminahumanmethylationepicanno.ilm10b2.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminahumanmethylationepicmanifest >=0.3.0,<0.4.0' + - 'bioconductor-maftools >=1.8.0,<1.9.0' + - 'bioconductor-minfi >=1.28.0,<1.29.0' + - 'bioconductor-pathview >=1.22.0,<1.23.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tcgabiolinks >=2.10.0,<2.11.0' + - 'bioconductor-tcgabiolinksgui.data >=1.2.0,<1.3.0' + - r-base + - r-caret + - r-colourpicker + - r-data.table + - 'r-downloader >=0.4' + - r-dt + - 'r-ggplot2 >=2.1.0' + - r-ggrepel + - r-plotly + - r-readr + - 'r-shiny >=0.14.1' + - 'r-shinybs >=0.61' + - 'r-shinydashboard >=0.5.3' + - 'r-shinyfiles >=0.6.2' + - 'r-shinyjs >=0.7' + - 'r-stringr >=1.1.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: '"TCGAbiolinksGUI: A Graphical User Interface to analyze cancer molecular and clinical data. A demo version of GUI is found in https://tcgabiolinksgui.shinyapps.io/tcgabiolinks/"' + diff --git a/recipes/bioconductor-tcgacrcmirna/meta.yaml b/recipes/bioconductor-tcgacrcmirna/meta.yaml new file mode 100644 index 0000000000000..d7f850593cf53 --- /dev/null +++ b/recipes/bioconductor-tcgacrcmirna/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "TCGAcrcmiRNA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 75d707e6d1c7feb9d4dfd5d6e62f9c3a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'colorectal cancer miRNA profile provided by TCGA' + diff --git a/recipes/bioconductor-tcgacrcmirna/post-link.sh b/recipes/bioconductor-tcgacrcmirna/post-link.sh new file mode 100644 index 0000000000000..fb226e8abee35 --- /dev/null +++ b/recipes/bioconductor-tcgacrcmirna/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TCGAcrcmiRNA_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAcrcmiRNA_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAcrcmiRNA_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmirna/bioconductor-tcgacrcmirna_1.2.0_src_all.tar.gz" +) +MD5="75d707e6d1c7feb9d4dfd5d6e62f9c3a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgacrcmirna/pre-unlink.sh b/recipes/bioconductor-tcgacrcmirna/pre-unlink.sh new file mode 100644 index 0000000000000..d1c90aa2cd9d7 --- /dev/null +++ b/recipes/bioconductor-tcgacrcmirna/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TCGAcrcmiRNA diff --git a/recipes/bioconductor-tcgacrcmrna/meta.yaml b/recipes/bioconductor-tcgacrcmrna/meta.yaml new file mode 100644 index 0000000000000..57acfef862434 --- /dev/null +++ b/recipes/bioconductor-tcgacrcmrna/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.2.0" %} +{% set name = "TCGAcrcmRNA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4d499e122eee3f40019b944889a63fe4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'colorectal cancer mRNA profile provided by TCGA' + diff --git a/recipes/bioconductor-tcgacrcmrna/post-link.sh b/recipes/bioconductor-tcgacrcmrna/post-link.sh new file mode 100644 index 0000000000000..b5abe21c42c1a --- /dev/null +++ b/recipes/bioconductor-tcgacrcmrna/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TCGAcrcmRNA_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAcrcmRNA_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAcrcmRNA_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgacrcmrna/bioconductor-tcgacrcmrna_1.2.0_src_all.tar.gz" +) +MD5="4d499e122eee3f40019b944889a63fe4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgacrcmrna/pre-unlink.sh b/recipes/bioconductor-tcgacrcmrna/pre-unlink.sh new file mode 100644 index 0000000000000..5c8bde4312004 --- /dev/null +++ b/recipes/bioconductor-tcgacrcmrna/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TCGAcrcmRNA diff --git a/recipes/bioconductor-tcgamethylation450k/meta.yaml b/recipes/bioconductor-tcgamethylation450k/meta.yaml new file mode 100644 index 0000000000000..ed92676c33c70 --- /dev/null +++ b/recipes/bioconductor-tcgamethylation450k/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "TCGAMethylation450k" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 71ce8ebbc5ddcf78fe3c6995ee2c64f5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'The Cancer Genome Atlas (TCGA) is applying genomics technologies to over 20 different types of cancer. This package contains a small set of 450k array data in idat format.' + diff --git a/recipes/bioconductor-tcgamethylation450k/post-link.sh b/recipes/bioconductor-tcgamethylation450k/post-link.sh new file mode 100644 index 0000000000000..7d5d3dcd1158f --- /dev/null +++ b/recipes/bioconductor-tcgamethylation450k/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TCGAMethylation450k_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAMethylation450k_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAMethylation450k_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgamethylation450k/bioconductor-tcgamethylation450k_1.18.0_src_all.tar.gz" +) +MD5="71ce8ebbc5ddcf78fe3c6995ee2c64f5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgamethylation450k/pre-unlink.sh b/recipes/bioconductor-tcgamethylation450k/pre-unlink.sh new file mode 100644 index 0000000000000..009f050c33541 --- /dev/null +++ b/recipes/bioconductor-tcgamethylation450k/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TCGAMethylation450k diff --git a/recipes/bioconductor-tcgautils/build.sh b/recipes/bioconductor-tcgautils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tcgautils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcgautils/meta.yaml b/recipes/bioconductor-tcgautils/meta.yaml new file mode 100644 index 0000000000000..0afd213ad4f68 --- /dev/null +++ b/recipes/bioconductor-tcgautils/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.2.1" %} +{% set name = "TCGAutils" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ded15c4190f16c090858878e53fab751 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, curatedTCGAData, devtools, impute, knitr, magrittr, mirbase.db, org.Hs.eg.db, readr, RTCGAToolbox (>= 2.7.5), testthat, TxDb.Hsapiens.UCSC.hg19.knownGene, +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rvest + - r-stringr + - r-xml2 + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicdatacommons >=1.6.0,<1.7.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-rvest + - r-stringr + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A suite of helper functions for checking and manipulating TCGA data including data obtained from the curatedTCGAData experiment package. These functions aim to simplify and make working with TCGA data more manageable.' + diff --git a/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml b/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml new file mode 100644 index 0000000000000..fb7688cbee2ee --- /dev/null +++ b/recipes/bioconductor-tcgawgbsdata.hg19/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "tcgaWGBSData.hg19" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e614d37504300366b89e08aae9d82902 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-knitr + run: + - 'bioconductor-bsseq >=1.18.0,<1.19.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - r-base + - r-knitr + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'Data package for WGBS Data in TCGA. Data is stored as SummarizedExperiment Format. See vignette on how to extract the data and perform differential methylation analysis.' + diff --git a/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh b/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh new file mode 100644 index 0000000000000..1afad2749d6b5 --- /dev/null +++ b/recipes/bioconductor-tcgawgbsdata.hg19/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tcgaWGBSData.hg19_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tcgaWGBSData.hg19_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/tcgaWGBSData.hg19_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgawgbsdata.hg19/bioconductor-tcgawgbsdata.hg19_1.0.0_src_all.tar.gz" +) +MD5="e614d37504300366b89e08aae9d82902" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgawgbsdata.hg19/pre-unlink.sh b/recipes/bioconductor-tcgawgbsdata.hg19/pre-unlink.sh new file mode 100644 index 0000000000000..3599d715e67d9 --- /dev/null +++ b/recipes/bioconductor-tcgawgbsdata.hg19/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tcgaWGBSData.hg19 diff --git a/recipes/bioconductor-tcgaworkflowdata/meta.yaml b/recipes/bioconductor-tcgaworkflowdata/meta.yaml new file mode 100644 index 0000000000000..bb1552eb7abd4 --- /dev/null +++ b/recipes/bioconductor-tcgaworkflowdata/meta.yaml @@ -0,0 +1,36 @@ +{% set version = "1.6.0" %} +{% set name = "TCGAWorkflowData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3c147bc7cf5ba811e359f12db8e7b42a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, pander, testthat +requirements: + host: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + run: + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This experimental data package contains 11 data sets necessary to follow the "TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages".' + diff --git a/recipes/bioconductor-tcgaworkflowdata/post-link.sh b/recipes/bioconductor-tcgaworkflowdata/post-link.sh new file mode 100644 index 0000000000000..cf88a138539df --- /dev/null +++ b/recipes/bioconductor-tcgaworkflowdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TCGAWorkflowData_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TCGAWorkflowData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/TCGAWorkflowData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tcgaworkflowdata/bioconductor-tcgaworkflowdata_1.6.0_src_all.tar.gz" +) +MD5="3c147bc7cf5ba811e359f12db8e7b42a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tcgaworkflowdata/pre-unlink.sh b/recipes/bioconductor-tcgaworkflowdata/pre-unlink.sh new file mode 100644 index 0000000000000..4ee424401adfa --- /dev/null +++ b/recipes/bioconductor-tcgaworkflowdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TCGAWorkflowData diff --git a/recipes/bioconductor-tcseq/build.sh b/recipes/bioconductor-tcseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tcseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tcseq/meta.yaml b/recipes/bioconductor-tcseq/meta.yaml new file mode 100644 index 0000000000000..abb0e960b3e88 --- /dev/null +++ b/recipes/bioconductor-tcseq/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.6.0" %} +{% set name = "TCseq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5300ccb82f5f6de70b89fa1b1a8cd01d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: testthat +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-e1071 + - r-ggplot2 + - r-locfit + - r-reshape2 + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-cluster + - r-e1071 + - r-ggplot2 + - r-locfit + - r-reshape2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of temporal patterns of time course data.' + diff --git a/recipes/bioconductor-tdaracne/build.sh b/recipes/bioconductor-tdaracne/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tdaracne/build.sh +++ b/recipes/bioconductor-tdaracne/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tdaracne/meta.yaml b/recipes/bioconductor-tdaracne/meta.yaml index 5ffbc48bbfc2d..07892dd058921 100644 --- a/recipes/bioconductor-tdaracne/meta.yaml +++ b/recipes/bioconductor-tdaracne/meta.yaml @@ -1,40 +1,46 @@ -{% set version = "1.30.0" %} +{% set version = "1.32.0" %} {% set name = "TDARACNE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e69fc502f8d3010247d0e455bfa5762a32c4642d13d473a6bf34a61332a1754d + md5: 5d2edadc66ee9cc1e3984fb1845314fb build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-genkern run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' - r-base - r-genkern test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 - summary: 'To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.' + summary: 'To infer gene networks from time-series measurements is a current challenge into bioinformatics research area. In order to detect dependencies between genes at different time delays, we propose an approach to infer gene regulatory networks from time-series measurements starting from a well known algorithm based on information theory. The proposed algorithm is expected to be useful in reconstruction of small biological directed networks from time course data.' extra: identifiers: - biotools:tdaracne - doi:10.1186/1471-2105-11-154 + parent_recipe: + name: bioconductor-tdaracne + path: recipes/bioconductor-tdaracne + version: 1.30.0 + diff --git a/recipes/bioconductor-tenxbraindata/meta.yaml b/recipes/bioconductor-tenxbraindata/meta.yaml new file mode 100644 index 0000000000000..1c587c5998fbb --- /dev/null +++ b/recipes/bioconductor-tenxbraindata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.2.0" %} +{% set name = "TENxBrainData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8f4e0317f3db09ed897fc30484e48115 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel, data.table +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'CC BY 4.0' + summary: 'Single-cell RNA-seq data for 1.3 million brain cells from E18 mice, generated by 10X Genomics.' + diff --git a/recipes/bioconductor-tenxbraindata/post-link.sh b/recipes/bioconductor-tenxbraindata/post-link.sh new file mode 100644 index 0000000000000..d64f3f7b7b21d --- /dev/null +++ b/recipes/bioconductor-tenxbraindata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TENxBrainData_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TENxBrainData_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/TENxBrainData_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tenxbraindata/bioconductor-tenxbraindata_1.2.0_src_all.tar.gz" +) +MD5="8f4e0317f3db09ed897fc30484e48115" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tenxbraindata/pre-unlink.sh b/recipes/bioconductor-tenxbraindata/pre-unlink.sh new file mode 100644 index 0000000000000..2d0d47641cc88 --- /dev/null +++ b/recipes/bioconductor-tenxbraindata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TENxBrainData diff --git a/recipes/bioconductor-tenxpbmcdata/meta.yaml b/recipes/bioconductor-tenxpbmcdata/meta.yaml new file mode 100644 index 0000000000000..757de2704bde7 --- /dev/null +++ b/recipes/bioconductor-tenxpbmcdata/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.0.0" %} +{% set name = "TENxPBMCData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 51a0e7d6a73413d7275fe368de4471bf +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, BiocStyle, snow, BiocFileCache, BiocParallel +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-experimenthub >=1.8.0,<1.9.0' + - 'bioconductor-hdf5array >=1.10.0,<1.11.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'CC BY 4.0' + summary: 'Single-cell RNA-seq data for on PBMC cells, generated by 10X Genomics.' + diff --git a/recipes/bioconductor-tenxpbmcdata/post-link.sh b/recipes/bioconductor-tenxpbmcdata/post-link.sh new file mode 100644 index 0000000000000..57618d3705910 --- /dev/null +++ b/recipes/bioconductor-tenxpbmcdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TENxPBMCData_1.0.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TENxPBMCData_1.0.0.tar.gz" + "https://bioarchive.galaxyproject.org/TENxPBMCData_1.0.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tenxpbmcdata/bioconductor-tenxpbmcdata_1.0.0_src_all.tar.gz" +) +MD5="51a0e7d6a73413d7275fe368de4471bf" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tenxpbmcdata/pre-unlink.sh b/recipes/bioconductor-tenxpbmcdata/pre-unlink.sh new file mode 100644 index 0000000000000..669a9b9ae458a --- /dev/null +++ b/recipes/bioconductor-tenxpbmcdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TENxPBMCData diff --git a/recipes/bioconductor-tenxplore/build.sh b/recipes/bioconductor-tenxplore/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tenxplore/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tenxplore/meta.yaml b/recipes/bioconductor-tenxplore/meta.yaml new file mode 100644 index 0000000000000..f43d8d8cdf4be --- /dev/null +++ b/recipes/bioconductor-tenxplore/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.4.0" %} +{% set name = "tenXplore" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 5976e4b5b299bcaebe96b3d2e9d3bd21 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: org.Hs.eg.db, testthat, knitr +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-ontoproc >=1.4.0,<1.5.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-restfulse >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-matrixstats + - r-shiny + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-ontoproc >=1.4.0,<1.5.0' + - 'bioconductor-org.mm.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-restfulse >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-matrixstats + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Perform ontological exploration of scRNA-seq of 1.3 million mouse neurons from 10x genomics.' + diff --git a/recipes/bioconductor-teqc/build.sh b/recipes/bioconductor-teqc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-teqc/build.sh +++ b/recipes/bioconductor-teqc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-teqc/meta.yaml b/recipes/bioconductor-teqc/meta.yaml index 33a6167550d35..badfe451541e4 100644 --- a/recipes/bioconductor-teqc/meta.yaml +++ b/recipes/bioconductor-teqc/meta.yaml @@ -1,44 +1,50 @@ -{% set version = "4.2.0" %} +{% set version = "4.4.0" %} {% set name = "TEQC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5266dd24cf9da014c564eb510f06a7a65efc9c83d76cfa143f92a5b80eaefb69 + md5: 85ceae4d51ead9716d90df8bc38e60a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-hwriter run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' - r-base - r-hwriter test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Target capture experiments combine hybridization-based (in solution or on microarrays) capture and enrichment of genomic regions of interest (e.g. the exome) with high throughput sequencing of the captured DNA fragments. This package provides functionalities for assessing and visualizing the quality of the target enrichment process, like specificity and sensitivity of the capture, per-target read coverage and so on.' extra: identifiers: - biotools:teqc - doi:10.1093/bioinformatics/btr122 + parent_recipe: + name: bioconductor-teqc + path: recipes/bioconductor-teqc + version: 4.2.0 + diff --git a/recipes/bioconductor-ternarynet/build.sh b/recipes/bioconductor-ternarynet/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-ternarynet/build.sh +++ b/recipes/bioconductor-ternarynet/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ternarynet/meta.yaml b/recipes/bioconductor-ternarynet/meta.yaml index b101bb94d691d..3ef2b456ffa54 100644 --- a/recipes/bioconductor-ternarynet/meta.yaml +++ b/recipes/bioconductor-ternarynet/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "ternarynet" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a13713ab4400a022d71ea22afb03893270742257367c0412a3bba59a39dbd4f7 + md5: fcc0042c1e0dbfc502572cd0f4b0a3cf build: number: 0 rpaths: @@ -31,9 +31,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'A computational Bayesian approach to ternary gene regulatory network estimation from gene perturbation experiments.' extra: identifiers: - biotools:ternarynet + parent_recipe: + name: bioconductor-ternarynet + path: recipes/bioconductor-ternarynet + version: 1.24.0 + diff --git a/recipes/bioconductor-test1cdf/meta.yaml b/recipes/bioconductor-test1cdf/meta.yaml new file mode 100644 index 0000000000000..5ee70a1d59358 --- /dev/null +++ b/recipes/bioconductor-test1cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "test1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8c94708b49ccc7bbf127485155970b9b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Test1.CDF file.' + diff --git a/recipes/bioconductor-test1cdf/post-link.sh b/recipes/bioconductor-test1cdf/post-link.sh new file mode 100644 index 0000000000000..3df39556854dc --- /dev/null +++ b/recipes/bioconductor-test1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="test1cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test1cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/test1cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test1cdf/bioconductor-test1cdf_2.18.0_src_all.tar.gz" +) +MD5="8c94708b49ccc7bbf127485155970b9b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-test1cdf/pre-unlink.sh b/recipes/bioconductor-test1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..5ec909ee1848c --- /dev/null +++ b/recipes/bioconductor-test1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ test1cdf diff --git a/recipes/bioconductor-test2cdf/meta.yaml b/recipes/bioconductor-test2cdf/meta.yaml new file mode 100644 index 0000000000000..4c0ec817e77ed --- /dev/null +++ b/recipes/bioconductor-test2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "test2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0d1c20d6450dfc83d62214be9dc46b5f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Test2.CDF file.' + diff --git a/recipes/bioconductor-test2cdf/post-link.sh b/recipes/bioconductor-test2cdf/post-link.sh new file mode 100644 index 0000000000000..91cb0cde4abf5 --- /dev/null +++ b/recipes/bioconductor-test2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="test2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/test2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test2cdf/bioconductor-test2cdf_2.18.0_src_all.tar.gz" +) +MD5="0d1c20d6450dfc83d62214be9dc46b5f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-test2cdf/pre-unlink.sh b/recipes/bioconductor-test2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..871fa8e13cd3a --- /dev/null +++ b/recipes/bioconductor-test2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ test2cdf diff --git a/recipes/bioconductor-test3cdf/meta.yaml b/recipes/bioconductor-test3cdf/meta.yaml new file mode 100644 index 0000000000000..772f1fe5d93fc --- /dev/null +++ b/recipes/bioconductor-test3cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "test3cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9904e7fa6599f68400a9b77d0caa159a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Test3.CDF file.' + diff --git a/recipes/bioconductor-test3cdf/post-link.sh b/recipes/bioconductor-test3cdf/post-link.sh new file mode 100644 index 0000000000000..512f346fe8dd7 --- /dev/null +++ b/recipes/bioconductor-test3cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="test3cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test3cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/test3cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test3cdf/bioconductor-test3cdf_2.18.0_src_all.tar.gz" +) +MD5="9904e7fa6599f68400a9b77d0caa159a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-test3cdf/pre-unlink.sh b/recipes/bioconductor-test3cdf/pre-unlink.sh new file mode 100644 index 0000000000000..ef74d42d28686 --- /dev/null +++ b/recipes/bioconductor-test3cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ test3cdf diff --git a/recipes/bioconductor-test3probe/meta.yaml b/recipes/bioconductor-test3probe/meta.yaml new file mode 100644 index 0000000000000..692d25074314a --- /dev/null +++ b/recipes/bioconductor-test3probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "test3probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ffcbfee4e5c486fd03b2b9b64820340c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Test3\_probe\_tab.' + diff --git a/recipes/bioconductor-test3probe/post-link.sh b/recipes/bioconductor-test3probe/post-link.sh new file mode 100644 index 0000000000000..7a23e0098c7a7 --- /dev/null +++ b/recipes/bioconductor-test3probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="test3probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/test3probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/test3probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-test3probe/bioconductor-test3probe_2.18.0_src_all.tar.gz" +) +MD5="ffcbfee4e5c486fd03b2b9b64820340c" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-test3probe/pre-unlink.sh b/recipes/bioconductor-test3probe/pre-unlink.sh new file mode 100644 index 0000000000000..b81bfd89823d8 --- /dev/null +++ b/recipes/bioconductor-test3probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ test3probe diff --git a/recipes/bioconductor-tfarm/build.sh b/recipes/bioconductor-tfarm/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tfarm/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tfarm/meta.yaml b/recipes/bioconductor-tfarm/meta.yaml new file mode 100644 index 0000000000000..58988e1ce47ac --- /dev/null +++ b/recipes/bioconductor-tfarm/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.4.0" %} +{% set name = "TFARM" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: de70bbb6c08b094687d9a0c8c1b80307 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, plyr +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-arules + - r-base + - r-fields + - r-stringr + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-arules + - r-base + - r-fields + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'It searches for relevant associations of transcription factors with a transcription factor target, in specific genomic regions. It also allows to evaluate the Importance Index distribution of transcription factors (and combinations of transcription factors) in association rules.' + diff --git a/recipes/bioconductor-tfbstools/build.sh b/recipes/bioconductor-tfbstools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tfbstools/build.sh +++ b/recipes/bioconductor-tfbstools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tfbstools/meta.yaml b/recipes/bioconductor-tfbstools/meta.yaml index d6a9992a9b727..7409bf5ce3c1d 100644 --- a/recipes/bioconductor-tfbstools/meta.yaml +++ b/recipes/bioconductor-tfbstools/meta.yaml @@ -1,37 +1,38 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TFBSTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: d15e80f4ab53ffe240b52a64cf00b82895bb6f9e8d414741fc07364c9ebb6bb8 + md5: e3c9e0fb66c9e32d883aaa5f22d86201 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle(>= 1.7.7), JASPAR2014(>= 1.4.0), knitr(>= 1.11), testthat, JASPAR2016(>= 1.0.0) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-cner >=1.16.1,<1.18.0' - - 'bioconductor-dirichletmultinomial >=1.22.0,<1.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-cner >=1.18.0,<1.19.0' + - 'bioconductor-dirichletmultinomial >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -40,20 +41,20 @@ requirements: - 'r-tfmpvalue >=0.0.5' - 'r-xml >=3.98-1.3' run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-cner >=1.16.1,<1.18.0' - - 'bioconductor-dirichletmultinomial >=1.22.0,<1.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-seqlogo >=1.46.0,<1.48.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-cner >=1.18.0,<1.19.0' + - 'bioconductor-dirichletmultinomial >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-seqlogo >=1.48.0,<1.49.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - 'r-catools >=1.17.1' - 'r-dbi >=0.6' @@ -68,9 +69,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.' extra: identifiers: - biotools:tfbstools + parent_recipe: + name: bioconductor-tfbstools + path: recipes/bioconductor-tfbstools + version: 1.18.0 + diff --git a/recipes/bioconductor-tfea.chip/build.sh b/recipes/bioconductor-tfea.chip/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tfea.chip/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tfea.chip/meta.yaml b/recipes/bioconductor-tfea.chip/meta.yaml new file mode 100644 index 0000000000000..b4587dfe23484 --- /dev/null +++ b/recipes/bioconductor-tfea.chip/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.2.0" %} +{% set name = "TFEA.ChIP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e7211803be520d45c2f1051aa1164482 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, S4Vectors, plotly, scales, tidyr, ggplot2, GSEABase, DESeq2, BiocGenerics +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - r-base + - r-dplyr + - r-r.utils + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - r-base + - r-dplyr + - r-r.utils +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package to analize transcription factor enrichment in a gene set using data from ChIP-Seq experiments.' + diff --git a/recipes/bioconductor-tfhaz/build.sh b/recipes/bioconductor-tfhaz/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tfhaz/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tfhaz/meta.yaml b/recipes/bioconductor-tfhaz/meta.yaml new file mode 100644 index 0000000000000..5c47b8284f660 --- /dev/null +++ b/recipes/bioconductor-tfhaz/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.4.0" %} +{% set name = "TFHAZ" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b2e9eef46b67621c17b58309ff630b22 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'It finds trascription factor (TF) high accumulation DNA zones, i.e., regions along the genome where there is a high presence of different transcription factors. Starting from a dataset containing the genomic positions of TF binding regions, for each base of the selected chromosome the accumulation of TFs is computed. Three different types of accumulation (TF, region and base accumulation) are available, together with the possibility of considering, in the single base accumulation computing, the TFs present not only in that single base, but also in its neighborhood, within a window of a given width. Two different methods for the search of TF high accumulation DNA zones, called "binding regions" and "overlaps", are available. In addition, some functions are provided in order to analyze, visualize and compare results obtained with different input parameters.' + diff --git a/recipes/bioconductor-tfutils/build.sh b/recipes/bioconductor-tfutils/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tfutils/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tfutils/meta.yaml b/recipes/bioconductor-tfutils/meta.yaml new file mode 100644 index 0000000000000..04fa46c734466 --- /dev/null +++ b/recipes/bioconductor-tfutils/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.2.0" %} +{% set name = "TFutils" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f8cdec899590e3cd9198bd3e63c27d01 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, data.table, GSEABase, testthat, AnnotationDbi, AnnotationFilter, Biobase, GenomicFeatures, GenomicRanges, Gviz, IRanges, Rsamtools, S4Vectors, org.Hs.eg.db, EnsDb.Hsapiens.v75, BiocParallel, BiocStyle, GO.db, GenomicFiles, GenomeInfoDb, SummarizedExperiment, UpSetR, ggplot2, png, gwascat +requirements: + host: + - r-base + - r-dplyr + - r-magrittr + - r-miniui + - r-shiny + run: + - r-base + - r-dplyr + - r-magrittr + - r-miniui + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Package to work with TF data.' + diff --git a/recipes/bioconductor-tigre/build.sh b/recipes/bioconductor-tigre/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tigre/build.sh +++ b/recipes/bioconductor-tigre/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tigre/meta.yaml b/recipes/bioconductor-tigre/meta.yaml index 49ea21d441d79..fb15aeeb75904 100644 --- a/recipes/bioconductor-tigre/meta.yaml +++ b/recipes/bioconductor-tigre/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.34.0" %} +{% set version = "1.36.0" %} {% set name = "tigre" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ce2d3f680a61019347c94d83e6f35826ee208505eaef7bd1faf72bca6e2b0a4b + md5: 96d6f5cdec071763b3695fab44ae87cb build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: drosgenome1.db, puma, lumi, BiocStyle, BiocManager requirements: host: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-dbi - r-gplots - r-rsqlite run: - - 'bioconductor-annotate >=1.58.0,<1.60.0' - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotate >=1.60.0,<1.61.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-dbi - r-gplots @@ -42,9 +43,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: AGPL-3 summary: 'The tigre package implements our methodology of Gaussian process differential equation models for analysis of gene expression time series from single input motif networks. The package can be used for inferring unobserved transcription factor (TF) protein concentrations from expression measurements of known target genes, or for ranking candidate targets of a TF.' extra: identifiers: - biotools:tigre + parent_recipe: + name: bioconductor-tigre + path: recipes/bioconductor-tigre + version: 1.34.0 + diff --git a/recipes/bioconductor-tilingarray/build.sh b/recipes/bioconductor-tilingarray/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tilingarray/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tilingarray/meta.yaml b/recipes/bioconductor-tilingarray/meta.yaml new file mode 100644 index 0000000000000..99bfcc26b88c1 --- /dev/null +++ b/recipes/bioconductor-tilingarray/meta.yaml @@ -0,0 +1,48 @@ +{% set version = "1.60.0" %} +{% set name = "tilingArray" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eae54973c3f6bd1f99ddb4df77d0377a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-pixmap + - r-rcolorbrewer + - r-strucchange + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' + - r-base + - r-pixmap + - r-rcolorbrewer + - r-strucchange + build: + - {{ compiler('c') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The package provides functionality that can be useful for the analysis of high-density tiling microarray data (such as from Affymetrix genechips) for measuring transcript abundance and architecture. The main functionalities of the package are: 1. the class ''segmentation'' for representing partitionings of a linear series of data; 2. the function ''segment'' for fitting piecewise constant models using a dynamic programming algorithm that is both fast and exact; 3. the function ''confint'' for calculating confidence intervals using the strucchange package; 4. the function ''plotAlongChrom'' for generating pretty plots; 5. the function ''normalizeByReference'' for probe-sequence dependent response adjustment from a (set of) reference hybridizations.' + diff --git a/recipes/bioconductor-timecourse/build.sh b/recipes/bioconductor-timecourse/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-timecourse/build.sh +++ b/recipes/bioconductor-timecourse/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-timecourse/meta.yaml b/recipes/bioconductor-timecourse/meta.yaml index c6a6d5a5ea2e6..1d0211b82203c 100644 --- a/recipes/bioconductor-timecourse/meta.yaml +++ b/recipes/bioconductor-timecourse/meta.yaml @@ -1,42 +1,48 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "timecourse" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a93caaa2e211c1ca0b51c8b691fd0d54a0d13b8d11517a7f4b5b425dbb782572 + md5: f951b9aa3b8398f16a99b0534c58c94f build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-mass run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-mass test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'Functions for data analysis and graphical displays for developmental microarray time course data.' extra: identifiers: - biotools:timecourse - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-timecourse + path: recipes/bioconductor-timecourse + version: 1.52.0 + diff --git a/recipes/bioconductor-timerquant/meta.yaml b/recipes/bioconductor-timerquant/meta.yaml new file mode 100644 index 0000000000000..1a5d03201edea --- /dev/null +++ b/recipes/bioconductor-timerquant/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "1.12.0" %} +{% set name = "TimerQuant" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6b6d3bd75b7a51740ede49802179a8e3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, reshape2, knitr, shinyBS +requirements: + host: + - r-base + - r-desolve + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-locfit + - r-shiny + run: + - r-base + - r-desolve + - r-dplyr + - r-ggplot2 + - r-gridextra + - r-locfit + - r-shiny + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Supplementary Data package for tandem timer methods paper by Barry et al. (2015) including TimerQuant shiny applications.' + diff --git a/recipes/bioconductor-timerquant/post-link.sh b/recipes/bioconductor-timerquant/post-link.sh new file mode 100644 index 0000000000000..d69dd6b8405c4 --- /dev/null +++ b/recipes/bioconductor-timerquant/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TimerQuant_1.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/TimerQuant_1.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/TimerQuant_1.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-timerquant/bioconductor-timerquant_1.12.0_src_all.tar.gz" +) +MD5="6b6d3bd75b7a51740ede49802179a8e3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-timerquant/pre-unlink.sh b/recipes/bioconductor-timerquant/pre-unlink.sh new file mode 100644 index 0000000000000..a8b56d0c69f0a --- /dev/null +++ b/recipes/bioconductor-timerquant/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TimerQuant diff --git a/recipes/bioconductor-timescape/build.sh b/recipes/bioconductor-timescape/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-timescape/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-timescape/meta.yaml b/recipes/bioconductor-timescape/meta.yaml new file mode 100644 index 0000000000000..ad57326f06681 --- /dev/null +++ b/recipes/bioconductor-timescape/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "1.6.0" %} +{% set name = "timescape" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 4559bf51a0edf576108683f5b8e96652 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - r-base + - 'r-dplyr >=0.4.3' + - 'r-gtools >=3.5.0' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-stringr >=1.0.0' + run: + - r-base + - 'r-dplyr >=0.4.3' + - 'r-gtools >=3.5.0' + - 'r-htmlwidgets >=0.5' + - 'r-jsonlite >=0.9.19' + - 'r-stringr >=1.0.0' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'TimeScape is an automated tool for navigating temporal clonal evolution data. The key attributes of this implementation involve the enumeration of clones, their evolutionary relationships and their shifting dynamics over time. TimeScape requires two inputs: (i) the clonal phylogeny and (ii) the clonal prevalences. Optionally, TimeScape accepts a data table of targeted mutations observed in each clone and their allele prevalences over time. The output is the TimeScape plot showing clonal prevalence vertically, time horizontally, and the plot height optionally encoding tumour volume during tumour-shrinking events. At each sampling time point (denoted by a faint white line), the height of each clone accurately reflects its proportionate prevalence. These prevalences form the anchors for bezier curves that visually represent the dynamic transitions between time points.' + diff --git a/recipes/bioconductor-timeseriesexperiment/build.sh b/recipes/bioconductor-timeseriesexperiment/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-timeseriesexperiment/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-timeseriesexperiment/meta.yaml b/recipes/bioconductor-timeseriesexperiment/meta.yaml new file mode 100644 index 0000000000000..c4891f04aab4b --- /dev/null +++ b/recipes/bioconductor-timeseriesexperiment/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "1.0.1" %} +{% set name = "TimeSeriesExperiment" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 86683c672fd6810957f14309b6bf092b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, BiocFileCache (>= 1.5.8), circlize, ComplexHeatmap, GO.db, grDevices, grid, knitr, org.Mm.eg.db, org.Hs.eg.db, MASS, RColorBrewer, rmarkdown, UpSetR, +requirements: + host: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-dynamictreecut + - 'r-ggplot2 >=3.0.0' + - r-hmisc + - r-magrittr + - r-proxy + - r-tibble + - r-tidyr + - r-vegan + - r-viridis + run: + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dplyr + - r-dynamictreecut + - 'r-ggplot2 >=3.0.0' + - r-hmisc + - r-magrittr + - r-proxy + - r-tibble + - r-tidyr + - r-vegan + - r-viridis +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'LGPL (>= 3)' + summary: 'Visualization and analysis toolbox for short time course data which includes dimensionality reduction, clustering, two-sample differential expression testing and gene ranking techniques. The package also provides methods for retrieving enriched pathways.' + diff --git a/recipes/bioconductor-tin/build.sh b/recipes/bioconductor-tin/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tin/build.sh +++ b/recipes/bioconductor-tin/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tin/meta.yaml b/recipes/bioconductor-tin/meta.yaml index e1dcb9f794391..a4f8840b38f6e 100644 --- a/recipes/bioconductor-tin/meta.yaml +++ b/recipes/bioconductor-tin/meta.yaml @@ -1,24 +1,26 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "TIN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ff3aa08c7673d3c45fc8926e07cdbef9ea518765171a6b5f5ed31c50c2dc291a + md5: 924d7dc26022c2ca5d9923d05de34c83 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, aroma.light, affxparser, RUnit, BiocGenerics requirements: host: - - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' - r-aroma.affymetrix - r-base - r-data.table @@ -26,7 +28,7 @@ requirements: - r-stringr - r-wgcna run: - - 'bioconductor-impute >=1.54.0,<1.56.0' + - 'bioconductor-impute >=1.56.0,<1.57.0' - r-aroma.affymetrix - r-base - r-data.table @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The TIN package implements a set of tools for transcriptome instability analysis based on exon expression profiles. Deviating exon usage is studied in the context of splicing factors to analyse to what degree transcriptome instability is correlated to splicing factor expression. In the transcriptome instability correlation analysis, the data is compared to both random permutations of alternative splicing scores and expression of random gene sets.' extra: identifiers: - biotools:tin - doi:10.4137/CIN.S31363 + parent_recipe: + name: bioconductor-tin + path: recipes/bioconductor-tin + version: 1.12.0 + diff --git a/recipes/bioconductor-tinesath1cdf/meta.yaml b/recipes/bioconductor-tinesath1cdf/meta.yaml new file mode 100644 index 0000000000000..38830397a9fe7 --- /dev/null +++ b/recipes/bioconductor-tinesath1cdf/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.20.0" %} +{% set name = "tinesath1cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 95e256c032576c0eb2eb21d479ae5e68 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A package containing an environment represeting the newcdf/tinesATH1.cdf.cdf file.' + diff --git a/recipes/bioconductor-tinesath1cdf/post-link.sh b/recipes/bioconductor-tinesath1cdf/post-link.sh new file mode 100644 index 0000000000000..11c278b350fd9 --- /dev/null +++ b/recipes/bioconductor-tinesath1cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tinesath1cdf_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tinesath1cdf_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/tinesath1cdf_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tinesath1cdf/bioconductor-tinesath1cdf_1.20.0_src_all.tar.gz" +) +MD5="95e256c032576c0eb2eb21d479ae5e68" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tinesath1cdf/pre-unlink.sh b/recipes/bioconductor-tinesath1cdf/pre-unlink.sh new file mode 100644 index 0000000000000..8e193c87a8557 --- /dev/null +++ b/recipes/bioconductor-tinesath1cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tinesath1cdf diff --git a/recipes/bioconductor-tinesath1probe/meta.yaml b/recipes/bioconductor-tinesath1probe/meta.yaml new file mode 100644 index 0000000000000..702c850aa16b8 --- /dev/null +++ b/recipes/bioconductor-tinesath1probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "tinesath1probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8c43dc2ede1e42e22779059c5a6925f0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package matchprobes version 1.4.0. The probe sequence data was obtained from http://www.affymetrix.com.' + diff --git a/recipes/bioconductor-tinesath1probe/post-link.sh b/recipes/bioconductor-tinesath1probe/post-link.sh new file mode 100644 index 0000000000000..31a46c0611e14 --- /dev/null +++ b/recipes/bioconductor-tinesath1probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tinesath1probe_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tinesath1probe_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/tinesath1probe_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tinesath1probe/bioconductor-tinesath1probe_1.20.0_src_all.tar.gz" +) +MD5="8c43dc2ede1e42e22779059c5a6925f0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tinesath1probe/pre-unlink.sh b/recipes/bioconductor-tinesath1probe/pre-unlink.sh new file mode 100644 index 0000000000000..c268eadef0712 --- /dev/null +++ b/recipes/bioconductor-tinesath1probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tinesath1probe diff --git a/recipes/bioconductor-tissueenrich/build.sh b/recipes/bioconductor-tissueenrich/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tissueenrich/build.sh +++ b/recipes/bioconductor-tissueenrich/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tissueenrich/conda_build_config.yaml b/recipes/bioconductor-tissueenrich/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-tissueenrich/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-tissueenrich/meta.yaml b/recipes/bioconductor-tissueenrich/meta.yaml index ee1dfab840e01..64e3abdb956dd 100644 --- a/recipes/bioconductor-tissueenrich/meta.yaml +++ b/recipes/bioconductor-tissueenrich/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.0.7" %} +{% set version = "1.2.0" %} {% set name = "TissueEnrich" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c910cdf72450093540ea05ed7bdd95733812ca18103f68f21c56f7496669e314 + md5: ad8ab5d572c9104d55e51de7aff80554 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat requirements: host: - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' - 'r-ggplot2 >=2.2.1' - 'r-tidyr >=0.8.0' run: - - 'bioconductor-gseabase >=1.42.0,<1.44.0' - - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + - 'bioconductor-gseabase >=1.44.0,<1.45.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - 'r-dplyr >=0.7.3' - 'r-ensurer >=1.1.0' @@ -37,6 +39,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'MIT + file LICENSE' summary: 'The TissueEnrich package is used to calculate enrichment of tissue-specific genes in a set of input genes. For example, the user can input the most highly expressed genes from RNA-Seq data, or gene co-expression modules to determine which tissue-specific genes are enriched in those datasets. Tissue-specific genes were defined by processing RNA-Seq data from the Human Protein Atlas (HPA) (Uhlén et al. 2015), GTEx (Ardlie et al. 2015), and mouse ENCODE (Shen et al. 2012) using the algorithm from the HPA (Uhlén et al. 2015).The hypergeometric test is being used to determine if the tissue-specific genes are enriched among the input genes. Along with tissue-specific gene enrichment, the TissueEnrich package can also be used to define tissue-specific genes from expression datasets provided by the user, which can then be used to calculate tissue-specific gene enrichments.' +extra: + parent_recipe: + name: bioconductor-tissueenrich + path: recipes/bioconductor-tissueenrich + version: 1.0.7 + diff --git a/recipes/bioconductor-tissuetreg/meta.yaml b/recipes/bioconductor-tissuetreg/meta.yaml new file mode 100644 index 0000000000000..f642ded770d16 --- /dev/null +++ b/recipes/bioconductor-tissuetreg/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "tissueTreg" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 36f57ef9bb4affda62e679798e2fca58 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, ExperimentHub, bsseq, SummarizedExperiment +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'The package provides ready to use epigenomes (obtained from TWGBS) and transcriptomes (RNA-seq) from various tissues as obtained in the study (Delacher and Imbusch 2017, PMID: 28783152). Regulatory T cells (Treg cells) perform two distinct functions: they maintain self-tolerance, and they support organ homeostasis by differentiating into specialized tissue Treg cells. The underlying dataset characterises the epigenetic and transcriptomic modifications for specialized tissue Treg cells.' + diff --git a/recipes/bioconductor-tissuetreg/post-link.sh b/recipes/bioconductor-tissuetreg/post-link.sh new file mode 100644 index 0000000000000..87f6e6d8d6ea5 --- /dev/null +++ b/recipes/bioconductor-tissuetreg/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tissueTreg_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tissueTreg_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/tissueTreg_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tissuetreg/bioconductor-tissuetreg_1.2.0_src_all.tar.gz" +) +MD5="36f57ef9bb4affda62e679798e2fca58" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tissuetreg/pre-unlink.sh b/recipes/bioconductor-tissuetreg/pre-unlink.sh new file mode 100644 index 0000000000000..3a9b260ea5ca1 --- /dev/null +++ b/recipes/bioconductor-tissuetreg/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tissueTreg diff --git a/recipes/bioconductor-titancna/build.sh b/recipes/bioconductor-titancna/build.sh index 3deb50a9e84ed..c1d13421f5f1e 100644 --- a/recipes/bioconductor-titancna/build.sh +++ b/recipes/bioconductor-titancna/build.sh @@ -1,22 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION -$R CMD INSTALL --build . - -outdir=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM -mkdir -p $outdir/scripts/R_scripts -mkdir -p $outdir/data -mkdir -p $PREFIX/bin - -perl -pi -e 'print "#!/opt/anaconda1anaconda2anaconda3/bin/Rscript\n" if $. == 1' scripts/R_scripts/selectSolution.R -sed -i.bak 's:/usr/bin/env Rscript:/opt/anaconda1anaconda2anaconda3/bin/Rscript:' scripts/R_scripts/titanCNA.R - -mv scripts/R_scripts/selectSolution.R $outdir/scripts/R_scripts/titanCNA_selectSolution.R -mv scripts/R_scripts/titanCNA.R $outdir/scripts/R_scripts/titanCNA.R - -chmod a+x $outdir/scripts/R_scripts/*.R -ln -s $outdir/scripts/R_scripts/titanCNA.R $PREFIX/bin -ln -s $outdir/scripts/R_scripts/titanCNA_selectSolution.R $PREFIX/bin - -# Retrieve external data we want to link into the run -wget --no-check-certificate -O $outdir/data/cytoBand_hg38.txt https://raw.githubusercontent.com/broadinstitute/ichorCNA/master/inst/extdata/cytoBand_hg38.txt +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-titancna/meta.yaml b/recipes/bioconductor-titancna/meta.yaml index 78f67541c81fa..4bf930561c487 100644 --- a/recipes/bioconductor-titancna/meta.yaml +++ b/recipes/bioconductor-titancna/meta.yaml @@ -1,64 +1,57 @@ -{% set version="1.19.1" %} -{% set name="TitanCNA" %} -{% set bioc="3.6" %} +{% set version = "1.20.0" %} +{% set name = "TitanCNA" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: - url: https://github.com/gavinha/TitanCNA/archive/e214ca3.tar.gz - # - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - # - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - # - 'https://depot.galaxyproject.org/software/{{ name }}/{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 990137a1b3ae6c6a94fb3ee7735171188393b34006d5053f6eb9746ea47ee82a + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2b7d63323a87458c78e13a26ea6f5f6b build: - number: 4 + number: 0 rpaths: - lib/R/lib/ - lib/ requirements: host: - - r-base 3.4.1 - - perl # for adding in correct path references to scripts - - 'bioconductor-genomeinfodb >=1.8.7' - - 'bioconductor-genomicranges >=1.24.3' - - 'bioconductor-iranges >=2.6.1' - - 'bioconductor-rsamtools >=1.20.4' - - 'bioconductor-variantannotation >=1.18.7' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.5.0' - 'r-foreach >=1.4.3' - - r-data.table - - r-dplyr - - r-optparse - - r-domc - - bioconductor-snpchip - - r-stringr run: - - r-base 3.4.1 - - 'bioconductor-genomeinfodb >=1.8.7' - - 'bioconductor-genomicranges >=1.24.3' - - 'bioconductor-iranges >=2.6.1' - - 'bioconductor-rsamtools >=1.24.0' - - 'bioconductor-variantannotation >=1.18.7' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - 'r-data.table >=1.10.4' + - 'r-dplyr >=0.5.0' - 'r-foreach >=1.4.3' - - r-data.table - - r-dplyr - - r-optparse - - r-domc - - bioconductor-snpchip - - r-stringr build: - {{ compiler('c') }} - make test: commands: - '$R -e "library(''{{ name }}'')"' - - titanCNA.R -h 2>&1 | grep Usage - - titanCNA_selectSolution.R -h 2>&1 | grep Usage about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Hidden Markov model to segment and predict regions of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH), and estimate cellular prevalenece of clonal clusters in tumour whole genome sequencing data.' - extra: identifiers: - biotools:titancna + parent_recipe: + name: bioconductor-titancna + path: recipes/bioconductor-titancna + version: 1.19.1 + diff --git a/recipes/bioconductor-tkwidgets/build.sh b/recipes/bioconductor-tkwidgets/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tkwidgets/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tkwidgets/meta.yaml b/recipes/bioconductor-tkwidgets/meta.yaml new file mode 100644 index 0000000000000..0335f3eaa14dd --- /dev/null +++ b/recipes/bioconductor-tkwidgets/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "1.60.0" %} +{% set name = "tkWidgets" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 0e005bd310c9b2eceacac768781a3a61 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, hgu95av2 +requirements: + host: + - 'bioconductor-dyndoc >=1.60.0,<1.61.0' + - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - r-base + run: + - 'bioconductor-dyndoc >=1.60.0,<1.61.0' + - 'bioconductor-widgettools >=1.60.0,<1.61.0' + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Widgets to provide user interfaces. tcltk should have been installed for the widgets to run.' + diff --git a/recipes/bioconductor-tmixclust/build.sh b/recipes/bioconductor-tmixclust/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tmixclust/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tmixclust/meta.yaml b/recipes/bioconductor-tmixclust/meta.yaml new file mode 100644 index 0000000000000..1e89ce63f6e66 --- /dev/null +++ b/recipes/bioconductor-tmixclust/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.4.0" %} +{% set name = "TMixClust" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 60760731b1fdae8cf110d2407173bdb5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: rmarkdown, knitr, BiocStyle, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-spem >=1.22.0,<1.23.0' + - r-base + - r-cluster + - r-flexclust + - r-gss + - r-mvtnorm + - r-zoo + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-spem >=1.22.0,<1.23.0' + - r-base + - r-cluster + - r-flexclust + - r-gss + - r-mvtnorm + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'Implementation of a clustering method for time series gene expression data based on mixed-effects models with Gaussian variables and non-parametric cubic splines estimation. The method can robustly account for the high levels of noise present in typical gene expression time series datasets.' + diff --git a/recipes/bioconductor-tnt/build.sh b/recipes/bioconductor-tnt/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tnt/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tnt/meta.yaml b/recipes/bioconductor-tnt/meta.yaml new file mode 100644 index 0000000000000..200b18bd17748 --- /dev/null +++ b/recipes/bioconductor-tnt/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.0" %} +{% set name = "TnT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: fe8a6e7598825b862f8fcba6bddebc71 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: GenomicFeatures, shiny, BiocManager, rmarkdown, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-htmlwidgets + - r-jsonlite + - r-knitr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-data.table + - r-htmlwidgets + - r-jsonlite + - r-knitr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'A R interface to the TnT javascript library (https://github.com/ tntvis) to provide interactive and flexible visualization of track-based genomic data.' + diff --git a/recipes/bioconductor-tofsims/build.sh b/recipes/bioconductor-tofsims/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tofsims/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tofsims/meta.yaml b/recipes/bioconductor-tofsims/meta.yaml new file mode 100644 index 0000000000000..a651ed8a36413 --- /dev/null +++ b/recipes/bioconductor-tofsims/meta.yaml @@ -0,0 +1,50 @@ +{% set version = "1.10.0" %} +{% set name = "tofsims" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c1f09ed1514f7979856ee3dab059a9cc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: EBImage, knitr, rmarkdown, testthat, tofsimsData, BiocParallel, RColorBrewer +requirements: + host: + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - r-als + - r-base + - r-chemometricswithr + - r-kernsmooth + - 'r-rcpp >=0.11.2' + - r-rcpparmadillo + - r-signal + run: + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - r-als + - r-base + - r-chemometricswithr + - r-kernsmooth + - 'r-rcpp >=0.11.2' + - r-rcpparmadillo + - r-signal + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'This packages offers a pipeline for import, processing and analysis of ToF-SIMS 2D image data. Import of Iontof and Ulvac-Phi raw or preprocessed data is supported. For rawdata, mass calibration, peak picking and peak integration exist. General funcionality includes data binning, scaling, image subsetting and visualization. A range of multivariate tools common in the ToF-SIMS community are implemented (PCA, MCR, MAF, MNF). An interface to the bioconductor image processing package EBImage offers image segmentation functionality.' + diff --git a/recipes/bioconductor-tofsimsdata/meta.yaml b/recipes/bioconductor-tofsimsdata/meta.yaml new file mode 100644 index 0000000000000..031f0fbcb6a9d --- /dev/null +++ b/recipes/bioconductor-tofsimsdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "tofsimsData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 545622a01ba2067b1cf805f07367a83a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, tools +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-3 + summary: 'This packages contains data to be used with the ''tofsims'' package.' + diff --git a/recipes/bioconductor-tofsimsdata/post-link.sh b/recipes/bioconductor-tofsimsdata/post-link.sh new file mode 100644 index 0000000000000..4c5ae5383dd65 --- /dev/null +++ b/recipes/bioconductor-tofsimsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tofsimsData_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tofsimsData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/tofsimsData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tofsimsdata/bioconductor-tofsimsdata_1.10.0_src_all.tar.gz" +) +MD5="545622a01ba2067b1cf805f07367a83a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tofsimsdata/pre-unlink.sh b/recipes/bioconductor-tofsimsdata/pre-unlink.sh new file mode 100644 index 0000000000000..1918835a11f79 --- /dev/null +++ b/recipes/bioconductor-tofsimsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tofsimsData diff --git a/recipes/bioconductor-tomatocdf/meta.yaml b/recipes/bioconductor-tomatocdf/meta.yaml new file mode 100644 index 0000000000000..32c723882b20a --- /dev/null +++ b/recipes/bioconductor-tomatocdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "tomatocdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 200efc0637788d4bd3263fc9183c1aa6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Tomato.cdf file.' + diff --git a/recipes/bioconductor-tomatocdf/post-link.sh b/recipes/bioconductor-tomatocdf/post-link.sh new file mode 100644 index 0000000000000..3fbf46a056613 --- /dev/null +++ b/recipes/bioconductor-tomatocdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tomatocdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/tomatocdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/tomatocdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tomatocdf/bioconductor-tomatocdf_2.18.0_src_all.tar.gz" +) +MD5="200efc0637788d4bd3263fc9183c1aa6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tomatocdf/pre-unlink.sh b/recipes/bioconductor-tomatocdf/pre-unlink.sh new file mode 100644 index 0000000000000..e226287e9808b --- /dev/null +++ b/recipes/bioconductor-tomatocdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tomatocdf diff --git a/recipes/bioconductor-tomatoprobe/meta.yaml b/recipes/bioconductor-tomatoprobe/meta.yaml new file mode 100644 index 0000000000000..bb918297ca172 --- /dev/null +++ b/recipes/bioconductor-tomatoprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "tomatoprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 72020469f35c19399fd0be9eaffd8e77 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Tomato\_probe\_tab.' + diff --git a/recipes/bioconductor-tomatoprobe/post-link.sh b/recipes/bioconductor-tomatoprobe/post-link.sh new file mode 100644 index 0000000000000..1755656e9498a --- /dev/null +++ b/recipes/bioconductor-tomatoprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tomatoprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/tomatoprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/tomatoprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tomatoprobe/bioconductor-tomatoprobe_2.18.0_src_all.tar.gz" +) +MD5="72020469f35c19399fd0be9eaffd8e77" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tomatoprobe/pre-unlink.sh b/recipes/bioconductor-tomatoprobe/pre-unlink.sh new file mode 100644 index 0000000000000..3a7a96f51dfc0 --- /dev/null +++ b/recipes/bioconductor-tomatoprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tomatoprobe diff --git a/recipes/bioconductor-topaseq/build.sh b/recipes/bioconductor-topaseq/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-topaseq/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-topaseq/meta.yaml b/recipes/bioconductor-topaseq/meta.yaml new file mode 100644 index 0000000000000..e8dfc81a7a1a1 --- /dev/null +++ b/recipes/bioconductor-topaseq/meta.yaml @@ -0,0 +1,42 @@ +{% set version = "1.16.0" %} +{% set name = "ToPASeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8282cfb442516b8e14e2b6a62c525a1d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: BiocStyle, EnrichmentBrowser, airway, knitr, rmarkdown +requirements: + host: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - r-base + - r-rcpp + run: + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-graphite >=1.28.0,<1.29.0' + - r-base + - r-rcpp + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: AGPL-3 + summary: 'Implementation of methods for topology-based pathway analysis of RNA-seq data. This includes Topological Analysis of Pathway Phenotype Association (TAPPA; Gao and Wang, 2007), PathWay Enrichment Analysis (PWEA; Hung et al., 2010), and the Pathway Regulation Score (PRS; Ibrahim et al., 2012).' + diff --git a/recipes/bioconductor-topdownr/build.sh b/recipes/bioconductor-topdownr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-topdownr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-topdownr/meta.yaml b/recipes/bioconductor-topdownr/meta.yaml new file mode 100644 index 0000000000000..3a3c131d7c491 --- /dev/null +++ b/recipes/bioconductor-topdownr/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.0" %} +{% set name = "topdownr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ea19cef97df4e5a6b9be320a8796e41a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: topdownrdata (>= 0.2), knitr, ranger, testthat, BiocStyle +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - 'r-matrix >=1.2.10' + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - 'r-ggplot2 >=2.2.1' + - 'r-matrix >=1.2.10' +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'The topdownr package allows automatic and systemic investigation of fragment conditions. It creates Thermo Orbitrap Fusion Lumos method files to test hundreds of fragmentation conditions. Additionally it provides functions to analyse and process the generated MS data and determine the best conditions to maximise overall fragment coverage.' + diff --git a/recipes/bioconductor-topdownrdata/meta.yaml b/recipes/bioconductor-topdownrdata/meta.yaml new file mode 100644 index 0000000000000..83730fe5c2441 --- /dev/null +++ b/recipes/bioconductor-topdownrdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.4.0" %} +{% set name = "topdownrdata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2e25621bd796b78859795b7f5158a289 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-topdownr >=1.4.0,<1.5.0' + - r-base + run: + - 'bioconductor-topdownr >=1.4.0,<1.5.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 3)' + summary: 'Example data for the topdownr package generated on a Thermo Orbitrap Fusion Lumos MS device.' + diff --git a/recipes/bioconductor-topdownrdata/post-link.sh b/recipes/bioconductor-topdownrdata/post-link.sh new file mode 100644 index 0000000000000..8a905529e3e13 --- /dev/null +++ b/recipes/bioconductor-topdownrdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="topdownrdata_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/topdownrdata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/topdownrdata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-topdownrdata/bioconductor-topdownrdata_1.4.0_src_all.tar.gz" +) +MD5="2e25621bd796b78859795b7f5158a289" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-topdownrdata/pre-unlink.sh b/recipes/bioconductor-topdownrdata/pre-unlink.sh new file mode 100644 index 0000000000000..ac424577595e5 --- /dev/null +++ b/recipes/bioconductor-topdownrdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ topdownrdata diff --git a/recipes/bioconductor-topgo/build.sh b/recipes/bioconductor-topgo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-topgo/build.sh +++ b/recipes/bioconductor-topgo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-topgo/meta.yaml b/recipes/bioconductor-topgo/meta.yaml index 194350d0528f9..36e71c90000c4 100644 --- a/recipes/bioconductor-topgo/meta.yaml +++ b/recipes/bioconductor-topgo/meta.yaml @@ -1,39 +1,41 @@ -{% set version = "2.32.0" %} +{% set version = "2.34.0" %} {% set name = "topGO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 81f758e507ac28ec341ecad1a8d67e50b6619e4b2e8254274dfc2dd4e2b4dd17 + md5: c46fdfda730504443c46c4b4bed95f00 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ALL, hgu95av2.db, hgu133a.db, genefilter, xtable, multtest, Rgraphviz, globaltest requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-dbi - r-lattice - r-matrixstats - 'r-sparsem >=0.73' run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-go.db >=3.6.0,<3.8.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-go.db >=3.7.0,<3.8.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - r-dbi - r-lattice @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'topGO package provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.' extra: identifiers: - biotools:topgo - doi:10.1093/bioinformatics/btl140 + parent_recipe: + name: bioconductor-topgo + path: recipes/bioconductor-topgo + version: 2.32.0 + diff --git a/recipes/bioconductor-tpp/build.sh b/recipes/bioconductor-tpp/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tpp/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tpp/meta.yaml b/recipes/bioconductor-tpp/meta.yaml new file mode 100644 index 0000000000000..444b6ab587fa9 --- /dev/null +++ b/recipes/bioconductor-tpp/meta.yaml @@ -0,0 +1,89 @@ +{% set version = "3.10.0" %} +{% set name = "TPP" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 12ade25322bf55da53207f15265802b8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobroom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-broom + - r-data.table + - r-doparallel + - r-dplyr + - r-foreach + - r-futile.logger + - r-ggplot2 + - r-gridextra + - r-knitr + - r-magrittr + - r-mass + - r-mefa + - r-nls2 + - 'r-openxlsx >=2.4.0' + - r-plyr + - r-purrr + - r-rcolorbrewer + - r-rcurl + - r-reshape2 + - r-rmarkdown + - r-sme + - r-stringr + - r-tidyr + - r-venndiagram + - r-vgam + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biobroom >=1.14.0,<1.15.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-broom + - r-data.table + - r-doparallel + - r-dplyr + - r-foreach + - r-futile.logger + - r-ggplot2 + - r-gridextra + - r-knitr + - r-magrittr + - r-mass + - r-mefa + - r-nls2 + - 'r-openxlsx >=2.4.0' + - r-plyr + - r-purrr + - r-rcolorbrewer + - r-rcurl + - r-reshape2 + - r-rmarkdown + - r-sme + - r-stringr + - r-tidyr + - r-venndiagram + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Analyze thermal proteome profiling (TPP) experiments with varying temperatures (TR) or compound concentrations (CCR).' + diff --git a/recipes/bioconductor-tracktables/build.sh b/recipes/bioconductor-tracktables/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tracktables/build.sh +++ b/recipes/bioconductor-tracktables/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tracktables/meta.yaml b/recipes/bioconductor-tracktables/meta.yaml index 2db160ec4d36c..e2183d3479dde 100644 --- a/recipes/bioconductor-tracktables/meta.yaml +++ b/recipes/bioconductor-tracktables/meta.yaml @@ -1,37 +1,39 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "tracktables" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 36442889139f0c5395be2704a132414b281061e91d6f277fc8bc331599e7b902 + md5: 838950811dd0ae1fc902181f7ecca4ab build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, BiocStyle requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-rcolorbrewer - r-stringr - r-tractor.base - r-xml run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-rcolorbrewer - r-stringr @@ -41,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 3)' summary: 'Methods to create complex IGV genome browser sessions and dynamic IGV reports in HTML pages.' extra: identifiers: - biotools:tracktables - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-tracktables + path: recipes/bioconductor-tracktables + version: 1.14.0 + diff --git a/recipes/bioconductor-trackviewer/build.sh b/recipes/bioconductor-trackviewer/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-trackviewer/build.sh +++ b/recipes/bioconductor-trackviewer/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trackviewer/conda_build_config.yaml b/recipes/bioconductor-trackviewer/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-trackviewer/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-trackviewer/meta.yaml b/recipes/bioconductor-trackviewer/meta.yaml index d8e7b4674ace4..e49957a6f508e 100644 --- a/recipes/bioconductor-trackviewer/meta.yaml +++ b/recipes/bioconductor-trackviewer/meta.yaml @@ -1,57 +1,59 @@ -{% set version = "1.16.1" %} +{% set version = "1.18.0" %} {% set name = "trackViewer" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 42d8d513d099d29764505ae646148b5954cc8cde5837e01af89a1970bba5eead + md5: 35615fefb813c4b05703a35cc04a7ea2 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: biomaRt, TxDb.Hsapiens.UCSC.hg19.knownGene, RUnit, org.Hs.eg.db, BiocStyle, knitr, VariantAnnotation requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-grimport - r-htmlwidgets - r-plotrix - r-scales run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-interactionset >=1.8.0,<1.10.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rgraphviz >=2.24.0,<2.26.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-interactionset >=1.10.0,<1.11.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-grimport - r-htmlwidgets @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Visualize mapped reads along with annotation as track layers for NGS dataset such as ChIP-seq, RNA-seq, miRNA-seq, DNA-seq, SNPs and methylation data.' extra: identifiers: - biotools:trackviewer - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trackviewer + path: recipes/bioconductor-trackviewer + version: 1.16.1 + diff --git a/recipes/bioconductor-transcriptogramer/build.sh b/recipes/bioconductor-transcriptogramer/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-transcriptogramer/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-transcriptogramer/meta.yaml b/recipes/bioconductor-transcriptogramer/meta.yaml new file mode 100644 index 0000000000000..06fc840350fb5 --- /dev/null +++ b/recipes/bioconductor-transcriptogramer/meta.yaml @@ -0,0 +1,58 @@ +{% set version = "1.4.1" %} +{% set name = "transcriptogramer" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f47441df0de365c755ad232153eb8082 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, RUnit, BiocGenerics +# SystemRequirements: Java Runtime Environment (>= 6) +requirements: + host: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-data.table + - r-dosnow + - r-foreach + - r-ggplot2 + - r-igraph + - r-progress + - r-snow + - r-tidyr + run: + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-reder >=1.30.0,<1.31.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' + - r-base + - r-data.table + - r-dosnow + - r-foreach + - r-ggplot2 + - r-igraph + - r-progress + - r-snow + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'R package for transcriptional analysis based on transcriptograms, a method to analyze transcriptomes that projects expression values on a set of ordered proteins, arranged such that the probability that gene products participate in the same metabolic pathway exponentially decreases with the increase of the distance between two proteins of the ordering. Transcriptograms are, hence, genome wide gene expression profiles that provide a global view for the cellular metabolism, while indicating gene sets whose expression are altered.' + diff --git a/recipes/bioconductor-transcriptr/build.sh b/recipes/bioconductor-transcriptr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-transcriptr/build.sh +++ b/recipes/bioconductor-transcriptr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-transcriptr/meta.yaml b/recipes/bioconductor-transcriptr/meta.yaml index d06d2de828545..57d2d42950ce7 100644 --- a/recipes/bioconductor-transcriptr/meta.yaml +++ b/recipes/bioconductor-transcriptr/meta.yaml @@ -1,33 +1,35 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "transcriptR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c83546052cd55ff2093f298f9a32c5c9491eaeb3155e24ce36a5bed16f1f2095 + md5: 5679fd797416d2b8b93daa5cf72acb27 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-caret - r-e1071 @@ -35,16 +37,16 @@ requirements: - r-proc - r-reshape2 run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-chipseq >=1.30.0,<1.32.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicalignments >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-chipseq >=1.32.0,<1.33.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-caret - r-e1071 @@ -55,10 +57,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.' extra: identifiers: - biotools:transcriptr - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-transcriptr + path: recipes/bioconductor-transcriptr + version: 1.8.0 + diff --git a/recipes/bioconductor-transite/build.sh b/recipes/bioconductor-transite/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-transite/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-transite/meta.yaml b/recipes/bioconductor-transite/meta.yaml new file mode 100644 index 0000000000000..4acb9da24c1cb --- /dev/null +++ b/recipes/bioconductor-transite/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.0.1" %} +{% set name = "transite" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3ea8de97f52ef44e0e45d27f81a95ee2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr (>= 1.20), rmarkdown (>= 1.10), roxygen2 (>= 6.1.0) +# SystemRequirements: C++11 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-ggplot2 >=3.0.0' + - 'r-ggseqlogo >=0.1' + - 'r-gridextra >=2.3' + - 'r-rcpp >=0.12.18' + - 'r-scales >=1.0.0' + - 'r-tfmpvalue >=0.0.8' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - r-base + - 'r-dplyr >=0.7.6' + - 'r-ggplot2 >=3.0.0' + - 'r-ggseqlogo >=0.1' + - 'r-gridextra >=2.3' + - 'r-rcpp >=0.12.18' + - 'r-scales >=1.0.0' + - 'r-tfmpvalue >=0.0.8' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'MIT + file LICENSE' + summary: 'transite is a computational method that allows comprehensive analysis of the regulatory role of RNA-binding proteins in various cellular processes by leveraging preexisting gene expression data and current knowledge of binding preferences of RNA-binding proteins.' + diff --git a/recipes/bioconductor-translatome/build.sh b/recipes/bioconductor-translatome/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-translatome/build.sh +++ b/recipes/bioconductor-translatome/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-translatome/meta.yaml b/recipes/bioconductor-translatome/meta.yaml index 0ef9481e811d6..b6c5782caaefa 100644 --- a/recipes/bioconductor-translatome/meta.yaml +++ b/recipes/bioconductor-translatome/meta.yaml @@ -1,49 +1,50 @@ -{% set version = "1.18.5" %} +{% set version = "1.20.0" %} {% set name = "tRanslatome" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: ba3713d72b18f107b2849c536790d80093e47aa769e2e899b313054f4a3c1749 + md5: b426345db745c8c6e163c2a6a15a533e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-anota >=1.28.0,<1.30.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-heatplus >=2.26.0,<2.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rankprod >=3.6.0,<3.8.0' - - 'bioconductor-sigpathway >=1.48.0,<1.50.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-anota >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-sigpathway >=1.50.0,<1.51.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-gplots - r-plotrix run: - - 'bioconductor-anota >=1.28.0,<1.30.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq >=1.32.0,<1.34.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-gosemsim >=2.6.2,<2.8.0' - - 'bioconductor-heatplus >=2.26.0,<2.28.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-org.hs.eg.db >=3.6.0,<3.8.0' - - 'bioconductor-rankprod >=3.6.0,<3.8.0' - - 'bioconductor-sigpathway >=1.48.0,<1.50.0' - - 'bioconductor-topgo >=2.32.0,<2.34.0' + - 'bioconductor-anota >=1.30.0,<1.31.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-gosemsim >=2.8.0,<2.9.0' + - 'bioconductor-heatplus >=2.28.0,<2.29.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-rankprod >=3.8.0,<3.9.0' + - 'bioconductor-sigpathway >=1.50.0,<1.51.0' + - 'bioconductor-topgo >=2.34.0,<2.35.0' - r-base - r-gplots - r-plotrix @@ -51,10 +52,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 - summary: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' + summary: 'Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions (treated vs. untreated, diseased vs. normal, mutant vs. wild-type) among different levels of gene expression (transcriptome ,translatome, proteome), using several statistical methods: Rank Product, Translational Efficiency, t-test, Limma, ANOTA, DESeq, edgeR. Possibility to plot the results with scatterplots, histograms, MA plots, standard deviation (SD) plots, coefficient of variation (CV) plots. Detection of significantly enriched post-transcriptional regulatory factors (RBPs, miRNAs, etc) and Gene Ontology terms in the lists of DEGs previously identified for the two expression levels. Comparison of GO terms enriched only in one of the levels or in both. Calculation of the semantic similarity score between the lists of enriched GO terms coming from the two expression levels. Visual examination and comparison of the enriched terms with heatmaps, radar plots and barplots.' extra: identifiers: - biotools:translatome - doi:10.1093/bioinformatics/btt634 + parent_recipe: + name: bioconductor-translatome + path: recipes/bioconductor-translatome + version: 1.18.5 + diff --git a/recipes/bioconductor-transview/build.sh b/recipes/bioconductor-transview/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-transview/build.sh +++ b/recipes/bioconductor-transview/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-transview/meta.yaml b/recipes/bioconductor-transview/meta.yaml index 8be74d39e4033..7a4305dbe0195 100644 --- a/recipes/bioconductor-transview/meta.yaml +++ b/recipes/bioconductor-transview/meta.yaml @@ -1,38 +1,39 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "TransView" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 49007bacd52ae273fa3216f399b9e32e3d2441c44011b2b8600a96b8a2da48a5 + md5: 88fdd4448b4e7c5d8b6e434e1079134f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, pasillaBamSubset, BiocManager requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-gplots run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-gplots build: @@ -42,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides efficient tools to generate, access and display read densities of sequencing based data sets such as from RNA-Seq and ChIP-Seq.' extra: identifiers: - biotools:transview - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-transview + path: recipes/bioconductor-transview + version: 1.24.0 + diff --git a/recipes/bioconductor-traser/build.sh b/recipes/bioconductor-traser/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-traser/build.sh +++ b/recipes/bioconductor-traser/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-traser/meta.yaml b/recipes/bioconductor-traser/meta.yaml index f049012fbe3bf..675f32fd398a6 100644 --- a/recipes/bioconductor-traser/meta.yaml +++ b/recipes/bioconductor-traser/meta.yaml @@ -1,40 +1,47 @@ -{% set version = "1.10.0" %} +{% set version = "1.12.0" %} {% set name = "traseR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 293f445a6729a71b7074a78bda52e092f54321262f847b73e71d07599d6da6cb + md5: bcd587ebb46cd8b95863d9e31fe95bbc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle,RUnit, BiocGenerics requirements: host: - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base run: - - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.6.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL summary: 'traseR performs GWAS trait-associated SNP enrichment analyses in genomic intervals using different hypothesis testing approaches, also provides various functionalities to explore and visualize the results.' extra: identifiers: - biotools:traser - doi:10.1093/bioinformatics/btv741 + parent_recipe: + name: bioconductor-traser + path: recipes/bioconductor-traser + version: 1.10.0 + diff --git a/recipes/bioconductor-treeio/build.sh b/recipes/bioconductor-treeio/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-treeio/build.sh +++ b/recipes/bioconductor-treeio/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-treeio/meta.yaml b/recipes/bioconductor-treeio/meta.yaml index 7b76ddbf81d52..a6e33649e3441 100644 --- a/recipes/bioconductor-treeio/meta.yaml +++ b/recipes/bioconductor-treeio/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.4.3" %} +{% set version = "1.6.1" %} {% set name = "treeio" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b546ef1c71b4029f8c5ae10311e78cb14f695355c043912dac288afbbf4b4256 + md5: 78c5700df0497b8c3918b7f3bd59c103 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: ggplot2, ggtree, knitr, prettydoc, testthat, tidyr requirements: host: - r-ape @@ -41,8 +43,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Base classes and functions for parsing and exporting phylogenetic trees. ''treeio'' supports parsing analysis findings from commonly used software packages, allows linking external data to phylogeny and merging tree data obtained from different sources. It also supports exporting phylogenetic tree with heterogeneous associated data to a single tree file.' - +extra: + parent_recipe: + name: bioconductor-treeio + path: recipes/bioconductor-treeio + version: 1.4.3 diff --git a/recipes/bioconductor-trena/build.sh b/recipes/bioconductor-trena/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-trena/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trena/meta.yaml b/recipes/bioconductor-trena/meta.yaml new file mode 100644 index 0000000000000..32fd5eb3166fc --- /dev/null +++ b/recipes/bioconductor-trena/meta.yaml @@ -0,0 +1,75 @@ +{% set version = "1.4.2" %} +{% set name = "trena" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 2860c7d847193071a608d566bcccf9ba +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: RUnit, plyr, knitr, BiocGenerics, rmarkdown +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=0.99.0,<0.100.0' + - r-base + - r-dbi + - r-flare + - 'r-glmnet >=2.0.3' + - r-lassopv + - r-randomforest + - r-rmariadb + - r-rpostgresql + - r-rsqlite + - r-vbsr + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg19 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg38 >=1.4.0,<1.5.0' + - 'bioconductor-bsgenome.mmusculus.ucsc.mm10 >=1.4.0,<1.5.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-motifdb >=1.24.0,<1.25.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - 'bioconductor-snplocs.hsapiens.dbsnp150.grch38 >=0.99.0,<0.100.0' + - r-base + - r-dbi + - r-flare + - 'r-glmnet >=2.0.3' + - r-lassopv + - r-randomforest + - r-rmariadb + - r-rpostgresql + - r-rsqlite + - r-vbsr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Methods for reconstructing transcriptional regulatory networks, especially in species for which genome-wide TF binding site information is available.' + diff --git a/recipes/bioconductor-trendy/build.sh b/recipes/bioconductor-trendy/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-trendy/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trendy/meta.yaml b/recipes/bioconductor-trendy/meta.yaml new file mode 100644 index 0000000000000..5c5196ebbee73 --- /dev/null +++ b/recipes/bioconductor-trendy/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.4.1" %} +{% set name = "Trendy" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e89cf377c4b22e192a49271456040a9a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, devtools +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dt + - r-gplots + - r-magrittr + - r-segmented + - r-shiny + - r-shinyfiles + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-dt + - r-gplots + - r-magrittr + - r-segmented + - r-shiny + - r-shinyfiles +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Trendy implements segmented (or breakpoint) regression models to estimate breakpoints which represent changes in expression for each feature/gene in high throughput data with ordered conditions.' + diff --git a/recipes/bioconductor-triform/build.sh b/recipes/bioconductor-triform/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-triform/build.sh +++ b/recipes/bioconductor-triform/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-triform/meta.yaml b/recipes/bioconductor-triform/meta.yaml index d15165779c502..3a3d8e75cee3e 100644 --- a/recipes/bioconductor-triform/meta.yaml +++ b/recipes/bioconductor-triform/meta.yaml @@ -1,39 +1,46 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "triform" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 79365c1345b1a6c4a62407afe2a9299b033da3c0e78aeefb8d492c0a3026fd17 + md5: 5d97100c4ecccc587a7c339338499e6a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-yaml run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' - r-base - r-yaml test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The Triform algorithm uses model-free statistics to identify peak-like distributions of TF ChIP sequencing reads, taking advantage of an improved peak definition in combination with known profile characteristics.' extra: identifiers: - biotools:triform + parent_recipe: + name: bioconductor-triform + path: recipes/bioconductor-triform + version: 1.22.0 + diff --git a/recipes/bioconductor-trigger/build.sh b/recipes/bioconductor-trigger/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-trigger/build.sh +++ b/recipes/bioconductor-trigger/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trigger/meta.yaml b/recipes/bioconductor-trigger/meta.yaml index 8de0588dbbef5..6f39bd91a7fb6 100644 --- a/recipes/bioconductor-trigger/meta.yaml +++ b/recipes/bioconductor-trigger/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "trigger" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 267ab711df8e70684ab6d7cfa8f49225840fd3dbf3df811ff9df44d48557644f + md5: 26b0b707b709215845adcd78059c142f build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-corpcor - r-qtl run: - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-sva >=3.28.0,<3.30.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-sva >=3.30.0,<3.31.0' - r-base - r-corpcor - r-qtl @@ -36,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This R package provides tools for the statistical analysis of integrative genomic data that involve some combination of: genotypes, high-dimensional intermediate traits (e.g., gene expression, protein abundance), and higher-order traits (phenotypes). The package includes functions to: (1) construct global linkage maps between genetic markers and gene expression; (2) analyze multiple-locus linkage (epistasis) for gene expression; (3) quantify the proportion of genome-wide variation explained by each locus and identify eQTL hotspots; (4) estimate pair-wise causal gene regulatory probabilities and construct gene regulatory networks; and (5) identify causal genes for a quantitative trait of interest.' extra: identifiers: - biotools:trigger - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trigger + path: recipes/bioconductor-trigger + version: 1.26.0 + diff --git a/recipes/bioconductor-trio/build.sh b/recipes/bioconductor-trio/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-trio/build.sh +++ b/recipes/bioconductor-trio/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trio/meta.yaml b/recipes/bioconductor-trio/meta.yaml index 0597a5a9e0c7f..437f1cb79d8ed 100644 --- a/recipes/bioconductor-trio/meta.yaml +++ b/recipes/bioconductor-trio/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "trio" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 9d5d4c09b6c57a1c26a4d8c123e9f77218979a33fa0ed324171dd0f327a83621 + md5: 742ef152b1d4cd230c557dba4bd308a8 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: survival, haplo.stats, mcbiopi, siggenes, splines, LogicReg (>= 1.5.3), logicFS (>= 1.28.1), KernSmooth, VariantAnnotation requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Testing SNPs and SNP interactions with a genotypic TDT. This package furthermore contains functions for computing pairwise values of LD measures and for identifying LD blocks, as well as functions for setting up matched case pseudo-control genotype data for case-parent trios in order to run trio logic regression, for imputing missing genotypes in trios, for simulating case-parent trios with disease risk dependent on SNP interaction, and for power and sample size calculation in trio data.' extra: identifiers: - biotools:trio - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-trio + path: recipes/bioconductor-trio + version: 3.18.0 + diff --git a/recipes/bioconductor-triplex/build.sh b/recipes/bioconductor-triplex/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-triplex/build.sh +++ b/recipes/bioconductor-triplex/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-triplex/meta.yaml b/recipes/bioconductor-triplex/meta.yaml index 163d96ef16113..e5225d61d9440 100644 --- a/recipes/bioconductor-triplex/meta.yaml +++ b/recipes/bioconductor-triplex/meta.yaml @@ -1,35 +1,36 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "triplex" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 3113d1456d357332296f12585a65cf403165fff660b17f5319b82ad98d026c38 + md5: a155c67050549f90fb2e1565b36e7f6f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: rgl (>= 0.93.932), BSgenome.Celegans.UCSC.ce10, rtracklayer, GenomeGraphs requirements: host: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base run: - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base build: - {{ compiler('c') }} @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'BSD_2_clause + file LICENSE' summary: 'This package provides functions for identification and visualization of potential intramolecular triplex patterns in DNA sequence. The main functionality is to detect the positions of subsequences capable of folding into an intramolecular triplex (H-DNA) in a much larger sequence. The potential H-DNA (triplexes) should be made of as many cannonical nucleotide triplets as possible. The package includes visualization showing the exact base-pairing in 1D, 2D or 3D.' extra: identifiers: - biotools:triplex + parent_recipe: + name: bioconductor-triplex + path: recipes/bioconductor-triplex + version: 1.20.0 + diff --git a/recipes/bioconductor-trna/build.sh b/recipes/bioconductor-trna/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-trna/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trna/meta.yaml b/recipes/bioconductor-trna/meta.yaml new file mode 100644 index 0000000000000..4ea286878ad00 --- /dev/null +++ b/recipes/bioconductor-trna/meta.yaml @@ -0,0 +1,53 @@ +{% set version = "1.0.0" %} +{% set name = "tRNA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f53b7c910a0519debc047e4df784a63a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, BiocStyle, tRNAscanImport +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-assertive + - r-base + - r-ggplot2 + - r-scales + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - r-assertive + - r-base + - r-ggplot2 + - r-scales + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'The tRNA package allows tRNA sequences and structures to be accessed and used for subsetting. In addition, it provides visualization tools to compare feature parameters of multiple tRNA sets and correlate them to additional data. The tRNA package uses GRanges objects as inputs requiring only few additional column data sets.' + diff --git a/recipes/bioconductor-trnadbimport/build.sh b/recipes/bioconductor-trnadbimport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-trnadbimport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trnadbimport/meta.yaml b/recipes/bioconductor-trnadbimport/meta.yaml new file mode 100644 index 0000000000000..5a79e0ab333da --- /dev/null +++ b/recipes/bioconductor-trnadbimport/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.0.0" %} +{% set name = "tRNAdbImport" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 97017b574dee15ec399bab8a5cf095c4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, httptest, BiocStyle, rtracklayer +requirements: + host: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-trna >=1.0.0,<1.1.0' + - r-assertive + - r-base + - r-httr + - r-stringr + - r-xml2 + run: + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-trna >=1.0.0,<1.1.0' + - r-assertive + - r-base + - r-httr + - r-stringr + - r-xml2 +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'tRNAdbImport imports the entries of the tRNAdb and mtRNAdb (http://trna.bioinf.uni-leipzig.de) as GRanges object.' + diff --git a/recipes/bioconductor-trnascanimport/build.sh b/recipes/bioconductor-trnascanimport/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-trnascanimport/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-trnascanimport/meta.yaml b/recipes/bioconductor-trnascanimport/meta.yaml new file mode 100644 index 0000000000000..fe89f53d71cef --- /dev/null +++ b/recipes/bioconductor-trnascanimport/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "tRNAscanImport" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 00c52e3ddec9433db1e2422ee3da4b4f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, testthat, ggplot2 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-trna >=1.0.0,<1.1.0' + - r-assertive + - r-base + - r-stringr + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-trna >=1.0.0,<1.1.0' + - r-assertive + - r-base + - r-stringr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 + file LICENSE' + summary: 'The package imports the result of tRNAscan-SE as a GRanges object.' + diff --git a/recipes/bioconductor-tronco/build.sh b/recipes/bioconductor-tronco/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tronco/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tronco/meta.yaml b/recipes/bioconductor-tronco/meta.yaml new file mode 100644 index 0000000000000..07c85f86600a5 --- /dev/null +++ b/recipes/bioconductor-tronco/meta.yaml @@ -0,0 +1,63 @@ +{% set version = "2.14.0" %} +{% set name = "TRONCO" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 96b9e31bf6a28adfdacafc85d0efab6c +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocGenerics, BiocStyle, testthat, knitr, +requirements: + host: + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-bnlearn + - r-cgdsr + - r-circlize + - r-doparallel + - r-foreach + - r-gridextra + - r-gtable + - r-gtools + - r-igraph + - r-iterators + - r-r.matlab + - r-rcolorbrewer + - r-scales + - r-xtable + run: + - 'bioconductor-rgraphviz >=2.26.0,<2.27.0' + - r-base + - r-bnlearn + - r-cgdsr + - r-circlize + - r-doparallel + - r-foreach + - r-gridextra + - r-gtable + - r-gtools + - r-igraph + - r-iterators + - r-r.matlab + - r-rcolorbrewer + - r-scales + - r-xtable +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'The TRONCO (TRanslational ONCOlogy) R package collects algorithms to infer progression models via the approach of Suppes-Bayes Causal Network, both from an ensemble of tumors (cross-sectional samples) and within an individual patient (multi-region or single-cell samples). The package provides parallel implementation of algorithms that process binary matrices where each row represents a tumor sample and each column a single-nucleotide or a structural variant driving the progression; a 0/1 value models the absence/presence of that alteration in the sample. The tool can import data from plain, MAF or GISTIC format files, and can fetch it from the cBioPortal for cancer genomics. Functions for data manipulation and visualization are provided, as well as functions to import/export such data to other bioinformatics tools for, e.g, clustering or detection of mutually exclusive alterations. Inferred models can be visualized and tested for their confidence via bootstrap and cross-validation. TRONCO is used for the implementation of the Pipeline for Cancer Inference (PICNIC).' + diff --git a/recipes/bioconductor-tscan/build.sh b/recipes/bioconductor-tscan/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tscan/build.sh +++ b/recipes/bioconductor-tscan/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tscan/meta.yaml b/recipes/bioconductor-tscan/meta.yaml index 2b3ade7f20423..cd08a4765b46a 100644 --- a/recipes/bioconductor-tscan/meta.yaml +++ b/recipes/bioconductor-tscan/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.18.0" %} +{% set version = "1.20.0" %} {% set name = "TSCAN" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 5c9007f51d20b908f737381ab300396572553c709d2073fb2141649d67180db1 + md5: 88f8eead43b40eeacfd6546d0f7ad3e5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr requirements: host: - r-base @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL(>=2) summary: 'TSCAN enables users to easily construct and tune pseudotemporal cell ordering as well as analyzing differentially expressed genes. TSCAN comes with a user-friendly GUI written in shiny. More features will come in the future.' extra: identifiers: - biotools:tscan - doi:10.1093/nar/gkw430 + parent_recipe: + name: bioconductor-tscan + path: recipes/bioconductor-tscan + version: 1.18.0 + diff --git a/recipes/bioconductor-tspair/build.sh b/recipes/bioconductor-tspair/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tspair/build.sh +++ b/recipes/bioconductor-tspair/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tspair/meta.yaml b/recipes/bioconductor-tspair/meta.yaml index 4d8efbc29440d..d68e891aca92b 100644 --- a/recipes/bioconductor-tspair/meta.yaml +++ b/recipes/bioconductor-tspair/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "tspair" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 8509a2f8003b33df8d9027fdaae15de28077fa76316f52b634d5500c31ac0409 + md5: 8f240fd93f65564edf17897732940e17 build: number: 0 rpaths: @@ -18,10 +18,10 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +30,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'These functions calculate the pair of genes that show the maximum difference in ranking between two user specified groups. This "top scoring pair" maximizes the average of sensitivity and specificity over all rank based classifiers using a pair of genes in the data set. The advantage of classifying samples based on only the relative rank of a pair of genes is (a) the classifiers are much simpler and often more interpretable than more complicated classification schemes and (b) if arrays can be classified using only a pair of genes, PCR based tests could be used for classification of samples. See the references for the tspcalc() function for references regarding TSP classifiers.' extra: identifiers: - biotools:tspair - doi:10.1093/bioinformatics/btp126 + parent_recipe: + name: bioconductor-tspair + path: recipes/bioconductor-tspair + version: 1.38.0 + diff --git a/recipes/bioconductor-tsrchitect/build.sh b/recipes/bioconductor-tsrchitect/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tsrchitect/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tsrchitect/meta.yaml b/recipes/bioconductor-tsrchitect/meta.yaml new file mode 100644 index 0000000000000..a11d5730ec407 --- /dev/null +++ b/recipes/bioconductor-tsrchitect/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.8.9" %} +{% set name = "TSRchitect" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ffb55c47e0e9ba14edd48bcd48bb0330 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: ENCODExplorer, ggplot2, knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gtools + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicalignments >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-gtools +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'In recent years, large-scale transcriptional sequence data has yielded considerable insights into the nature of gene expression and regulation in eukaryotes. Techniques that identify the 5'' end of mRNAs, most notably CAGE, have mapped the promoter landscape across a number of model organisms. Due to the variability of TSS distributions and the transcriptional noise present in datasets, precisely identifying the active promoter(s) for genes from these datasets is not straightforward. TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq). In addition, (new with version 1.3.0) TSRchitect provides the ability to import aligned EST and cDNA data. Along with the coordiantes of identified TSRs, TSRchitect also calculates the width, abundance and two forms of the Shape Index, and handles biological replicates for expression profiling. Finally, TSRchitect imports annotation files, allowing the user to associate identified promoters with genes and other genomic features. Three detailed examples of TSRchitect''s utility are provided in the User''s Guide, included with this package.' + diff --git a/recipes/bioconductor-tssi/build.sh b/recipes/bioconductor-tssi/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tssi/build.sh +++ b/recipes/bioconductor-tssi/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tssi/meta.yaml b/recipes/bioconductor-tssi/meta.yaml index 69e357607c2a4..abc18cd0572c2 100644 --- a/recipes/bioconductor-tssi/meta.yaml +++ b/recipes/bioconductor-tssi/meta.yaml @@ -1,36 +1,37 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "TSSi" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 51c7131ed78586561100307e31a75ad592fe18c02a5b70ccec7322ca5c9a00ac + md5: 71fb81d19b05b106eaf0a34f8975d6b1 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: rtracklayer requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc - r-minqa - r-plyr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-hmisc - r-minqa @@ -42,10 +43,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'Identify and normalize transcription start sites in high-throughput sequencing data.' extra: identifiers: - biotools:tssi - doi:10.1093/bioinformatics/bts189 + parent_recipe: + name: bioconductor-tssi + path: recipes/bioconductor-tssi + version: 1.26.0 + diff --git a/recipes/bioconductor-ttmap/build.sh b/recipes/bioconductor-ttmap/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ttmap/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ttmap/meta.yaml b/recipes/bioconductor-ttmap/meta.yaml new file mode 100644 index 0000000000000..dbf3b43674055 --- /dev/null +++ b/recipes/bioconductor-ttmap/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.4.0" %} +{% set name = "TTMap" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b9749313b878fae1dd4ed81a16b7271d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, airway +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-colorramps + - r-rgl + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-colorramps + - r-rgl +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'TTMap is a clustering method that groups together samples with the same deviation in comparison to a control group. It is specially useful when the data is small. It is parameter free.' + diff --git a/recipes/bioconductor-turbonorm/build.sh b/recipes/bioconductor-turbonorm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-turbonorm/build.sh +++ b/recipes/bioconductor-turbonorm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-turbonorm/conda_build_config.yaml b/recipes/bioconductor-turbonorm/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-turbonorm/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-turbonorm/meta.yaml b/recipes/bioconductor-turbonorm/meta.yaml index 087840bcee23e..2b9bf2de99d92 100644 --- a/recipes/bioconductor-turbonorm/meta.yaml +++ b/recipes/bioconductor-turbonorm/meta.yaml @@ -1,34 +1,35 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "TurboNorm" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 7e381ff66918cfbe2a1f277fa7f8f6c569e8efb31d52088402c261a91c52dd89 + md5: c258665eba34296ed6a5f6e4b7e8ddd5 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, affydata requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-convert >=1.56.0,<1.58.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-convert >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-lattice run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-convert >=1.56.0,<1.58.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-marray >=1.58.0,<1.60.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-convert >=1.58.0,<1.59.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-marray >=1.60.0,<1.61.0' - r-base - r-lattice build: @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL summary: 'A fast scatterplot smoother based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available.' extra: identifiers: - biotools:turbonorm + parent_recipe: + name: bioconductor-turbonorm + path: recipes/bioconductor-turbonorm + version: 1.28.0 + diff --git a/recipes/bioconductor-tvtb/build.sh b/recipes/bioconductor-tvtb/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tvtb/build.sh +++ b/recipes/bioconductor-tvtb/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tvtb/meta.yaml b/recipes/bioconductor-tvtb/meta.yaml index 654c040847fa5..984fc50961aa5 100644 --- a/recipes/bioconductor-tvtb/meta.yaml +++ b/recipes/bioconductor-tvtb/meta.yaml @@ -1,58 +1,60 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "TVTB" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4a30a085640cb5e77ef9bbf9f32f8e0033d94146cfd3912790749f1937fbcca2 + md5: cba10d6dc0358c99d2ab92e861786a9b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: EnsDb.Hsapiens.v75 (>= 0.99.7), shiny (>= 0.13.2.9005), DT (>= 0.1.67), rtracklayer, BiocStyle (>= 2.5.19), knitr (>= 1.12), rmarkdown, testthat, covr, pander requirements: host: - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-ensemblvep >=1.22.0,<1.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensemblvep >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggally - r-ggplot2 - r-reshape2 run: - - 'bioconductor-annotationfilter >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-ensembldb >=2.4.1,<2.6.0' - - 'bioconductor-ensemblvep >=1.22.0,<1.24.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-annotationfilter >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-ensemblvep >=1.24.0,<1.25.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-ggally - r-ggplot2 @@ -61,10 +63,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package provides S4 classes and methods to filter, summarise and visualise genetic variation data stored in VCF files. In particular, the package extends the FilterRules class (S4Vectors package) to define news classes of filter rules applicable to the various slots of VCF objects. Functionalities are integrated and demonstrated in a Shiny web-application, the Shiny Variant Explorer (tSVE).' extra: identifiers: - biotools:tvtb - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-tvtb + path: recipes/bioconductor-tvtb + version: 1.6.0 + diff --git a/recipes/bioconductor-tweedeseq/build.sh b/recipes/bioconductor-tweedeseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tweedeseq/build.sh +++ b/recipes/bioconductor-tweedeseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tweedeseq/meta.yaml b/recipes/bioconductor-tweedeseq/meta.yaml index b6157c637c7d5..6bd50fdc5f021 100644 --- a/recipes/bioconductor-tweedeseq/meta.yaml +++ b/recipes/bioconductor-tweedeseq/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "tweeDEseq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 55bc0add0f651ef5fc66f7b34b073ca691694b6b786c0e16edf380b1abc4fef8 + md5: bec81583ff3cabe5b429104aacf47acc build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: tweeDEseqCountData, xtable requirements: host: - - 'bioconductor-cqn >=1.26.0,<1.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-cqn >=1.28.0,<1.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-mass run: - - 'bioconductor-cqn >=1.26.0,<1.28.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-cqn >=1.28.0,<1.29.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-mass build: @@ -36,9 +37,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Differential expression analysis of RNA-seq using the Poisson-Tweedie family of distributions.' extra: identifiers: - biotools:tweedeseq + parent_recipe: + name: bioconductor-tweedeseq + path: recipes/bioconductor-tweedeseq + version: 1.26.0 + diff --git a/recipes/bioconductor-tweedeseqcountdata/meta.yaml b/recipes/bioconductor-tweedeseqcountdata/meta.yaml new file mode 100644 index 0000000000000..65255c5193550 --- /dev/null +++ b/recipes/bioconductor-tweedeseqcountdata/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "1.20.0" %} +{% set name = "tweeDEseqCountData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: aaea601e98d23f6e80db25f3eabe68c3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>=2)' + summary: 'RNA-seq count data from Pickrell et al. (2010) employed to illustrate the use of the Poisson-Tweedie family of distributions with the tweeDEseq package.' + diff --git a/recipes/bioconductor-tweedeseqcountdata/post-link.sh b/recipes/bioconductor-tweedeseqcountdata/post-link.sh new file mode 100644 index 0000000000000..66f8ac45b7693 --- /dev/null +++ b/recipes/bioconductor-tweedeseqcountdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tweeDEseqCountData_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tweeDEseqCountData_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/tweeDEseqCountData_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tweedeseqcountdata/bioconductor-tweedeseqcountdata_1.20.0_src_all.tar.gz" +) +MD5="aaea601e98d23f6e80db25f3eabe68c3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tweedeseqcountdata/pre-unlink.sh b/recipes/bioconductor-tweedeseqcountdata/pre-unlink.sh new file mode 100644 index 0000000000000..db59b3be8ec52 --- /dev/null +++ b/recipes/bioconductor-tweedeseqcountdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tweeDEseqCountData diff --git a/recipes/bioconductor-twilight/build.sh b/recipes/bioconductor-twilight/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-twilight/build.sh +++ b/recipes/bioconductor-twilight/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-twilight/meta.yaml b/recipes/bioconductor-twilight/meta.yaml index 20fcc784cf5dd..5c549ed78e3ac 100644 --- a/recipes/bioconductor-twilight/meta.yaml +++ b/recipes/bioconductor-twilight/meta.yaml @@ -1,27 +1,28 @@ -{% set version = "1.56.0" %} +{% set version = "1.58.0" %} {% set name = "twilight" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 76db531c1798882fdf620232a767869ba855293a56358d360565fd8014c4bb4d + md5: bdc31d1f7e094aa3d2e3eb436b9b6306 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: golubEsets (>= 1.4.2), vsn (>= 1.7.2) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base build: - {{ compiler('c') }} @@ -30,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'In a typical microarray setting with gene expression data observed under two conditions, the local false discovery rate describes the probability that a gene is not differentially expressed between the two conditions given its corrresponding observed score or p-value level. The resulting curve of p-values versus local false discovery rate offers an insight into the twilight zone between clear differential and clear non-differential gene expression. Package ''twilight'' contains two main functions: Function twilight.pval performs a two-condition test on differences in means for a given input matrix or expression set and computes permutation based p-values. Function twilight performs a stochastic downhill search to estimate local false discovery rates and effect size distributions. The package further provides means to filter for permutations that describe the null distribution correctly. Using filtered permutations, the influence of hidden confounders could be diminished.' extra: identifiers: - biotools:twilight - doi:10.1093/bioinformatics/bti436 + parent_recipe: + name: bioconductor-twilight + path: recipes/bioconductor-twilight + version: 1.56.0 + diff --git a/recipes/bioconductor-twoddpcr/build.sh b/recipes/bioconductor-twoddpcr/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-twoddpcr/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-twoddpcr/meta.yaml b/recipes/bioconductor-twoddpcr/meta.yaml new file mode 100644 index 0000000000000..5b6fc8a34fed6 --- /dev/null +++ b/recipes/bioconductor-twoddpcr/meta.yaml @@ -0,0 +1,47 @@ +{% set version = "1.6.0" %} +{% set name = "twoddpcr" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 42ab6dd8305e75b8029b4c69abeb5b7d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: devtools, knitr, reshape2, rmarkdown, testthat, BiocStyle +requirements: + host: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-class + - r-ggplot2 + - r-hexbin + - r-rcolorbrewer + - r-scales + - r-shiny + run: + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - r-class + - r-ggplot2 + - r-hexbin + - r-rcolorbrewer + - r-scales + - r-shiny +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'The twoddpcr package takes Droplet Digital PCR (ddPCR) droplet amplitude data from Bio-Rad''s QuantaSoft and can classify the droplets. A summary of the positive/negative droplet counts can be generated, which can then be used to estimate the number of molecules using the Poisson distribution. This is the first open source package that facilitates the automatic classification of general two channel ddPCR data. Previous work includes ''definetherain'' (Jones et al., 2014) and ''ddpcRquant'' (Trypsteen et al., 2015) which both handle one channel ddPCR experiments only. The ''ddpcr'' package available on CRAN (Attali et al., 2016) supports automatic gating of a specific class of two channel ddPCR experiments only.' + diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml new file mode 100644 index 0000000000000..3af100f1da538 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.0.1" %} +{% set name = "TxDb.Athaliana.BioMart.plantsmart22" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 3bab54295e300fedba99eef521220e50 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh new file mode 100644 index 0000000000000..75f00aba1fe80 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart22_3.0.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart22/bioconductor-txdb.athaliana.biomart.plantsmart22_3.0.1_src_all.tar.gz" +) +MD5="3bab54295e300fedba99eef521220e50" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/pre-unlink.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/pre-unlink.sh new file mode 100644 index 0000000000000..643d9ab5d69a2 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart22/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Athaliana.BioMart.plantsmart22 diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml new file mode 100644 index 0000000000000..213070cbbc969 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.1.3" %} +{% set name = "TxDb.Athaliana.BioMart.plantsmart25" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eb007c07317b9717c76949e5ed999978 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh new file mode 100644 index 0000000000000..2453fb11731e2 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart25_3.1.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart25/bioconductor-txdb.athaliana.biomart.plantsmart25_3.1.3_src_all.tar.gz" +) +MD5="eb007c07317b9717c76949e5ed999978" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/pre-unlink.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/pre-unlink.sh new file mode 100644 index 0000000000000..6281dfc6d1b79 --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart25/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Athaliana.BioMart.plantsmart25 diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml new file mode 100644 index 0000000000000..6fae92861abab --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.2.2" %} +{% set name = "TxDb.Athaliana.BioMart.plantsmart28" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 9ed52284f01e08fc382db179b544bb17 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh new file mode 100644 index 0000000000000..c6d708042efbe --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Athaliana.BioMart.plantsmart28_3.2.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.athaliana.biomart.plantsmart28/bioconductor-txdb.athaliana.biomart.plantsmart28_3.2.2_src_all.tar.gz" +) +MD5="9ed52284f01e08fc382db179b544bb17" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/pre-unlink.sh b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/pre-unlink.sh new file mode 100644 index 0000000000000..390ffb1b97fbf --- /dev/null +++ b/recipes/bioconductor-txdb.athaliana.biomart.plantsmart28/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Athaliana.BioMart.plantsmart28 diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml new file mode 100644 index 0000000000000..991a1f35ea4b6 --- /dev/null +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Btaurus.UCSC.bosTau8.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4c5973c4153ff02dd768324291631d1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh new file mode 100644 index 0000000000000..0b7574d57c815 --- /dev/null +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Btaurus.UCSC.bosTau8.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/bioconductor-txdb.btaurus.ucsc.bostau8.refgene_3.4.4_src_all.tar.gz" +) +MD5="4c5973c4153ff02dd768324291631d1e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..b5e589d2f50fa --- /dev/null +++ b/recipes/bioconductor-txdb.btaurus.ucsc.bostau8.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Btaurus.UCSC.bosTau8.refGene diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml index 12834a2b54fa9..a8b67190e557c 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.3" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Celegans.UCSC.ce11.refGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 89873961267cd0a6e729ff3c09eb6eb3617cae61d707fb940e8ad423916ec8e0 + md5: 3952ad139ed6e3cc7d210cc994c53b3e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.celegans.ucsc.ce11.refgene + path: recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene + version: 3.4.3 diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh index 645ce9de9f796..1fc822ae2a775 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce11.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" +FN="TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.3.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.3_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce11.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce11.refgene/bioconductor-txdb.celegans.ucsc.ce11.refgene_3.4.4_src_all.tar.gz" ) -MD5="62144dbefc0beb1bb1c2e0db3757179c" +MD5="3952ad139ed6e3cc7d210cc994c53b3e" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml index faec0530fa0ae..f001c182cc657 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Celegans.UCSC.ce6.ensGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 20c51a06664f1135500b3ce1b9eeacf5154995ab4847217524beb131d4bef7e9 + md5: 215c2edd440a3df8229fe6a75b431aa8 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.celegans.ucsc.ce6.ensgene + path: recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh index 49215dd6fd9b2..ead01900cdb01 100644 --- a/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.celegans.ucsc.ce6.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Celegans.UCSC.ce6.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.celegans.ucsc.ce6.ensgene/bioconductor-txdb.celegans.ucsc.ce6.ensgene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml new file mode 100644 index 0000000000000..5acc9d8140230 --- /dev/null +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Cfamiliaris.UCSC.canFam3.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 8bc49815d284a193ab9c1db2fa32cb64 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh new file mode 100644 index 0000000000000..4e54219278311 --- /dev/null +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Cfamiliaris.UCSC.canFam3.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene_3.4.4_src_all.tar.gz" +) +MD5="8bc49815d284a193ab9c1db2fa32cb64" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..2ba72c08aef19 --- /dev/null +++ b/recipes/bioconductor-txdb.cfamiliaris.ucsc.canfam3.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Cfamiliaris.UCSC.canFam3.refGene diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml index 95519a3675bbe..34734014178b0 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm3.ensGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 879d366e7c6ca9734a059c060e0b36019e11f32c42e83a90fa31d69687e8678c + md5: 46b7ffe0c516edf8a2a3b5d78e0d8b67 build: - number: 4 + number: 5 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene + path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh index 160fc4fc37928..6b14a5faa8769 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm3.ensgene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml index 436dc9fc1b551..c7cd4bb3fcfb5 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.1" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Dmelanogaster.UCSC.dm6.ensGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 01cc6196b2660348d6ec3c7eb707966b07f803c0a40bef63958e1234d703bc69 + md5: 7cad715c42d1f960c0e54905ec6612d7 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene + path: recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene + version: 3.4.1 diff --git a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh index d47728c075d58..c52879c46ddf5 100644 --- a/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/post-link.sh @@ -1,12 +1,11 @@ #!/bin/bash -FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" +FN="TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.1.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.1_src_all.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.1_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Dmelanogaster.UCSC.dm6.ensGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene/bioconductor-txdb.dmelanogaster.ucsc.dm6.ensgene_3.4.4_src_all.tar.gz" ) -MD5="539737dcb0b3d6d0134f5fe2ecf4e835" +MD5="7cad715c42d1f960c0e54905ec6612d7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml index 3529a953fda80..8c1d181205c0f 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.3" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Drerio.UCSC.danRer10.refGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 794989712cfc2f6d9cc0cca6216326b8536c2e2215643a39a62f24bc448c5c0d + md5: aba2cc25f7893d09c3f64e32f0771691 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.drerio.ucsc.danrer10.refgene + path: recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene + version: 3.4.3 diff --git a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh index 4bbb49e809b76..018fae9b6ad3d 100644 --- a/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.drerio.ucsc.danrer10.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" +FN="TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.3.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.3_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Drerio.UCSC.danRer10.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.drerio.ucsc.danrer10.refgene/bioconductor-txdb.drerio.ucsc.danrer10.refgene_3.4.4_src_all.tar.gz" ) -MD5="db746342bff2cd07c9e02b5f5840fb2b" +MD5="aba2cc25f7893d09c3f64e32f0771691" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml new file mode 100644 index 0000000000000..8855443d7d2a5 --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Ggallus.UCSC.galGal4.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: ed0a1620fa3031845720d5373a1a7716 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh new file mode 100644 index 0000000000000..42e51aed34abb --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal4.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/bioconductor-txdb.ggallus.ucsc.galgal4.refgene_3.4.4_src_all.tar.gz" +) +MD5="ed0a1620fa3031845720d5373a1a7716" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..2a9e70b2b1d4b --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal4.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Ggallus.UCSC.galGal4.refGene diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml new file mode 100644 index 0000000000000..49a68faa60acd --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Ggallus.UCSC.galGal5.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: bab2647bf88285a3e417524b9801cb29 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh new file mode 100644 index 0000000000000..944ff30d1f5e5 --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ggallus.UCSC.galGal5.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/bioconductor-txdb.ggallus.ucsc.galgal5.refgene_3.4.4_src_all.tar.gz" +) +MD5="bab2647bf88285a3e417524b9801cb29" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..265f5874d4112 --- /dev/null +++ b/recipes/bioconductor-txdb.ggallus.ucsc.galgal5.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Ggallus.UCSC.galGal5.refGene diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml new file mode 100644 index 0000000000000..bf2655bce7c74 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.3.2" %} +{% set name = "TxDb.Hsapiens.BioMart.igis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 75b793928d29bcd3f069b5986bc2cfae +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh b/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh new file mode 100644 index 0000000000000..e9d62d98e57f3 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.BioMart.igis_2.3.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.biomart.igis/bioconductor-txdb.hsapiens.biomart.igis_2.3.2_src_all.tar.gz" +) +MD5="75b793928d29bcd3f069b5986bc2cfae" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.hsapiens.biomart.igis/pre-unlink.sh b/recipes/bioconductor-txdb.hsapiens.biomart.igis/pre-unlink.sh new file mode 100644 index 0000000000000..ad88b113757e3 --- /dev/null +++ b/recipes/bioconductor-txdb.hsapiens.biomart.igis/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Hsapiens.BioMart.igis diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml index 262094f36a3c9..5bbb9221149b4 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg18.knownGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: bc9ca40b4eab87f5ca64a4b876d42502b9b8e9f5983d745bfe0ee349d97b69fa + md5: e8b32a672e87345c72bb30be73d1e2d6 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg18.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh index 6c561280b58d5..be11859325656 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg18.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene/bioconductor-txdb.hsapiens.ucsc.hg18.knowngene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml index 84572b048ae3e..a1111cc3df693 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.knownGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 063de2b1174782a0b2b8ab7f04a0bdf3c43252cb67c685a9f8ef2b8e318352e9 + md5: 61be88a81433958571b57d0952be48a0 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh index 4fa0165f6ef81..0a43adeff4d3f 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene/bioconductor-txdb.hsapiens.ucsc.hg19.knowngene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml index 4539913ea4b2e..0341ee6495102 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4f68ee75c1722b53de4a5382a455730673dab8c0fd7585f86771efe6e7b9ab2e + md5: a0d61cd90639c40b3d0bb6bdb043cf12 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh index 0d715bcfcac5c..6c08f9edf1b4e 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg19.lincRNAsTranscripts_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts/bioconductor-txdb.hsapiens.ucsc.hg19.lincrnastranscripts_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml index 1e040d4da4789..e207abf3b0650 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Hsapiens.UCSC.hg38.knownGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: c5e6ebd84690e00eed966e4569dbd5abccf478b60dcb1842ca0310cb2ae01d44 + md5: 1d5e07631ea58e96b11905d39e76ca6e build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + path: recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene + version: 3.4.0 diff --git a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh index fe0d79fd8e074..ca419c728fb28 100644 --- a/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Hsapiens.UCSC.hg38.knownGene_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene/bioconductor-txdb.hsapiens.ucsc.hg38.knowngene_3.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml new file mode 100644 index 0000000000000..f36a0a803c163 --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Mmulatta.UCSC.rheMac3.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f395dba94db765148ac814a1330f7ade +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh new file mode 100644 index 0000000000000..407e8d791d1e7 --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac3.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene_3.4.4_src_all.tar.gz" +) +MD5="f395dba94db765148ac814a1330f7ade" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..477b8170670d1 --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac3.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Mmulatta.UCSC.rheMac3.refGene diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml new file mode 100644 index 0000000000000..1d2c548b05f1c --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Mmulatta.UCSC.rheMac8.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: b4a10fc4c1a277f8eba66da3ab697ff5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh new file mode 100644 index 0000000000000..2e310cd7520f5 --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmulatta.UCSC.rheMac8.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene_3.4.4_src_all.tar.gz" +) +MD5="b4a10fc4c1a277f8eba66da3ab697ff5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..5f5b7891de5b9 --- /dev/null +++ b/recipes/bioconductor-txdb.mmulatta.ucsc.rhemac8.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Mmulatta.UCSC.rheMac8.refGene diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml index be309abb5459d..a8faa2c8de940 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.4.0" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.ensGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3abd4f50b358ed1d1996da6c894ab82b13b247b33e07bf9d46a3f1d85c885d69 + md5: 88d65b714d1f86b456aee2b8524e9d84 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm10.ensgene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene + version: 3.4.0 diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh index d6bf203d9f539..dc07e46ba4753 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene/bioconductor-txdb.mmusculus.ucsc.mm10.ensgene_3.4.0_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml index 79984396f0ef9..21fd3bbade05f 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.0" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Mmusculus.UCSC.mm10.knownGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6b2e9ce3b2050cb770cca989b14b09c50e20ef88568b19cac7ec6ecd93daea21 + md5: 48c7efbd3a3004a0760b56b4858cc6c7 build: - number: 3 + number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm10.knowngene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene + version: 3.4.0 diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh index 4f47f3f82d372..6cf573cd948bf 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/post-link.sh @@ -1,12 +1,11 @@ #!/bin/bash -FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" +FN="TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.0_src_all.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm10.knownGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene/bioconductor-txdb.mmusculus.ucsc.mm10.knowngene_3.4.4_src_all.tar.gz" ) -MD5="86b7dca1b7d0d957c1794d261fc5bb81" +MD5="48c7efbd3a3004a0760b56b4858cc6c7" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml index 04299049e5603..079710f54bec6 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Mmusculus.UCSC.mm9.knownGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a2d760206336d0c1ba48108ba3e23b201aa429a6b88a19437270980180ef7299 + md5: cb72af039b011033477363bda8ed9104 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.mmusculus.ucsc.mm9.knowngene + path: recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh index 7bb559a168511..47194c9c45f5c 100644 --- a/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh +++ b/recipes/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Mmusculus.UCSC.mm9.knownGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene/bioconductor-txdb.mmusculus.ucsc.mm9.knowngene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml new file mode 100644 index 0000000000000..64f743e7eaa79 --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Ptroglodytes.UCSC.panTro4.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 85e52cd67bc1433b4cc4553022778fec +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh new file mode 100644 index 0000000000000..a1203dfa2bd68 --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro4.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene_3.4.4_src_all.tar.gz" +) +MD5="85e52cd67bc1433b4cc4553022778fec" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..97be7c1ed01fc --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro4.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Ptroglodytes.UCSC.panTro4.refGene diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml new file mode 100644 index 0000000000000..71cd837ec2737 --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Ptroglodytes.UCSC.panTro5.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 778842f0216030a8d60674c7e04fbc47 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh new file mode 100644 index 0000000000000..1c210dd028388 --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Ptroglodytes.UCSC.panTro5.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene_3.4.4_src_all.tar.gz" +) +MD5="778842f0216030a8d60674c7e04fbc47" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..0d28a33f72099 --- /dev/null +++ b/recipes/bioconductor-txdb.ptroglodytes.ucsc.pantro5.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Ptroglodytes.UCSC.panTro5.refGene diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml new file mode 100644 index 0000000000000..c53a22c366db2 --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "2.3.2" %} +{% set name = "TxDb.Rnorvegicus.BioMart.igis" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: eaf695f63cd021074d68c76d148cdfb7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from BioMart by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh new file mode 100644 index 0000000000000..6f862f7744371 --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.BioMart.igis_2.3.2.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.biomart.igis/bioconductor-txdb.rnorvegicus.biomart.igis_2.3.2_src_all.tar.gz" +) +MD5="eaf695f63cd021074d68c76d148cdfb7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/pre-unlink.sh b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/pre-unlink.sh new file mode 100644 index 0000000000000..e520ce76969aa --- /dev/null +++ b/recipes/bioconductor-txdb.rnorvegicus.biomart.igis/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Rnorvegicus.BioMart.igis diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml index 5596886011a4d..9eb62dbc3b7ee 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn4.ensGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 15325d09a9da4292678768164e1850a78595dd96351970553844f5eeac5f683f + md5: 6bf2ebc522c2828c036e52b2028792c1 build: - number: 3 + number: 4 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh index 5eef393d3801f..4ae5817baed38 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn4.ensGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene/bioconductor-txdb.rnorvegicus.ucsc.rn4.ensgene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml index 99f5e1d42c333..a5b597e00b2cd 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.3" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn5.refGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 82a9597c56c1181f26363601f9618fa203c50f04a5a3386c0f66c137747af34a + md5: edb5a69c1aab095e285d902b8edddddc build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene + version: 3.4.3 diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh index 090cc1bacd076..8df704c5ee456 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.3.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.3_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn5.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn5.refgene_3.4.4_src_all.tar.gz" ) -MD5="4dafbc7e60e8fb947d40571fa3812699" +MD5="edb5a69c1aab095e285d902b8edddddc" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml index 4d68f80fb327b..336a2e70125ac 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/meta.yaml @@ -1,37 +1,42 @@ -{% set version = "3.4.3" %} +{% set version = "3.4.4" %} {% set name = "TxDb.Rnorvegicus.UCSC.rn6.refGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4325ad6b56fe6de8f17eae445327f4cac8731530a46e5fa4775d242bfb730296 + md5: 517b65f7a796f7c7c4f4cce2673bbb0c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene + path: recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene + version: 3.4.3 diff --git a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh index 3b8b82daa4d17..94338ff73ac9e 100644 --- a/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh +++ b/recipes/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" +FN="TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" - "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.3.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.3_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Rnorvegicus.UCSC.rn6.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene/bioconductor-txdb.rnorvegicus.ucsc.rn6.refgene_3.4.4_src_all.tar.gz" ) -MD5="502c29bc0eb476938794a01c2d8ce269" +MD5="517b65f7a796f7c7c4f4cce2673bbb0c" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml index 1e70b4eab380b..a020901cb197b 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer2.sgdGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: eaf35b5a3e4706328e7a5b89d7de846055f5ac0aa34109d305a6ffbd2067af50 + md5: 8ce83ef2ba6cfc69f9b4435a0a047819 build: - number: 5 + number: 6 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene + path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh index 616af4ba2ab51..40fb88d833a30 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer2.sgdGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer2.sgdgene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml index 58ff21afdd9af..3896cc46db8ee 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/meta.yaml @@ -1,37 +1,42 @@ {% set version = "3.2.2" %} {% set name = "TxDb.Scerevisiae.UCSC.sacCer3.sgdGene" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6dac0b4f88ce54c8543bb0ce236507cd46dd78ff7b3e3457ef7fd0b1dca15cea + md5: afb23b3265730b9e59c2f07ab37cc3a0 build: - number: 9 + number: 10 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' license: Artistic-2.0 summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' - +extra: + parent_recipe: + name: bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene + path: recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene + version: 3.2.2 diff --git a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh index a3773b0b6b287..32d7dfa5fc6ca 100644 --- a/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh +++ b/recipes/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/post-link.sh @@ -1,7 +1,7 @@ #!/bin/bash FN="TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" "https://bioarchive.galaxyproject.org/TxDb.Scerevisiae.UCSC.sacCer3.sgdGene_3.2.2.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" "https://depot.galaxyproject.org/software/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene/bioconductor-txdb.scerevisiae.ucsc.saccer3.sgdgene_3.2.2_src_all.tar.gz" diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml new file mode 100644 index 0000000000000..927d6d8177410 --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Sscrofa.UCSC.susScr11.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 7db4a04d14f707e53e5a921f125f8ea1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh new file mode 100644 index 0000000000000..651c4a9c44181 --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr11.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene_3.4.4_src_all.tar.gz" +) +MD5="7db4a04d14f707e53e5a921f125f8ea1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..7f0243864a593 --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr11.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Sscrofa.UCSC.susScr11.refGene diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml new file mode 100644 index 0000000000000..e333266050793 --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "3.4.4" %} +{% set name = "TxDb.Sscrofa.UCSC.susScr3.refGene" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a98f0f01b07cfac30de6c028cb79f747 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Exposes an annotation databases generated from UCSC by exposing these as TxDb objects' + diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh new file mode 100644 index 0000000000000..b918b0d37500b --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" + "https://bioarchive.galaxyproject.org/TxDb.Sscrofa.UCSC.susScr3.refGene_3.4.4.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene_3.4.4_src_all.tar.gz" +) +MD5="a98f0f01b07cfac30de6c028cb79f747" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/pre-unlink.sh b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/pre-unlink.sh new file mode 100644 index 0000000000000..ca9defd75599e --- /dev/null +++ b/recipes/bioconductor-txdb.sscrofa.ucsc.susscr3.refgene/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ TxDb.Sscrofa.UCSC.susScr3.refGene diff --git a/recipes/bioconductor-tximeta/build.sh b/recipes/bioconductor-tximeta/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-tximeta/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tximeta/meta.yaml b/recipes/bioconductor-tximeta/meta.yaml new file mode 100644 index 0000000000000..66597187f8820 --- /dev/null +++ b/recipes/bioconductor-tximeta/meta.yaml @@ -0,0 +1,55 @@ +{% set version = "1.0.1" %} +{% set name = "tximeta" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6f4773e54743943053be78b631570491 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, tximportData, org.Dm.eg.db, DESeq2, devtools +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tximport >=1.10.0,<1.11.0' + - r-base + - r-jsonlite + - r-rappdirs + - r-tibble + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-ensembldb >=2.6.0,<2.7.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-tximport >=1.10.0,<1.11.0' + - r-base + - r-jsonlite + - r-rappdirs + - r-tibble +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-2 + summary: 'Transcript quantification import from Salmon with automatic population of metadata and transcript ranges. Filtered, combined, or de novo transcriptomes can be linked to the appropriate sources with linkedTxomes and shared for reproducible analyses.' + diff --git a/recipes/bioconductor-tximport/build.sh b/recipes/bioconductor-tximport/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-tximport/build.sh +++ b/recipes/bioconductor-tximport/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-tximport/meta.yaml b/recipes/bioconductor-tximport/meta.yaml index 8d527f4c0b7cd..c82ca01d3958d 100644 --- a/recipes/bioconductor-tximport/meta.yaml +++ b/recipes/bioconductor-tximport/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.8.0" %} +{% set version = "1.10.0" %} {% set name = "tximport" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 375224ca34750e5064bb3db0e0f7347d84af2c2633dd2cd9be8cfd96a03a4ce2 + md5: cda7c7b351304fbe4feaf8e53434e483 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, tximportData, TxDb.Hsapiens.UCSC.hg19.knownGene, readr (>= 0.2.2), limma, edgeR, DESeq2 (>= 1.11.6), rhdf5, jsonlite, matrixStats requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.' extra: identifiers: - biotools:tximport + parent_recipe: + name: bioconductor-tximport + path: recipes/bioconductor-tximport + version: 1.8.0 + diff --git a/recipes/bioconductor-tximportdata/meta.yaml b/recipes/bioconductor-tximportdata/meta.yaml new file mode 100644 index 0000000000000..eaffa39e5fd40 --- /dev/null +++ b/recipes/bioconductor-tximportdata/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.10.0" %} +{% set name = "tximportData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 54178cc67ba022548272a2474fcecaac +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package provides the output of running various transcript abundance quantifiers on a set of 6 RNA-seq samples from the GEUVADIS project. The quantifiers were Cufflinks, RSEM, kallisto, Salmon and Sailfish. For details on version numbers, sample information, and details on calls, see the package vignette.' + diff --git a/recipes/bioconductor-tximportdata/post-link.sh b/recipes/bioconductor-tximportdata/post-link.sh new file mode 100644 index 0000000000000..048a7fc28f072 --- /dev/null +++ b/recipes/bioconductor-tximportdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="tximportData_1.10.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/tximportData_1.10.0.tar.gz" + "https://bioarchive.galaxyproject.org/tximportData_1.10.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-tximportdata/bioconductor-tximportdata_1.10.0_src_all.tar.gz" +) +MD5="54178cc67ba022548272a2474fcecaac" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-tximportdata/pre-unlink.sh b/recipes/bioconductor-tximportdata/pre-unlink.sh new file mode 100644 index 0000000000000..fe4581681db0d --- /dev/null +++ b/recipes/bioconductor-tximportdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ tximportData diff --git a/recipes/bioconductor-txreginfra/build.sh b/recipes/bioconductor-txreginfra/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-txreginfra/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-txreginfra/meta.yaml b/recipes/bioconductor-txreginfra/meta.yaml new file mode 100644 index 0000000000000..f9f282c0a6fdd --- /dev/null +++ b/recipes/bioconductor-txreginfra/meta.yaml @@ -0,0 +1,51 @@ +{% set version = "1.2.0" %} +{% set name = "TxRegInfra" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c09e95c44aca076760777fa3c89538eb +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, GenomicFiles, EnsDb.Hsapiens.v75, testthat, biovizBase (>= 1.27.2), Gviz, AnnotationFilter, ensembldb +requirements: + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mongolite + - r-rjson + run: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-raggedexperiment >=1.6.0,<1.7.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-mongolite + - r-rjson +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package provides interfaces to genomic metadata employed in regulatory network creation, with a focus on noSQL solutions. Currently quantitative representations of eQTLs, DnaseI hypersensitivity sites and digital genomic footprints are assembled using an out-of-memory extension of the RaggedExperiment API.' + diff --git a/recipes/bioconductor-typeinfo/build.sh b/recipes/bioconductor-typeinfo/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-typeinfo/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-typeinfo/meta.yaml b/recipes/bioconductor-typeinfo/meta.yaml new file mode 100644 index 0000000000000..a607feed620f3 --- /dev/null +++ b/recipes/bioconductor-typeinfo/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.48.0" %} +{% set name = "TypeInfo" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 1923e893a75108abebee8fc64984144e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: BSD + summary: 'A prototype for a mechanism for specifying the types of parameters and the return value for an R function. This is meta-information that can be used to generate stubs for servers and various interfaces to these functions. Additionally, the arguments in a call to a typed function can be validated using the type specifications. We allow types to be specified as either i) by class name using either inheritance - is(x, className), or strict instance of - class(x) %in% className, or ii) a dynamic test given as an R expression which is evaluated at run-time. More precise information and interesting tests can be done via ii), but it is harder to use this information as meta-data as it requires more effort to interpret it and it is of course run-time information. It is typically more meaningful.' + diff --git a/recipes/bioconductor-u133aaofav2cdf/meta.yaml b/recipes/bioconductor-u133aaofav2cdf/meta.yaml new file mode 100644 index 0000000000000..cb166ddff5ae9 --- /dev/null +++ b/recipes/bioconductor-u133aaofav2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "u133aaofav2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 716483ddb6664b8b7f0c58cd21136e8b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the U133AAofAv2.CDF file.' + diff --git a/recipes/bioconductor-u133aaofav2cdf/post-link.sh b/recipes/bioconductor-u133aaofav2cdf/post-link.sh new file mode 100644 index 0000000000000..fd172e0d773b4 --- /dev/null +++ b/recipes/bioconductor-u133aaofav2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="u133aaofav2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133aaofav2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/u133aaofav2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133aaofav2cdf/bioconductor-u133aaofav2cdf_2.18.0_src_all.tar.gz" +) +MD5="716483ddb6664b8b7f0c58cd21136e8b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-u133aaofav2cdf/pre-unlink.sh b/recipes/bioconductor-u133aaofav2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..00ac89386b86b --- /dev/null +++ b/recipes/bioconductor-u133aaofav2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ u133aaofav2cdf diff --git a/recipes/bioconductor-u133x3p.db/meta.yaml b/recipes/bioconductor-u133x3p.db/meta.yaml new file mode 100644 index 0000000000000..9787bea5308f2 --- /dev/null +++ b/recipes/bioconductor-u133x3p.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "u133x3p.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 1a36a09dc64b94728bf6ac75600b40c6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.hs.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Human X3P Array annotation data (chip u133x3p) assembled using data from public repositories' + diff --git a/recipes/bioconductor-u133x3p.db/post-link.sh b/recipes/bioconductor-u133x3p.db/post-link.sh new file mode 100644 index 0000000000000..8b5f650a67943 --- /dev/null +++ b/recipes/bioconductor-u133x3p.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="u133x3p.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3p.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/u133x3p.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3p.db/bioconductor-u133x3p.db_3.2.3_src_all.tar.gz" +) +MD5="1a36a09dc64b94728bf6ac75600b40c6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-u133x3p.db/pre-unlink.sh b/recipes/bioconductor-u133x3p.db/pre-unlink.sh new file mode 100644 index 0000000000000..4f7d874c35d91 --- /dev/null +++ b/recipes/bioconductor-u133x3p.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ u133x3p.db diff --git a/recipes/bioconductor-u133x3pcdf/meta.yaml b/recipes/bioconductor-u133x3pcdf/meta.yaml new file mode 100644 index 0000000000000..dc9cb442ead45 --- /dev/null +++ b/recipes/bioconductor-u133x3pcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "u133x3pcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ee4e62041bc8c63813e8cf8400ece2f3 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the U133_X3P.cdf file.' + diff --git a/recipes/bioconductor-u133x3pcdf/post-link.sh b/recipes/bioconductor-u133x3pcdf/post-link.sh new file mode 100644 index 0000000000000..32627ff8d312f --- /dev/null +++ b/recipes/bioconductor-u133x3pcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="u133x3pcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3pcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/u133x3pcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3pcdf/bioconductor-u133x3pcdf_2.18.0_src_all.tar.gz" +) +MD5="ee4e62041bc8c63813e8cf8400ece2f3" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-u133x3pcdf/pre-unlink.sh b/recipes/bioconductor-u133x3pcdf/pre-unlink.sh new file mode 100644 index 0000000000000..d55f4f7feedc3 --- /dev/null +++ b/recipes/bioconductor-u133x3pcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ u133x3pcdf diff --git a/recipes/bioconductor-u133x3pprobe/meta.yaml b/recipes/bioconductor-u133x3pprobe/meta.yaml new file mode 100644 index 0000000000000..d981fe282b9e2 --- /dev/null +++ b/recipes/bioconductor-u133x3pprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "u133x3pprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 81e2b00985688160805147bef0c638be +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was U133\_X3P\_probe\_tab.' + diff --git a/recipes/bioconductor-u133x3pprobe/post-link.sh b/recipes/bioconductor-u133x3pprobe/post-link.sh new file mode 100644 index 0000000000000..25a8fe1f784ec --- /dev/null +++ b/recipes/bioconductor-u133x3pprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="u133x3pprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/u133x3pprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/u133x3pprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-u133x3pprobe/bioconductor-u133x3pprobe_2.18.0_src_all.tar.gz" +) +MD5="81e2b00985688160805147bef0c638be" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-u133x3pprobe/pre-unlink.sh b/recipes/bioconductor-u133x3pprobe/pre-unlink.sh new file mode 100644 index 0000000000000..6144ffc45ac23 --- /dev/null +++ b/recipes/bioconductor-u133x3pprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ u133x3pprobe diff --git a/recipes/bioconductor-ularcirc/build.sh b/recipes/bioconductor-ularcirc/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-ularcirc/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-ularcirc/meta.yaml b/recipes/bioconductor-ularcirc/meta.yaml new file mode 100644 index 0000000000000..76af3ce0453a1 --- /dev/null +++ b/recipes/bioconductor-ularcirc/meta.yaml @@ -0,0 +1,65 @@ +{% set version = "1.0.0" %} +{% set name = "Ularcirc" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e8b3ed9cba2d1b3f52f2a1252107ec0f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' + - 'bioconductor-sushi >=1.20.0,<1.21.0' + - r-base + - 'r-data.table >=1.9.4' + - r-dt + - r-gsubfn + - r-httpuv + - r-moments + - r-shiny + - r-shinyfiles + - r-yaml + run: + - 'bioconductor-annotationhub >=2.14.0,<2.15.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomeinfodbdata >=1.2.0,<1.3.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-mirbase.db >=1.2.0,<1.3.0' + - 'bioconductor-sushi >=1.20.0,<1.21.0' + - r-base + - 'r-data.table >=1.9.4' + - r-dt + - r-gsubfn + - r-httpuv + - r-moments + - r-shiny + - r-shinyfiles + - r-yaml +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'file LICENSE' + summary: 'Ularcirc reads in STAR aligned splice junction files and provides visualisation and analysis tools for splicing analysis. Users can assess backsplice junctions and forward canonical junctions.' + diff --git a/recipes/bioconductor-undo/build.sh b/recipes/bioconductor-undo/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-undo/build.sh +++ b/recipes/bioconductor-undo/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-undo/meta.yaml b/recipes/bioconductor-undo/meta.yaml index d547ca9ea0f4e..7dd6b0b917a6c 100644 --- a/recipes/bioconductor-undo/meta.yaml +++ b/recipes/bioconductor-undo/meta.yaml @@ -1,32 +1,33 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "UNDO" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: b92e02e3ef692d7a40c4e5fe7aaf7443004765b45df439e8afeb23d28dd71698 + md5: f1e2a4e8cc746b0f2e99793229b09d79 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-boot - r-mass - r-nnls run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-boot - r-mass @@ -35,10 +36,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'UNDO is an R package for unsupervised deconvolution of tumor and stromal mixed expression data. It detects marker genes and deconvolutes the mixing expression data without any prior knowledge.' extra: identifiers: - biotools:undo - doi:10.1093/bioinformatics/btu607 + parent_recipe: + name: bioconductor-undo + path: recipes/bioconductor-undo + version: 1.22.0 + diff --git a/recipes/bioconductor-unifiedwmwqpcr/build.sh b/recipes/bioconductor-unifiedwmwqpcr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/build.sh +++ b/recipes/bioconductor-unifiedwmwqpcr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml b/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-unifiedwmwqpcr/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml index b8f1ad179ae73..4aa69fdf1d468 100644 --- a/recipes/bioconductor-unifiedwmwqpcr/meta.yaml +++ b/recipes/bioconductor-unifiedwmwqpcr/meta.yaml @@ -1,37 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "unifiedWMWqPCR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6ba1920b69895745d5b7cc0a85ef2ec957fd628f01f912019737fe5fec856268 + md5: d0bc72990976a0e11766f9f46402a588 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-htqpcr >=1.34.0,<1.36.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-htqpcr >=1.36.0,<1.37.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-htqpcr >=1.34.0,<1.36.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-htqpcr >=1.36.0,<1.37.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This packages implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.' extra: identifiers: - biotools:unifiedwmwqpcr + parent_recipe: + name: bioconductor-unifiedwmwqpcr + path: recipes/bioconductor-unifiedwmwqpcr + version: 1.16.0 + diff --git a/recipes/bioconductor-uniprot.ws/build.sh b/recipes/bioconductor-uniprot.ws/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-uniprot.ws/build.sh +++ b/recipes/bioconductor-uniprot.ws/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-uniprot.ws/meta.yaml b/recipes/bioconductor-uniprot.ws/meta.yaml index dd14915f1daec..963fc3b9feb03 100644 --- a/recipes/bioconductor-uniprot.ws/meta.yaml +++ b/recipes/bioconductor-uniprot.ws/meta.yaml @@ -1,34 +1,36 @@ -{% set version = "2.20.4" %} +{% set version = "2.22.0" %} {% set name = "UniProt.ws" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 38f80df3370c7beb0de96666b5df08efddbb66bd91c2a58aed2ac20d7dfa60ab + md5: 54f202f10a75478ae02ca20a309c231b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-rappdirs - r-rcurl - r-rsqlite run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biocfilecache >=1.4.0,<1.6.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biocfilecache >=1.6.0,<1.7.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' - r-base - r-rappdirs - r-rcurl @@ -37,10 +39,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic License 2.0' summary: 'A collection of functions for retrieving, processing and repackaging the UniProt web services.' extra: identifiers: - biotools:uniprot.ws - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-uniprot.ws + path: recipes/bioconductor-uniprot.ws + version: 2.20.4 + diff --git a/recipes/bioconductor-uniquorn/build.sh b/recipes/bioconductor-uniquorn/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-uniquorn/build.sh +++ b/recipes/bioconductor-uniquorn/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-uniquorn/meta.yaml b/recipes/bioconductor-uniquorn/meta.yaml index 40a0105686389..ee0bae0160544 100644 --- a/recipes/bioconductor-uniquorn/meta.yaml +++ b/recipes/bioconductor-uniquorn/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "2.0.0" %} +{% set version = "2.2.0" %} {% set name = "Uniquorn" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 2b82752fc5f2ec01bba3e71e9fa1fdda65db22ad5e598b1eb91f7fd10de997eb + md5: 2306a39e0dba09bf225b18f83cb40153 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: testthat, knitr, rmarkdown, BiocGenerics, RUnit requirements: host: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - r-doparallel @@ -29,9 +31,9 @@ requirements: - r-stringr - r-writexls run: - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-data.table - r-doparallel @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'This packages enables users to identify cancer cell lines. Cancer cell line misidentification and cross-contamination reprents a significant challenge for cancer researchers. The identification is vital and in the frame of this package based on the locations/ loci of somatic and germline mutations/ variations. The input format is vcf/ vcf.gz and the files have to contain a single cancer cell line sample (i.e. a single member/genotype/gt column in the vcf file). The implemented method is optimized for the Next-generation whole exome and whole genome DNA-sequencing technology. RNA-seq data is very likely to work as well but hasn''t been rigiously tested yet. Panel-seq will require manual adjustment of thresholds' extra: identifiers: - biotools:uniquorn - doi:10.18632/oncotarget.16110 + parent_recipe: + name: bioconductor-uniquorn + path: recipes/bioconductor-uniquorn + version: 2.0.0 + diff --git a/recipes/bioconductor-universalmotif/build.sh b/recipes/bioconductor-universalmotif/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-universalmotif/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-universalmotif/meta.yaml b/recipes/bioconductor-universalmotif/meta.yaml new file mode 100644 index 0000000000000..f1e3232bb158f --- /dev/null +++ b/recipes/bioconductor-universalmotif/meta.yaml @@ -0,0 +1,56 @@ +{% set version = "1.0.0" %} +{% set name = "universalmotif" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c71cb837cc9811cfc1d9540b042e920e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: knitr, BiocStyle, TFBSTools, MotIV, PWMEnrich, motifStack, seqLogo, rmarkdown, MotifDb, testthat, rGADEM, motifRG, motifbreakR, RcisTarget, motifcounter, Logolas, BiocParallel, BCRANK +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - r-ape + - r-base + - r-ggplot2 + - r-ggseqlogo + - r-gtools + - r-processx + - r-rcpp + - 'r-rdpack >=0.7' + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-ggtree >=1.14.0,<1.15.0' + - r-ape + - r-base + - r-ggplot2 + - r-ggseqlogo + - r-gtools + - r-processx + - r-rcpp + - 'r-rdpack >=0.7' + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'Allows for importing most common motif types into R for use by functions provided by other Bioconductor motif-related packages. Motifs can be exported into most major motif formats from various classes as defined by other Bioconductor packages. A suite of motif and sequence manipulation and analysis functions are included, including enrichment, comparison, P-value calculation, shuffling, trimming, higher-order motifs, and others.' + diff --git a/recipes/bioconductor-usort/build.sh b/recipes/bioconductor-usort/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-usort/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-usort/meta.yaml b/recipes/bioconductor-usort/meta.yaml new file mode 100644 index 0000000000000..79a2c6fafeabe --- /dev/null +++ b/recipes/bioconductor-usort/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.8.0" %} +{% set name = "uSORT" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e92645ff56f39c741d9c721c91648168 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, RUnit, testthat, ggplot2 +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-monocle >=2.10.0,<2.11.0' + - r-base + - r-cluster + - r-fpc + - r-gplots + - r-igraph + - r-matrix + - r-plyr + - r-rann + - r-rspectra + - r-vgam + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-monocle >=2.10.0,<2.11.0' + - r-base + - r-cluster + - r-fpc + - r-gplots + - r-igraph + - r-matrix + - r-plyr + - r-rann + - r-rspectra + - r-vgam +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'This package is designed to uncover the intrinsic cell progression path from single-cell RNA-seq data. It incorporates data pre-processing, preliminary PCA gene selection, preliminary cell ordering, feature selection, refined cell ordering, and post-analysis interpretation and visualization.' + diff --git a/recipes/bioconductor-vanillaice/build.sh b/recipes/bioconductor-vanillaice/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-vanillaice/build.sh +++ b/recipes/bioconductor-vanillaice/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vanillaice/conda_build_config.yaml b/recipes/bioconductor-vanillaice/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-vanillaice/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-vanillaice/meta.yaml b/recipes/bioconductor-vanillaice/meta.yaml index d6c6e57f8bf1d..4c07ef39297c2 100644 --- a/recipes/bioconductor-vanillaice/meta.yaml +++ b/recipes/bioconductor-vanillaice/meta.yaml @@ -1,49 +1,50 @@ -{% set version = "1.42.4" %} +{% set version = "1.44.0" %} {% set name = "VanillaICE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 0f744caf4e2dcceb4d25dccfcf06147e479db8145289c27eb204a73893fb3763 + md5: ea6bd436eab15fa26a9809990494a9a2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, SNPchip, human610quadv1bCrlmm, ArrayTV requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.1000,<1.5.0' - - 'bioconductor-crlmm >=1.38.0,<1.40.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - 'bioconductor-crlmm >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-foreach - r-lattice - r-matrixstats run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.1000,<1.5.0' - - 'bioconductor-crlmm >=1.38.0,<1.40.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome.hsapiens.ucsc.hg18 >=1.3.0,<1.4.0' + - 'bioconductor-crlmm >=1.40.0,<1.41.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-foreach @@ -56,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Hidden Markov Models for characterizing chromosomal alterations in high throughput SNP arrays.' extra: identifiers: - biotools:vanillaice + parent_recipe: + name: bioconductor-vanillaice + path: recipes/bioconductor-vanillaice + version: 1.42.4 + diff --git a/recipes/bioconductor-variancepartition/build.sh b/recipes/bioconductor-variancepartition/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-variancepartition/build.sh +++ b/recipes/bioconductor-variancepartition/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-variancepartition/meta.yaml b/recipes/bioconductor-variancepartition/meta.yaml index bc8a8f6312176..a72cbea6ba70d 100644 --- a/recipes/bioconductor-variancepartition/meta.yaml +++ b/recipes/bioconductor-variancepartition/meta.yaml @@ -1,25 +1,27 @@ -{% set version = "1.10.4" %} +{% set version = "1.12.0" %} {% set name = "variancePartition" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 24a6bc59c65bc97d0818010c489bd16eb7c746d9c45f0c53b90e581e9fbc5b2f + md5: 9620d92b1e585edd567a01c86d74a0e6 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, pander, rmarkdown, edgeR, dendextend, tximport, tximportData, ballgown, DESeq2, RUnit, BiocGenerics, r2glmm, readr requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-colorramps - r-doparallel @@ -34,8 +36,8 @@ requirements: - r-reshape2 - r-scales run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-colorramps - r-doparallel @@ -53,9 +55,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Quantify and interpret multiple sources of biological and technical variation in gene expression experiments. Uses a linear mixed model to quantify variation in gene expression attributable to individual, tissue, time point, or technical variables. Includes dream differential expression analysis for repeated measures.' extra: identifiers: - biotools:variancepartition + parent_recipe: + name: bioconductor-variancepartition + path: recipes/bioconductor-variancepartition + version: 1.10.4 + diff --git a/recipes/bioconductor-variantannotation/build.sh b/recipes/bioconductor-variantannotation/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-variantannotation/build.sh +++ b/recipes/bioconductor-variantannotation/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-variantannotation/meta.yaml b/recipes/bioconductor-variantannotation/meta.yaml index ceb5276d433cd..74d5342454a7f 100644 --- a/recipes/bioconductor-variantannotation/meta.yaml +++ b/recipes/bioconductor-variantannotation/meta.yaml @@ -1,56 +1,57 @@ -{% set version = "1.26.1" %} +{% set version = "1.28.3" %} {% set name = "VariantAnnotation" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 59a2859fddc9ed6ddc98969bd2e6df65c6643c73768ee3370e48b650529ca5e4 + md5: 794af6309fedd19426ef39df2a0907e2 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, AnnotationHub, BSgenome.Hsapiens.UCSC.hg19, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP.20101109, SIFT.Hsapiens.dbSNP132, SIFT.Hsapiens.dbSNP137, PolyPhen.Hsapiens.dbSNP131, snpStats, ggplot2, BiocStyle requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-dbi run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base - r-dbi build: @@ -60,9 +61,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Annotate variants, compute amino acid coding changes, predict coding outcomes.' extra: identifiers: - biotools:variantannotation + parent_recipe: + name: bioconductor-variantannotation + path: recipes/bioconductor-variantannotation + version: 1.26.1 + diff --git a/recipes/bioconductor-variantfiltering/build.sh b/recipes/bioconductor-variantfiltering/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-variantfiltering/build.sh +++ b/recipes/bioconductor-variantfiltering/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-variantfiltering/conda_build_config.yaml b/recipes/bioconductor-variantfiltering/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-variantfiltering/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-variantfiltering/meta.yaml b/recipes/bioconductor-variantfiltering/meta.yaml index 891040a80c2d2..c6d42d6ccd67d 100644 --- a/recipes/bioconductor-variantfiltering/meta.yaml +++ b/recipes/bioconductor-variantfiltering/meta.yaml @@ -1,42 +1,43 @@ -{% set version = "1.16.0" %} +{% set version = "1.18.0" %} {% set name = "VariantFiltering" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 96013d7fde2454ac565a36fd01ef9593c338b0f6d25ed2ac491810350c801395 + md5: 1ce3cd46b70fd5e9ca215f125d36317f build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: RUnit, BiocStyle, org.Hs.eg.db, BSgenome.Hsapiens.1000genomes.hs37d5, TxDb.Hsapiens.UCSC.hg19.knownGene, SNPlocs.Hsapiens.dbSNP144.GRCh37, MafDb.1Kgenomes.phase1.hs37d5, phastCons100way.UCSC.hg19, PolyPhen.Hsapiens.dbSNP131, SIFT.Hsapiens.dbSNP137 requirements: host: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dt - r-shiny @@ -44,25 +45,25 @@ requirements: - r-shinythemes - r-shinytree run: - - 'bioconductor-annotationdbi >=1.42.1,<1.44.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-genomicscores >=1.4.1,<1.6.0' - - 'bioconductor-graph >=1.58.0,<1.60.0' - - 'bioconductor-gviz >=1.24.0,<1.26.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rbgl >=1.56.0,<1.58.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' - - 'bioconductor-xvector >=0.20.0,<0.22.0' + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-genomicscores >=1.6.0,<1.7.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gviz >=1.26.0,<1.27.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rbgl >=1.58.0,<1.59.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - 'bioconductor-xvector >=0.22.0,<0.23.0' - r-base - r-dt - r-shiny @@ -76,10 +77,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.' extra: identifiers: - biotools:variantfiltering - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-variantfiltering + path: recipes/bioconductor-variantfiltering + version: 1.16.0 + diff --git a/recipes/bioconductor-varianttools/build.sh b/recipes/bioconductor-varianttools/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-varianttools/build.sh +++ b/recipes/bioconductor-varianttools/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-varianttools/meta.yaml b/recipes/bioconductor-varianttools/meta.yaml index f4d29d38804ca..649a5523b0c5e 100644 --- a/recipes/bioconductor-varianttools/meta.yaml +++ b/recipes/bioconductor-varianttools/meta.yaml @@ -1,62 +1,69 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "VariantTools" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 945d1d7f611094b7cfebf46583ebe431b644af071c385be5481e2cc8e78570f4 + md5: 58f5a5c644464fcac6ee6eb7ef3b1aa9 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, LungCancerLines (>= 0.0.6), RBGL, graph, gmapR (>= 1.21.3) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-matrix run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-bsgenome >=1.48.0,<1.50.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-matrix test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Explore, diagnose, and compare variant calls using filters.' extra: identifiers: - biotools:varianttools - doi:10.1101/027227 + parent_recipe: + name: bioconductor-varianttools + path: recipes/bioconductor-varianttools + version: 1.22.0 + diff --git a/recipes/bioconductor-varianttoolsdata/meta.yaml b/recipes/bioconductor-varianttoolsdata/meta.yaml new file mode 100644 index 0000000000000..417fc548956f5 --- /dev/null +++ b/recipes/bioconductor-varianttoolsdata/meta.yaml @@ -0,0 +1,40 @@ +{% set version = "1.6.0" %} +{% set name = "VariantToolsData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 6d1a1707b091b0d4beeb7f2cf0f9fb7f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: VariantTools (>= 1.3.4), gmapR (>= 1.3.3), BiocStyle +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Data from the sequencing of a 50/50 mixture of HapMap trio samples NA12878 (CEU) and NA19240 (YRI), subset to the TP53 region.' + diff --git a/recipes/bioconductor-varianttoolsdata/post-link.sh b/recipes/bioconductor-varianttoolsdata/post-link.sh new file mode 100644 index 0000000000000..35c1c81836b4f --- /dev/null +++ b/recipes/bioconductor-varianttoolsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="VariantToolsData_1.6.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/VariantToolsData_1.6.0.tar.gz" + "https://bioarchive.galaxyproject.org/VariantToolsData_1.6.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-varianttoolsdata/bioconductor-varianttoolsdata_1.6.0_src_all.tar.gz" +) +MD5="6d1a1707b091b0d4beeb7f2cf0f9fb7f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-varianttoolsdata/pre-unlink.sh b/recipes/bioconductor-varianttoolsdata/pre-unlink.sh new file mode 100644 index 0000000000000..a9964d150abc0 --- /dev/null +++ b/recipes/bioconductor-varianttoolsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ VariantToolsData diff --git a/recipes/bioconductor-vbmp/build.sh b/recipes/bioconductor-vbmp/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-vbmp/build.sh +++ b/recipes/bioconductor-vbmp/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vbmp/meta.yaml b/recipes/bioconductor-vbmp/meta.yaml index 4b91eeadddd3b..cde6a125b98f2 100644 --- a/recipes/bioconductor-vbmp/meta.yaml +++ b/recipes/bioconductor-vbmp/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.48.0" %} +{% set version = "1.50.0" %} {% set name = "vbmp" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 6e0eaa285699b910c8f7dc3da040d774dc1b04c170d74884e0c73f14e556e8df + md5: 775146794e65565df652e53d0330aff5 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase (>= 2.5.5), statmod requirements: host: - r-base @@ -25,10 +27,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'Variational Bayesian Multinomial Probit Regression with Gaussian Process Priors. It estimates class membership posterior probability employing variational and sparse approximation to the full posterior. This software also incorporates feature weighting by means of Automatic Relevance Determination.' extra: identifiers: - biotools:vbmp - doi:10.1093/bioinformatics/btm535 + parent_recipe: + name: bioconductor-vbmp + path: recipes/bioconductor-vbmp + version: 1.48.0 + diff --git a/recipes/bioconductor-vega/build.sh b/recipes/bioconductor-vega/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-vega/build.sh +++ b/recipes/bioconductor-vega/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vega/meta.yaml b/recipes/bioconductor-vega/meta.yaml index 95dfbfd56add3..f8b577d3139ff 100644 --- a/recipes/bioconductor-vega/meta.yaml +++ b/recipes/bioconductor-vega/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.28.0" %} +{% set version = "1.30.0" %} {% set name = "Vega" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: fb8f664b4b98bf2143bf215fa949fde00a8906915c9b9d004f6c242ff931f78c + md5: 909008499be8b351162b36976db05a5b build: number: 0 rpaths: @@ -28,10 +28,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'Vega (Variational Estimator for Genomic Aberrations) is an algorithm that adapts a very popular variational model (Mumford and Shah) used in image segmentation so that chromosomal aberrant regions can be efficiently detected.' extra: identifiers: - biotools:vega - doi:10.1093/bioinformatics/btq586 + parent_recipe: + name: bioconductor-vega + path: recipes/bioconductor-vega + version: 1.28.0 + diff --git a/recipes/bioconductor-vegamc/build.sh b/recipes/bioconductor-vegamc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-vegamc/build.sh +++ b/recipes/bioconductor-vegamc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vegamc/meta.yaml b/recipes/bioconductor-vegamc/meta.yaml index a276db1b721e2..5e47bd6025c9d 100644 --- a/recipes/bioconductor-vegamc/meta.yaml +++ b/recipes/bioconductor-vegamc/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "3.18.0" %} +{% set version = "3.20.0" %} {% set name = "VegaMC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 4abeb54d7a68466198c47961c6bed5ae0b7699cf3f039a9db203e911b1caa711 + md5: c3e60f589acb272536f80e01eb14e83f build: number: 0 rpaths: @@ -18,14 +18,14 @@ build: - lib/ requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genoset >=1.36.0,<1.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genoset >=1.38.0,<1.39.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-genoset >=1.36.0,<1.38.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-genoset >=1.38.0,<1.39.0' - r-base build: - {{ compiler('c') }} @@ -34,10 +34,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package enables the detection of driver chromosomal imbalances including loss of heterozygosity (LOH) from array comparative genomic hybridization (aCGH) data. VegaMC performs a joint segmentation of a dataset and uses a statistical framework to distinguish between driver and passenger mutation. VegaMC has been implemented so that it can be immediately integrated with the output produced by PennCNV tool. In addition, VegaMC produces in output two web pages that allows a rapid navigation between both the detected regions and the altered genes. In the web page that summarizes the altered genes, the link to the respective Ensembl gene web page is reported.' extra: identifiers: - biotools:vegamc - doi:10.1093/bioinformatics/bts453 + parent_recipe: + name: bioconductor-vegamc + path: recipes/bioconductor-vegamc + version: 3.18.0 + diff --git a/recipes/bioconductor-vidger/build.sh b/recipes/bioconductor-vidger/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-vidger/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vidger/meta.yaml b/recipes/bioconductor-vidger/meta.yaml new file mode 100644 index 0000000000000..51e9f28d3f5b2 --- /dev/null +++ b/recipes/bioconductor-vidger/meta.yaml @@ -0,0 +1,57 @@ +{% set version = "1.2.0" %} +{% set name = "vidger" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d4f2fe186eca458410c0b57f166f8500 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, testthat +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggally + - r-ggplot2 + - r-ggrepel + - r-knitr + - r-rcolorbrewer + - r-rmarkdown + - r-scales + - r-tidyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - r-base + - r-ggally + - r-ggplot2 + - r-ggrepel + - r-knitr + - r-rcolorbrewer + - r-rmarkdown + - r-scales + - r-tidyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL-3 | file LICENSE' + summary: 'The aim of vidger is to rapidly generate information-rich visualizations for the interpretation of differential gene expression results from three widely-used tools: Cuffdiff, DESeq2, and edgeR.' + diff --git a/recipes/bioconductor-viper/build.sh b/recipes/bioconductor-viper/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-viper/build.sh +++ b/recipes/bioconductor-viper/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-viper/meta.yaml b/recipes/bioconductor-viper/meta.yaml index f4b14539805cb..68d4287efedf9 100644 --- a/recipes/bioconductor-viper/meta.yaml +++ b/recipes/bioconductor-viper/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.14.0" %} +{% set version = "1.16.0" %} {% set name = "viper" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: afb1a611e36c40cd3b1b58ae2f1bcd20df028bee9e01981788d735283c348203 + md5: 88466e58bd88dc075343d450c2688b68 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: bcellViper requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 - r-kernsmooth - r-mixtools run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - r-e1071 - r-kernsmooth @@ -33,9 +35,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'file LICENSE' summary: 'Inference of protein activity from gene expression data, including the VIPER and msVIPER algorithms' extra: identifiers: - biotools:viper + parent_recipe: + name: bioconductor-viper + path: recipes/bioconductor-viper + version: 1.14.0 + diff --git a/recipes/bioconductor-vitisviniferacdf/meta.yaml b/recipes/bioconductor-vitisviniferacdf/meta.yaml new file mode 100644 index 0000000000000..ed6b179d4aec2 --- /dev/null +++ b/recipes/bioconductor-vitisviniferacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "vitisviniferacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 8eb491f3ffa3ff0814f5c155787ae160 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Vitis_Vinifera.cdf file.' + diff --git a/recipes/bioconductor-vitisviniferacdf/post-link.sh b/recipes/bioconductor-vitisviniferacdf/post-link.sh new file mode 100644 index 0000000000000..30da75c70b202 --- /dev/null +++ b/recipes/bioconductor-vitisviniferacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="vitisviniferacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/vitisviniferacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/vitisviniferacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vitisviniferacdf/bioconductor-vitisviniferacdf_2.18.0_src_all.tar.gz" +) +MD5="8eb491f3ffa3ff0814f5c155787ae160" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-vitisviniferacdf/pre-unlink.sh b/recipes/bioconductor-vitisviniferacdf/pre-unlink.sh new file mode 100644 index 0000000000000..d1d902342e10c --- /dev/null +++ b/recipes/bioconductor-vitisviniferacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ vitisviniferacdf diff --git a/recipes/bioconductor-vitisviniferaprobe/meta.yaml b/recipes/bioconductor-vitisviniferaprobe/meta.yaml new file mode 100644 index 0000000000000..5e201142ef935 --- /dev/null +++ b/recipes/bioconductor-vitisviniferaprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "vitisviniferaprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 386c0d5e37896d073ac20970e88b3160 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Vitis\_Vinifera\_probe\_tab.' + diff --git a/recipes/bioconductor-vitisviniferaprobe/post-link.sh b/recipes/bioconductor-vitisviniferaprobe/post-link.sh new file mode 100644 index 0000000000000..4fabb354f6bdf --- /dev/null +++ b/recipes/bioconductor-vitisviniferaprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="vitisviniferaprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/vitisviniferaprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/vitisviniferaprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vitisviniferaprobe/bioconductor-vitisviniferaprobe_2.18.0_src_all.tar.gz" +) +MD5="386c0d5e37896d073ac20970e88b3160" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-vitisviniferaprobe/pre-unlink.sh b/recipes/bioconductor-vitisviniferaprobe/pre-unlink.sh new file mode 100644 index 0000000000000..867a2f8f4821d --- /dev/null +++ b/recipes/bioconductor-vitisviniferaprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ vitisviniferaprobe diff --git a/recipes/bioconductor-vsn/build.sh b/recipes/bioconductor-vsn/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-vsn/build.sh +++ b/recipes/bioconductor-vsn/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vsn/conda_build_config.yaml b/recipes/bioconductor-vsn/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-vsn/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-vsn/meta.yaml b/recipes/bioconductor-vsn/meta.yaml index 1b40a9a5e68cb..e2851a42f7d6b 100644 --- a/recipes/bioconductor-vsn/meta.yaml +++ b/recipes/bioconductor-vsn/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "3.48.1" %} +{% set version = "3.50.0" %} {% set name = "vsn" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: f0948b5041b216e92af04571de5150a210ebc88bbbf630ae720bfff10654d54c + md5: bf53a681b9b9bdfce2b27cb556e2b9d0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: affydata, hgu95av2cdf, BiocStyle, knitr, dplyr, testthat requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 - r-lattice run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' - r-base - r-ggplot2 - r-lattice @@ -38,9 +39,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'The package implements a method for normalising microarray intensities, and works for single- and multiple-color arrays. It can also be used for data from other technologies, as long as they have similar format. The method uses a robust variant of the maximum-likelihood estimator for an additive-multiplicative error model and affine calibration. The model incorporates data calibration step (a.k.a. normalization), a model for the dependence of the variance on the mean intensity and a variance stabilizing data transformation. Differences between transformed intensities are analogous to "normalized log-ratios". However, in contrast to the latter, their variance is independent of the mean, and they are usually more sensitive and specific in detecting differential transcription.' extra: identifiers: - biotools:vsn + parent_recipe: + name: bioconductor-vsn + path: recipes/bioconductor-vsn + version: 3.48.1 + diff --git a/recipes/bioconductor-vtpnet/build.sh b/recipes/bioconductor-vtpnet/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-vtpnet/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vtpnet/meta.yaml b/recipes/bioconductor-vtpnet/meta.yaml new file mode 100644 index 0000000000000..d51d1a3fd1991 --- /dev/null +++ b/recipes/bioconductor-vtpnet/meta.yaml @@ -0,0 +1,43 @@ +{% set version = "0.22.0" %} +{% set name = "vtpnet" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: c72d10bf3d20932c1847fa2aad5f914e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: MotifDb, VariantAnnotation, Rgraphviz +requirements: + host: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gwascat >=2.14.0,<2.15.0' + - r-base + - r-doparallel + - r-foreach + run: + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' + - 'bioconductor-gwascat >=2.14.0,<2.15.0' + - r-base + - r-doparallel + - r-foreach +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'variant-transcription factor-phenotype networks, inspired by Maurano et al., Science (2012), PMID 22955828' + diff --git a/recipes/bioconductor-vulcan/build.sh b/recipes/bioconductor-vulcan/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-vulcan/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-vulcan/meta.yaml b/recipes/bioconductor-vulcan/meta.yaml new file mode 100644 index 0000000000000..cfbfaa539b091 --- /dev/null +++ b/recipes/bioconductor-vulcan/meta.yaml @@ -0,0 +1,61 @@ +{% set version = "1.4.0" %} +{% set name = "vulcan" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bdec6ffd2a60d2f83183dd2c76bcb637 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: vulcandata +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-diffbind >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-catools + - r-gplots + - r-locfit + - r-wordcloud + - r-zoo + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-chippeakanno >=3.16.0,<3.17.0' + - 'bioconductor-csaw >=1.16.0,<1.17.0' + - 'bioconductor-deseq >=1.34.0,<1.35.0' + - 'bioconductor-diffbind >=2.10.0,<2.11.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-txdb.hsapiens.ucsc.hg19.knowngene >=3.2.0,<3.3.0' + - 'bioconductor-viper >=1.16.0,<1.17.0' + - r-base + - r-catools + - r-gplots + - r-locfit + - r-wordcloud + - r-zoo +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL-3 + summary: 'Vulcan (VirtUaL ChIP-Seq Analysis through Networks) is a package that interrogates gene regulatory networks to infer cofactors significantly enriched in a differential binding signature coming from ChIP-Seq data. In order to do so, our package combines strategies from different BioConductor packages: DESeq for data normalization, ChIPpeakAnno and DiffBind for annotation and definition of ChIP-Seq genomic peaks, csaw to define optimal peak width and viper for applying a regulatory network over a differential binding signature.' + diff --git a/recipes/bioconductor-vulcandata/meta.yaml b/recipes/bioconductor-vulcandata/meta.yaml new file mode 100644 index 0000000000000..7c0efa4ece950 --- /dev/null +++ b/recipes/bioconductor-vulcandata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.4.0" %} +{% set name = "vulcandata" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 65a1dc1a4c75edacf512fe57434790e2 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: LGPL-3 + summary: 'This package provides a dummy regulatory network and ChIP-Seq dataset for running examples in the vulcan package' + diff --git a/recipes/bioconductor-vulcandata/post-link.sh b/recipes/bioconductor-vulcandata/post-link.sh new file mode 100644 index 0000000000000..90d30a95d00cc --- /dev/null +++ b/recipes/bioconductor-vulcandata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="vulcandata_1.4.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/vulcandata_1.4.0.tar.gz" + "https://bioarchive.galaxyproject.org/vulcandata_1.4.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-vulcandata/bioconductor-vulcandata_1.4.0_src_all.tar.gz" +) +MD5="65a1dc1a4c75edacf512fe57434790e2" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-vulcandata/pre-unlink.sh b/recipes/bioconductor-vulcandata/pre-unlink.sh new file mode 100644 index 0000000000000..0cbbb62c0f2b1 --- /dev/null +++ b/recipes/bioconductor-vulcandata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ vulcandata diff --git a/recipes/bioconductor-watermelon/build.sh b/recipes/bioconductor-watermelon/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-watermelon/build.sh +++ b/recipes/bioconductor-watermelon/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-watermelon/conda_build_config.yaml b/recipes/bioconductor-watermelon/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-watermelon/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-watermelon/meta.yaml b/recipes/bioconductor-watermelon/meta.yaml index 3ee7290b89461..d3ebfb2c86c8d 100644 --- a/recipes/bioconductor-watermelon/meta.yaml +++ b/recipes/bioconductor-watermelon/meta.yaml @@ -1,49 +1,56 @@ -{% set version = "1.24.0" %} +{% set version = "1.26.0" %} {% set name = "wateRmelon" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 01a311de4db43001c9fa0f2695fe6737aee266f67672dcd5fa3dab9f9ddc2db4 + md5: 850367d09d233968ac5b418f29de23a4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RPMM, IlluminaHumanMethylationEPICanno.ilm10b2.hg19, IlluminaHumanMethylationEPICmanifest, irlba requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-matrixstats run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.8.0' - - 'bioconductor-illuminaio >=0.22.0,<0.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-lumi >=2.32.0,<2.34.0' - - 'bioconductor-methylumi >=2.26.0,<2.28.0' - - 'bioconductor-roc >=1.56.0,<1.58.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-illuminahumanmethylation450kanno.ilmn12.hg19 >=0.6.0,<0.7.0' + - 'bioconductor-illuminaio >=0.24.0,<0.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-lumi >=2.34.0,<2.35.0' + - 'bioconductor-methylumi >=2.28.0,<2.29.0' + - 'bioconductor-roc >=1.58.0,<1.59.0' - r-base - r-matrixstats test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: '15 flavours of betas and three performance metrics, with methods for objects produced by methylumi and minfi packages.' extra: identifiers: - biotools:watermelon + parent_recipe: + name: bioconductor-watermelon + path: recipes/bioconductor-watermelon + version: 1.24.0 + diff --git a/recipes/bioconductor-wavcluster/build.sh b/recipes/bioconductor-wavcluster/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-wavcluster/build.sh +++ b/recipes/bioconductor-wavcluster/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-wavcluster/meta.yaml b/recipes/bioconductor-wavcluster/meta.yaml index 30637d195e8d4..9dae9a0067d92 100644 --- a/recipes/bioconductor-wavcluster/meta.yaml +++ b/recipes/bioconductor-wavcluster/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "2.14.0" %} +{% set version = "2.16.0" %} {% set name = "wavClusteR" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: f5076a5fa67e32d22faa10e696558dc5b9bd251bac83070ba8ef8ebca8ab8526 + md5: c27ac709b57b39907a298c5d8233757a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, BSgenome.Hsapiens.UCSC.hg19 requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-foreach - r-ggplot2 @@ -35,14 +37,14 @@ requirements: - r-stringr - r-wmtsa run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomicfeatures >=1.32.2,<1.34.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rsamtools >=1.32.3,<1.34.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomicfeatures >=1.34.0,<1.35.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rsamtools >=1.34.0,<1.35.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-foreach - r-ggplot2 @@ -55,9 +57,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'The package provides an integrated pipeline for the analysis of PAR-CLIP data. PAR-CLIP-induced transitions are first discriminated from sequencing errors, SNPs and additional non-experimental sources by a non- parametric mixture model. The protein binding sites (clusters) are then resolved at high resolution and cluster statistics are estimated using a rigorous Bayesian framework. Post-processing of the results, data export for UCSC genome browser visualization and motif search analysis are provided. In addition, the package allows to integrate RNA-Seq data to estimate the False Discovery Rate of cluster detection. Key functions support parallel multicore computing. Note: while wavClusteR was designed for PAR-CLIP data analysis, it can be applied to the analysis of other NGS data obtained from experimental procedures that induce nucleotide substitutions (e.g. BisSeq).' extra: identifiers: - biotools:wavcluster + parent_recipe: + name: bioconductor-wavcluster + path: recipes/bioconductor-wavcluster + version: 2.14.0 + diff --git a/recipes/bioconductor-wavetiling/build.sh b/recipes/bioconductor-wavetiling/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-wavetiling/build.sh +++ b/recipes/bioconductor-wavetiling/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-wavetiling/conda_build_config.yaml b/recipes/bioconductor-wavetiling/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-wavetiling/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-wavetiling/meta.yaml b/recipes/bioconductor-wavetiling/meta.yaml index a136d9d3c44f3..4c1ec00237381 100644 --- a/recipes/bioconductor-wavetiling/meta.yaml +++ b/recipes/bioconductor-wavetiling/meta.yaml @@ -1,44 +1,45 @@ -{% set version = "1.22.0" %} +{% set version = "1.24.0" %} {% set name = "waveTiling" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 771257e7925bf8ae57b042f6885eb251184c285149d81e9c374fed49bdf82fb1 + md5: 80d2a5104b88c2621ded2314d7a986ba build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BSgenome, BSgenome.Athaliana.TAIR.TAIR9, waveTilingData, pd.atdschip.tiling, TxDb.Athaliana.BioMart.plantsmart22 requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-waveslim run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biostrings >=2.48.0,<2.50.0' - - 'bioconductor-genomegraphs >=1.40.0,<1.42.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-oligo >=1.44.0,<1.46.0' - - 'bioconductor-oligoclasses >=1.42.0,<1.44.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biostrings >=2.50.0,<2.51.0' + - 'bioconductor-genomegraphs >=1.42.0,<1.43.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-oligo >=1.46.0,<1.47.0' + - 'bioconductor-oligoclasses >=1.44.0,<1.45.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' - r-base - r-waveslim build: @@ -48,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=2)' summary: 'This package is designed to conduct transcriptome analysis for tiling arrays based on fast wavelet-based functional models.' extra: identifiers: - biotools:wavetiling - doi:10.1186/1471-2105-13-234 + parent_recipe: + name: bioconductor-wavetiling + path: recipes/bioconductor-wavetiling + version: 1.22.0 + diff --git a/recipes/bioconductor-wavetilingdata/meta.yaml b/recipes/bioconductor-wavetilingdata/meta.yaml new file mode 100644 index 0000000000000..3f7383a954a10 --- /dev/null +++ b/recipes/bioconductor-wavetilingdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "waveTilingData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 4fe1e828f7c998a4d3c9621886e5c5f1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'Experiment and Annotation Data files used by the examples / vignette in the waveTiling package' + diff --git a/recipes/bioconductor-wavetilingdata/post-link.sh b/recipes/bioconductor-wavetilingdata/post-link.sh new file mode 100644 index 0000000000000..223c3ba3a8318 --- /dev/null +++ b/recipes/bioconductor-wavetilingdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="waveTilingData_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/waveTilingData_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/waveTilingData_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wavetilingdata/bioconductor-wavetilingdata_1.18.0_src_all.tar.gz" +) +MD5="4fe1e828f7c998a4d3c9621886e5c5f1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-wavetilingdata/pre-unlink.sh b/recipes/bioconductor-wavetilingdata/pre-unlink.sh new file mode 100644 index 0000000000000..172d5e328bb1f --- /dev/null +++ b/recipes/bioconductor-wavetilingdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ waveTilingData diff --git a/recipes/bioconductor-weaver/build.sh b/recipes/bioconductor-weaver/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-weaver/build.sh +++ b/recipes/bioconductor-weaver/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-weaver/meta.yaml b/recipes/bioconductor-weaver/meta.yaml index 8291f6e4ab46a..f9d779dba3583 100644 --- a/recipes/bioconductor-weaver/meta.yaml +++ b/recipes/bioconductor-weaver/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.46.0" %} +{% set version = "1.48.0" %} {% set name = "weaver" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: d87b51bf4c5b15c2c17f9c4310b535b7eb3abe9d2ee2918167e7193543e025cc + md5: 9b2abdd081e7f54dff55bfd0fe27512c build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: codetools requirements: host: - r-base @@ -29,10 +31,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-2 summary: 'This package provides enhancements on the Sweave() function in the base package. In particular a facility for caching code chunk results is included.' extra: identifiers: - biotools:weaver - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-weaver + path: recipes/bioconductor-weaver + version: 1.46.0 + diff --git a/recipes/bioconductor-webbioc/build.sh b/recipes/bioconductor-webbioc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-webbioc/build.sh +++ b/recipes/bioconductor-webbioc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-webbioc/conda_build_config.yaml b/recipes/bioconductor-webbioc/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-webbioc/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-webbioc/meta.yaml b/recipes/bioconductor-webbioc/meta.yaml index 593165c34993e..fa011d9b174f3 100644 --- a/recipes/bioconductor-webbioc/meta.yaml +++ b/recipes/bioconductor-webbioc/meta.yaml @@ -1,50 +1,57 @@ -{% set version = "1.52.0" %} +{% set version = "1.54.0" %} {% set name = "webbioc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 89dee6b8f11fa13f49f128a629fa0dc101b3f9ffdfba186a533e4c4b943d697c + md5: d08d8ccc53dc8c06d1472dc5e6e528d4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# SystemRequirements: Unix, Perl (>= 5.6.0), Netpbm requirements: host: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base + - r-biocmanager run: - - 'bioconductor-affy >=1.58.0,<1.60.0' - - 'bioconductor-annaffy >=1.52.0,<1.54.0' - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocinstaller >=1.30.0,<1.32.0' - - 'bioconductor-gcrma >=2.52.0,<2.54.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-qvalue >=2.12.0,<2.14.0' - - 'bioconductor-vsn >=3.48.1,<3.50.0' + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-annaffy >=1.54.0,<1.55.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-gcrma >=2.54.0,<2.55.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-qvalue >=2.14.0,<2.15.0' + - 'bioconductor-vsn >=3.50.0,<3.51.0' - r-base + - r-biocmanager test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2)' summary: 'An integrated web interface for doing microarray analysis using several of the Bioconductor packages. It is intended to be deployed as a centralized bioinformatics resource for use by many users. (Currently only Affymetrix oligonucleotide analysis is supported.)' extra: identifiers: - biotools:webbioc - doi:10.1007/0-387-29362-0_18 + parent_recipe: + name: bioconductor-webbioc + path: recipes/bioconductor-webbioc + version: 1.52.0 + diff --git a/recipes/bioconductor-wes.1kg.wugsc/meta.yaml b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml new file mode 100644 index 0000000000000..454eca7497d3a --- /dev/null +++ b/recipes/bioconductor-wes.1kg.wugsc/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.14.0" %} +{% set name = "WES.1KG.WUGSC" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: d1013abff0fe02136aab55a3354529ee +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL-2 + summary: 'The assembled .bam files of whole exome sequencing data from the 1000 Genomes Project. 46 samples sequenced by the Washington University Genome Sequencing Center are included.' + diff --git a/recipes/bioconductor-wes.1kg.wugsc/post-link.sh b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh new file mode 100644 index 0000000000000..bb8e8e3a080f9 --- /dev/null +++ b/recipes/bioconductor-wes.1kg.wugsc/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="WES.1KG.WUGSC_1.14.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/WES.1KG.WUGSC_1.14.0.tar.gz" + "https://bioarchive.galaxyproject.org/WES.1KG.WUGSC_1.14.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wes.1kg.wugsc/bioconductor-wes.1kg.wugsc_1.14.0_src_all.tar.gz" +) +MD5="d1013abff0fe02136aab55a3354529ee" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-wes.1kg.wugsc/pre-unlink.sh b/recipes/bioconductor-wes.1kg.wugsc/pre-unlink.sh new file mode 100644 index 0000000000000..607efb9acfa4f --- /dev/null +++ b/recipes/bioconductor-wes.1kg.wugsc/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ WES.1KG.WUGSC diff --git a/recipes/bioconductor-wheatcdf/meta.yaml b/recipes/bioconductor-wheatcdf/meta.yaml new file mode 100644 index 0000000000000..a85e44f45821a --- /dev/null +++ b/recipes/bioconductor-wheatcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "wheatcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0abeeeb9700b8d93a1a83769bdd8480f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the wheat.cdf file.' + diff --git a/recipes/bioconductor-wheatcdf/post-link.sh b/recipes/bioconductor-wheatcdf/post-link.sh new file mode 100644 index 0000000000000..5658a300de096 --- /dev/null +++ b/recipes/bioconductor-wheatcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="wheatcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/wheatcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/wheatcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wheatcdf/bioconductor-wheatcdf_2.18.0_src_all.tar.gz" +) +MD5="0abeeeb9700b8d93a1a83769bdd8480f" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-wheatcdf/pre-unlink.sh b/recipes/bioconductor-wheatcdf/pre-unlink.sh new file mode 100644 index 0000000000000..317a3226abc02 --- /dev/null +++ b/recipes/bioconductor-wheatcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ wheatcdf diff --git a/recipes/bioconductor-wheatprobe/meta.yaml b/recipes/bioconductor-wheatprobe/meta.yaml new file mode 100644 index 0000000000000..fa8d527d7836b --- /dev/null +++ b/recipes/bioconductor-wheatprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "wheatprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: b602d5050239850515be9dce12286360 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was wheat\_probe\_tab.' + diff --git a/recipes/bioconductor-wheatprobe/post-link.sh b/recipes/bioconductor-wheatprobe/post-link.sh new file mode 100644 index 0000000000000..fcf9571ef0b4f --- /dev/null +++ b/recipes/bioconductor-wheatprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="wheatprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/wheatprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/wheatprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-wheatprobe/bioconductor-wheatprobe_2.18.0_src_all.tar.gz" +) +MD5="b602d5050239850515be9dce12286360" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-wheatprobe/pre-unlink.sh b/recipes/bioconductor-wheatprobe/pre-unlink.sh new file mode 100644 index 0000000000000..5473c98ba8453 --- /dev/null +++ b/recipes/bioconductor-wheatprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ wheatprobe diff --git a/recipes/bioconductor-widgettools/build.sh b/recipes/bioconductor-widgettools/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-widgettools/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-widgettools/meta.yaml b/recipes/bioconductor-widgettools/meta.yaml new file mode 100644 index 0000000000000..5d3ccaf1c957d --- /dev/null +++ b/recipes/bioconductor-widgettools/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.60.0" %} +{% set name = "widgetTools" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c317790521ce4176632769af78d89b4f +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase +requirements: + host: + - r-base + run: + - r-base +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: LGPL + summary: 'This packages contains tools to support the construction of tcltk widgets' + diff --git a/recipes/bioconductor-wiggleplotr/build.sh b/recipes/bioconductor-wiggleplotr/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-wiggleplotr/build.sh +++ b/recipes/bioconductor-wiggleplotr/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-wiggleplotr/meta.yaml b/recipes/bioconductor-wiggleplotr/meta.yaml index 1c4eb374b3e83..6c8a0a54a703a 100644 --- a/recipes/bioconductor-wiggleplotr/meta.yaml +++ b/recipes/bioconductor-wiggleplotr/meta.yaml @@ -1,28 +1,30 @@ -{% set version = "1.4.0" %} +{% set version = "1.6.0" %} {% set name = "wiggleplotr" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a1996015e41c68a01d2985c6f0447426d1cff870489c7ec3240fb0c9e2c819ea + md5: 4385b0b448bb77ee6948c0a42a08962e build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, biomaRt, GenomicFeatures, testthat, ensembldb, EnsDb.Hsapiens.v86, org.Hs.eg.db, TxDb.Hsapiens.UCSC.hg38.knownGene, AnnotationDbi, AnnotationFilter requirements: host: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-assertthat - r-base - r-cowplot @@ -30,11 +32,11 @@ requirements: - 'r-ggplot2 >=2.2.0' - r-purrr run: - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-rtracklayer >=1.40.6,<1.42.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-rtracklayer >=1.42.0,<1.43.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-assertthat - r-base - r-cowplot @@ -45,8 +47,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Apache License 2.0' summary: 'Tools to visualise read coverage from sequencing experiments together with genomic annotations (genes, transcripts, peaks). Introns of long transcripts can be rescaled to a fixed length for better visualisation of exonic read coverage.' - +extra: + parent_recipe: + name: bioconductor-wiggleplotr + path: recipes/bioconductor-wiggleplotr + version: 1.4.0 diff --git a/recipes/bioconductor-worm.db0/meta.yaml b/recipes/bioconductor-worm.db0/meta.yaml new file mode 100644 index 0000000000000..68bc101fb78da --- /dev/null +++ b/recipes/bioconductor-worm.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "worm.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 65473df3ea58399054f7c71a53d33362 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for worm, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-worm.db0/post-link.sh b/recipes/bioconductor-worm.db0/post-link.sh new file mode 100644 index 0000000000000..a529de249585a --- /dev/null +++ b/recipes/bioconductor-worm.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="worm.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/worm.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/worm.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-worm.db0/bioconductor-worm.db0_3.7.1_src_all.tar.gz" +) +MD5="65473df3ea58399054f7c71a53d33362" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-worm.db0/pre-unlink.sh b/recipes/bioconductor-worm.db0/pre-unlink.sh new file mode 100644 index 0000000000000..881e4cceefb19 --- /dev/null +++ b/recipes/bioconductor-worm.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ worm.db0 diff --git a/recipes/bioconductor-wrench/build.sh b/recipes/bioconductor-wrench/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-wrench/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-wrench/meta.yaml b/recipes/bioconductor-wrench/meta.yaml new file mode 100644 index 0000000000000..0b9112230adef --- /dev/null +++ b/recipes/bioconductor-wrench/meta.yaml @@ -0,0 +1,39 @@ +{% set version = "1.0.0" %} +{% set name = "Wrench" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a13adf697da0006944f1f36b3c5748e5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, metagenomeSeq, DESeq2, edgeR +requirements: + host: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-locfit + - r-matrixstats + run: + - 'bioconductor-limma >=3.38.0,<3.39.0' + - r-base + - r-locfit + - r-matrixstats +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Wrench is a package for normalization sparse genomic count data, like that arising from 16s metagenomic surveys.' + diff --git a/recipes/bioconductor-xbseq/build.sh b/recipes/bioconductor-xbseq/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-xbseq/build.sh +++ b/recipes/bioconductor-xbseq/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xbseq/meta.yaml b/recipes/bioconductor-xbseq/meta.yaml index 01f4735da943e..3a7552ef45c76 100644 --- a/recipes/bioconductor-xbseq/meta.yaml +++ b/recipes/bioconductor-xbseq/meta.yaml @@ -1,26 +1,28 @@ -{% set version = "1.12.0" %} +{% set version = "1.14.0" %} {% set name = "XBSeq" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 3d566b6c678dbd5a3fa93100a24d4ec43b9e8a5c5ae1ad538a355fd2a8abd3ea + md5: fdc86bd68c94758b19a8a3fdefe2294a build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, DESeq, rmarkdown, BiocStyle, testthat requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-roar >=1.16.0,<1.18.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-roar >=1.18.0,<1.19.0' - r-base - r-dplyr - r-ggplot2 @@ -29,9 +31,9 @@ requirements: - r-matrixstats - r-pracma run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-deseq2 >=1.20.0,<1.22.0' - - 'bioconductor-roar >=1.16.0,<1.18.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-deseq2 >=1.22.0,<1.23.0' + - 'bioconductor-roar >=1.18.0,<1.19.0' - r-base - r-dplyr - r-ggplot2 @@ -43,10 +45,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>=3)' summary: 'We developed a novel algorithm, XBSeq, where a statistical model was established based on the assumption that observed signals are the convolution of true expression signals and sequencing noises. The mapped reads in non-exonic regions are considered as sequencing noises, which follows a Poisson distribution. Given measureable observed and noise signals from RNA-seq data, true expression signals, assuming governed by the negative binomial distribution, can be delineated and thus the accurate detection of differential expressed genes.' extra: identifiers: - biotools:xbseq - doi:10.1186/1471-2164-16-S7-S14 + parent_recipe: + name: bioconductor-xbseq + path: recipes/bioconductor-xbseq + version: 1.12.0 + diff --git a/recipes/bioconductor-xcms/build.sh b/recipes/bioconductor-xcms/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-xcms/build.sh +++ b/recipes/bioconductor-xcms/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xcms/meta.yaml b/recipes/bioconductor-xcms/meta.yaml index a5f8e3b32d408..ded78b96e8c45 100644 --- a/recipes/bioconductor-xcms/meta.yaml +++ b/recipes/bioconductor-xcms/meta.yaml @@ -1,52 +1,55 @@ -{% set version = "3.2.0" %} +{% set version = "3.4.1" %} {% set name = "xcms" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: af86ad398169f2ed955bb5fbfea86ca3913fda3431cbaac59ec0ca7b99e91a77 + md5: 8b2683e6ffcea74e126a2846fcc887b9 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: BiocStyle, caTools, knitr (>= 1.1.0), faahKO, msdata, ncdf4, rgl, microbenchmark, testthat, pander, magrittr, MALDIquant requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - r-plyr - r-rann - r-rcolorbrewer + - r-robustbase run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-biocparallel >=1.14.2,<1.16.0' - - 'bioconductor-massspecwavelet >=1.46.0,<1.48.0' - - 'bioconductor-msnbase >=2.6.4,<2.8.0' - - 'bioconductor-multtest >=2.36.0,<2.38.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-protgenerics >=1.12.0,<1.14.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-massspecwavelet >=1.48.0,<1.49.0' + - 'bioconductor-msnbase >=2.8.0,<2.9.0' + - 'bioconductor-multtest >=2.38.0,<2.39.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-protgenerics >=1.14.0,<1.15.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' - r-base - r-lattice - r-plyr - r-rann - r-rcolorbrewer + - r-robustbase build: - {{ compiler('c') }} - {{ compiler('cxx') }} @@ -55,9 +58,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL (>= 2) + file LICENSE' summary: 'Framework for processing and visualization of chromatographically separated and single-spectra mass spectral data. Imports from AIA/ANDI NetCDF, mzXML, mzData and mzML files. Preprocesses data for high-throughput, untargeted analyte profiling.' extra: identifiers: - biotools:xcms + parent_recipe: + name: bioconductor-xcms + path: recipes/bioconductor-xcms + version: 3.2.0 + diff --git a/recipes/bioconductor-xde/build.sh b/recipes/bioconductor-xde/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-xde/build.sh +++ b/recipes/bioconductor-xde/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xde/meta.yaml b/recipes/bioconductor-xde/meta.yaml index 93feaccbceff3..751c72ab8ce2a 100644 --- a/recipes/bioconductor-xde/meta.yaml +++ b/recipes/bioconductor-xde/meta.yaml @@ -1,40 +1,41 @@ -{% set version = "2.26.0" %} +{% set version = "2.28.0" %} {% set name = "XDE" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: a9e0c589824eecc5b5c2d8a7b2032c20922987ed7bcabd68b8317c02d8889929 + md5: be18c127b068e92c2811ceaf408326e0 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: MASS, RUnit requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genemeta >=1.52.0,<1.54.0' - - 'bioconductor-mergemaid >=2.52.0,<2.54.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genemeta >=1.54.0,<1.55.0' + - 'bioconductor-mergemaid >=2.54.0,<2.55.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-gtools - r-mvtnorm - r-rcolorbrewer run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-genemeta >=1.52.0,<1.54.0' - - 'bioconductor-mergemaid >=2.52.0,<2.54.0' - - 'bioconductor-siggenes >=1.54.0,<1.56.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-genemeta >=1.54.0,<1.55.0' + - 'bioconductor-mergemaid >=2.54.0,<2.55.0' + - 'bioconductor-siggenes >=1.56.0,<1.57.0' - r-base - r-gtools - r-mvtnorm @@ -47,9 +48,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-2 summary: 'Multi-level model for cross-study detection of differential gene expression.' extra: identifiers: - biotools:xde + parent_recipe: + name: bioconductor-xde + path: recipes/bioconductor-xde + version: 2.26.0 + diff --git a/recipes/bioconductor-xenopus.db0/meta.yaml b/recipes/bioconductor-xenopus.db0/meta.yaml new file mode 100644 index 0000000000000..5e7f0076609dc --- /dev/null +++ b/recipes/bioconductor-xenopus.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "xenopus.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6a34dd176e70d66d4acda7a141e09ef5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for xenopus, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-xenopus.db0/post-link.sh b/recipes/bioconductor-xenopus.db0/post-link.sh new file mode 100644 index 0000000000000..c4321ffd699de --- /dev/null +++ b/recipes/bioconductor-xenopus.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xenopus.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopus.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/xenopus.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopus.db0/bioconductor-xenopus.db0_3.7.1_src_all.tar.gz" +) +MD5="6a34dd176e70d66d4acda7a141e09ef5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xenopus.db0/pre-unlink.sh b/recipes/bioconductor-xenopus.db0/pre-unlink.sh new file mode 100644 index 0000000000000..464ddebcced21 --- /dev/null +++ b/recipes/bioconductor-xenopus.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xenopus.db0 diff --git a/recipes/bioconductor-xenopuslaeviscdf/meta.yaml b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml new file mode 100644 index 0000000000000..69bf07308b8f9 --- /dev/null +++ b/recipes/bioconductor-xenopuslaeviscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xenopuslaeviscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9d09ff76471ae60faf71090e0638f240 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Xenopus_laevis.cdf file.' + diff --git a/recipes/bioconductor-xenopuslaeviscdf/post-link.sh b/recipes/bioconductor-xenopuslaeviscdf/post-link.sh new file mode 100644 index 0000000000000..cbdd908f7ad6f --- /dev/null +++ b/recipes/bioconductor-xenopuslaeviscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xenopuslaeviscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopuslaeviscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xenopuslaeviscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopuslaeviscdf/bioconductor-xenopuslaeviscdf_2.18.0_src_all.tar.gz" +) +MD5="9d09ff76471ae60faf71090e0638f240" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xenopuslaeviscdf/pre-unlink.sh b/recipes/bioconductor-xenopuslaeviscdf/pre-unlink.sh new file mode 100644 index 0000000000000..8abfb1e901c98 --- /dev/null +++ b/recipes/bioconductor-xenopuslaeviscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xenopuslaeviscdf diff --git a/recipes/bioconductor-xenopuslaevisprobe/meta.yaml b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml new file mode 100644 index 0000000000000..cdf4f6aac5897 --- /dev/null +++ b/recipes/bioconductor-xenopuslaevisprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xenopuslaevisprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 06a25268a5ab57bddf28bbb364ea977b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Xenopus\_laevis\_probe\_tab.' + diff --git a/recipes/bioconductor-xenopuslaevisprobe/post-link.sh b/recipes/bioconductor-xenopuslaevisprobe/post-link.sh new file mode 100644 index 0000000000000..3f8831f84392d --- /dev/null +++ b/recipes/bioconductor-xenopuslaevisprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xenopuslaevisprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xenopuslaevisprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xenopuslaevisprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xenopuslaevisprobe/bioconductor-xenopuslaevisprobe_2.18.0_src_all.tar.gz" +) +MD5="06a25268a5ab57bddf28bbb364ea977b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xenopuslaevisprobe/pre-unlink.sh b/recipes/bioconductor-xenopuslaevisprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e8a60156c3aa2 --- /dev/null +++ b/recipes/bioconductor-xenopuslaevisprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xenopuslaevisprobe diff --git a/recipes/bioconductor-xhybcasneuf/meta.yaml b/recipes/bioconductor-xhybcasneuf/meta.yaml new file mode 100644 index 0000000000000..c6aaebd59fc6c --- /dev/null +++ b/recipes/bioconductor-xhybcasneuf/meta.yaml @@ -0,0 +1,41 @@ +{% set version = "1.20.0" %} +{% set name = "XhybCasneuf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: e31cf97fb07e30678b32d6db51a6cea5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' + - 'bioconductor-tinesath1cdf >=1.20.0,<1.21.0' + - r-base + - r-rcolorbrewer + run: + - 'bioconductor-affy >=1.60.0,<1.61.0' + - 'bioconductor-ath1121501cdf >=2.18.0,<2.19.0' + - 'bioconductor-tinesath1cdf >=1.20.0,<1.21.0' + - r-base + - r-rcolorbrewer + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Cross-hybridisation study on the ATH1 Affymetrix GeneChip' + diff --git a/recipes/bioconductor-xhybcasneuf/post-link.sh b/recipes/bioconductor-xhybcasneuf/post-link.sh new file mode 100644 index 0000000000000..94cb795e2cc1c --- /dev/null +++ b/recipes/bioconductor-xhybcasneuf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="XhybCasneuf_1.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/XhybCasneuf_1.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/XhybCasneuf_1.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xhybcasneuf/bioconductor-xhybcasneuf_1.20.0_src_all.tar.gz" +) +MD5="e31cf97fb07e30678b32d6db51a6cea5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xhybcasneuf/pre-unlink.sh b/recipes/bioconductor-xhybcasneuf/pre-unlink.sh new file mode 100644 index 0000000000000..72c80a2af7354 --- /dev/null +++ b/recipes/bioconductor-xhybcasneuf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ XhybCasneuf diff --git a/recipes/bioconductor-xina/build.sh b/recipes/bioconductor-xina/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-xina/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xina/meta.yaml b/recipes/bioconductor-xina/meta.yaml new file mode 100644 index 0000000000000..063c709a6b28b --- /dev/null +++ b/recipes/bioconductor-xina/meta.yaml @@ -0,0 +1,49 @@ +{% set version = "1.0.0" %} +{% set name = "XINA" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: be400c7b246c0dc3067b45e62f881067 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: knitr, rmarkdown +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-alluvial + - r-base + - r-ggplot2 + - r-gridextra + - r-igraph + - r-mclust + - r-plyr + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-stringdb >=1.22.0,<1.23.0' + - r-alluvial + - r-base + - r-ggplot2 + - r-gridextra + - r-igraph + - r-mclust + - r-plyr +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: GPL-3 + summary: 'An intuitive R package simplifies network analyses output from multiplexed high-dimensional proteomics/trascriptomics kinetics data.' + diff --git a/recipes/bioconductor-xlaevis.db/meta.yaml b/recipes/bioconductor-xlaevis.db/meta.yaml new file mode 100644 index 0000000000000..8ae2c0b49841a --- /dev/null +++ b/recipes/bioconductor-xlaevis.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "xlaevis.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: deaffe47b4ee48a7edb159d8104dc241 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.xl.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.xl.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Xenopus laevis annotation data (chip xlaevis) assembled using data from public repositories' + diff --git a/recipes/bioconductor-xlaevis.db/post-link.sh b/recipes/bioconductor-xlaevis.db/post-link.sh new file mode 100644 index 0000000000000..a04b02ff38346 --- /dev/null +++ b/recipes/bioconductor-xlaevis.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xlaevis.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/xlaevis.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis.db/bioconductor-xlaevis.db_3.2.3_src_all.tar.gz" +) +MD5="deaffe47b4ee48a7edb159d8104dc241" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xlaevis.db/pre-unlink.sh b/recipes/bioconductor-xlaevis.db/pre-unlink.sh new file mode 100644 index 0000000000000..64cb4d7c2fdb2 --- /dev/null +++ b/recipes/bioconductor-xlaevis.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xlaevis.db diff --git a/recipes/bioconductor-xlaevis2cdf/meta.yaml b/recipes/bioconductor-xlaevis2cdf/meta.yaml new file mode 100644 index 0000000000000..28a8484285f0e --- /dev/null +++ b/recipes/bioconductor-xlaevis2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xlaevis2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 9e4a80d66397299b4e66a8d6715ca4aa +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the X_laevis_2.CDF file.' + diff --git a/recipes/bioconductor-xlaevis2cdf/post-link.sh b/recipes/bioconductor-xlaevis2cdf/post-link.sh new file mode 100644 index 0000000000000..bf1672f70f2f7 --- /dev/null +++ b/recipes/bioconductor-xlaevis2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xlaevis2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xlaevis2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis2cdf/bioconductor-xlaevis2cdf_2.18.0_src_all.tar.gz" +) +MD5="9e4a80d66397299b4e66a8d6715ca4aa" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xlaevis2cdf/pre-unlink.sh b/recipes/bioconductor-xlaevis2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..4e927c403f7bd --- /dev/null +++ b/recipes/bioconductor-xlaevis2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xlaevis2cdf diff --git a/recipes/bioconductor-xlaevis2probe/meta.yaml b/recipes/bioconductor-xlaevis2probe/meta.yaml new file mode 100644 index 0000000000000..0d0faa1a6c2d0 --- /dev/null +++ b/recipes/bioconductor-xlaevis2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xlaevis2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d86f8a05e106eb3123435da233ff851d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_laevis\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-xlaevis2probe/post-link.sh b/recipes/bioconductor-xlaevis2probe/post-link.sh new file mode 100644 index 0000000000000..ac5de06d54476 --- /dev/null +++ b/recipes/bioconductor-xlaevis2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xlaevis2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xlaevis2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xlaevis2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xlaevis2probe/bioconductor-xlaevis2probe_2.18.0_src_all.tar.gz" +) +MD5="d86f8a05e106eb3123435da233ff851d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xlaevis2probe/pre-unlink.sh b/recipes/bioconductor-xlaevis2probe/pre-unlink.sh new file mode 100644 index 0000000000000..3c9f41153665e --- /dev/null +++ b/recipes/bioconductor-xlaevis2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xlaevis2probe diff --git a/recipes/bioconductor-xmapbridge/build.sh b/recipes/bioconductor-xmapbridge/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-xmapbridge/build.sh +++ b/recipes/bioconductor-xmapbridge/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xmapbridge/meta.yaml b/recipes/bioconductor-xmapbridge/meta.yaml index 183a1b3bfdb2f..4964240880db1 100644 --- a/recipes/bioconductor-xmapbridge/meta.yaml +++ b/recipes/bioconductor-xmapbridge/meta.yaml @@ -1,21 +1,23 @@ -{% set version = "1.38.0" %} +{% set version = "1.40.0" %} {% set name = "xmapbridge" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: b07cc4776287820b8ef16153a1265a071c285711056043e653051c116f1bc09f + md5: aad45dacbe7c31b2569b42e38cea5131 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: RUnit, RColorBrewer requirements: host: - r-base @@ -25,9 +27,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: LGPL-3 summary: 'xmapBridge can plot graphs in the X:Map genome browser. This package exports plotting files in a suitable format.' extra: identifiers: - biotools:xmapbridge + parent_recipe: + name: bioconductor-xmapbridge + path: recipes/bioconductor-xmapbridge + version: 1.38.0 + diff --git a/recipes/bioconductor-xps/build.sh b/recipes/bioconductor-xps/build.sh new file mode 100644 index 0000000000000..c1d13421f5f1e --- /dev/null +++ b/recipes/bioconductor-xps/build.sh @@ -0,0 +1,11 @@ +#!/bin/bash +mv DESCRIPTION DESCRIPTION.old +grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars +$R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xps/meta.yaml b/recipes/bioconductor-xps/meta.yaml new file mode 100644 index 0000000000000..22968a6433a9c --- /dev/null +++ b/recipes/bioconductor-xps/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "1.42.0" %} +{% set name = "xps" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 7778907ce1572ac8dddb9cf753dd1b68 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ +# Suggests: tools +# SystemRequirements: GNU make, root_v5.34.36 - See README file for installation instructions. +requirements: + host: + - r-base + run: + - r-base + build: + - {{ compiler('c') }} + - {{ compiler('cxx') }} + - automake + - make +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: 'GPL (>= 2.0)' + summary: 'The package handles pre-processing, normalization, filtering and analysis of Affymetrix GeneChip expression arrays, including exon arrays (Exon 1.0 ST: core, extended, full probesets), gene arrays (Gene 1.0 ST) and plate arrays on computers with 1 GB RAM only. It imports Affymetrix .CDF, .CLF, .PGF and .CEL as well as annotation files, and computes e.g. RMA, MAS5, FARMS, DFW, FIRMA, tRMA, MAS5-calls, DABG-calls, I/NI-calls. It is an R wrapper to XPS (eXpression Profiling System), which is based on ROOT, an object-oriented framework developed at CERN. Thus, the prior installation of ROOT is a prerequisite for the usage of this package, however, no knowledge of ROOT is required. ROOT is licensed under LGPL and can be downloaded from http://root.cern.ch.' + diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml new file mode 100644 index 0000000000000..bc86a8b4443b2 --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/meta.yaml @@ -0,0 +1,44 @@ +{% set version = "0.99.12" %} +{% set name = "XtraSNPlocs.Hsapiens.dbSNP141.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 2b9d4036b9baff400a811fd69c910cff +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: SNPlocs.Hsapiens.dbSNP141.GRCh38, BSgenome.Hsapiens.NCBI.GRCh38 (>= 1.3.19) +requirements: + host: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 141. The source data files used for this package were created by NCBI on May 1st, 2014, and contain SNPs mapped to reference genome GRCh38. While the SNPlocs.Hsapiens.dbSNP141.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).' + diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh new file mode 100644 index 0000000000000..de42b0f4e3d9a --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" + "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP141.GRCh38_0.99.12.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38_0.99.12_src_all.tar.gz" +) +MD5="2b9d4036b9baff400a811fd69c910cff" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..e6eebe5c0ad27 --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp141.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ XtraSNPlocs.Hsapiens.dbSNP141.GRCh38 diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml new file mode 100644 index 0000000000000..a6690b4736687 --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.12" %} +{% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh37" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 758d024c50d2349036dc27cc689b4e5a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg19, SNPlocs.Hsapiens.dbSNP144.GRCh37 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 29-30, 2015, and contain SNPs mapped to reference genome GRCh37.p13 (a patched version of GRCh37 that doesn''t alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh37 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).' + diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh new file mode 100644 index 0000000000000..92864657f21b7 --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" + "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh37_0.99.12.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37_0.99.12_src_all.tar.gz" +) +MD5="758d024c50d2349036dc27cc689b4e5a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh new file mode 100644 index 0000000000000..7d4e51d93e82b --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch37/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ XtraSNPlocs.Hsapiens.dbSNP144.GRCh37 diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml new file mode 100644 index 0000000000000..5ad8fc00478b8 --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/meta.yaml @@ -0,0 +1,46 @@ +{% set version = "0.99.12" %} +{% set name = "XtraSNPlocs.Hsapiens.dbSNP144.GRCh38" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c617aa805c7ecf60ee9283eb3c51b1c7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biostrings, BSgenome.Hsapiens.UCSC.hg38, SNPlocs.Hsapiens.dbSNP144.GRCh38 +requirements: + host: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + run: + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-bsgenome >=1.50.0,<1.51.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Extra SNP locations and alleles for Homo sapiens extracted from NCBI dbSNP Build 144. The source data files used for this package were created by NCBI on May 30, 2015, and contain SNPs mapped to reference genome GRCh38.p2 (a patched version of GRCh38 that doesn''t alter chromosomes 1-22, X, Y, MT). While the SNPlocs.Hsapiens.dbSNP144.GRCh38 package contains only molecular variations of class "snp", this package contains molecular variations of other classes (in-del, heterozygous, microsatellite, named-locus, no-variation, mixed, and multinucleotide-polymorphism).' + diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh new file mode 100644 index 0000000000000..a8a9c5f4167cf --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" + "https://bioarchive.galaxyproject.org/XtraSNPlocs.Hsapiens.dbSNP144.GRCh38_0.99.12.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38_0.99.12_src_all.tar.gz" +) +MD5="c617aa805c7ecf60ee9283eb3c51b1c7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh new file mode 100644 index 0000000000000..05ddc542e99eb --- /dev/null +++ b/recipes/bioconductor-xtrasnplocs.hsapiens.dbsnp144.grch38/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ XtraSNPlocs.Hsapiens.dbSNP144.GRCh38 diff --git a/recipes/bioconductor-xtropicaliscdf/meta.yaml b/recipes/bioconductor-xtropicaliscdf/meta.yaml new file mode 100644 index 0000000000000..07b3e0407711b --- /dev/null +++ b/recipes/bioconductor-xtropicaliscdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xtropicaliscdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 253e3cde76a393789e124f395820e947 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the X_tropicalis.cdf file.' + diff --git a/recipes/bioconductor-xtropicaliscdf/post-link.sh b/recipes/bioconductor-xtropicaliscdf/post-link.sh new file mode 100644 index 0000000000000..fecf7eda931b4 --- /dev/null +++ b/recipes/bioconductor-xtropicaliscdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xtropicaliscdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xtropicaliscdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xtropicaliscdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtropicaliscdf/bioconductor-xtropicaliscdf_2.18.0_src_all.tar.gz" +) +MD5="253e3cde76a393789e124f395820e947" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xtropicaliscdf/pre-unlink.sh b/recipes/bioconductor-xtropicaliscdf/pre-unlink.sh new file mode 100644 index 0000000000000..72907bbe05aae --- /dev/null +++ b/recipes/bioconductor-xtropicaliscdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xtropicaliscdf diff --git a/recipes/bioconductor-xtropicalisprobe/meta.yaml b/recipes/bioconductor-xtropicalisprobe/meta.yaml new file mode 100644 index 0000000000000..e712ce373fc29 --- /dev/null +++ b/recipes/bioconductor-xtropicalisprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "xtropicalisprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 43d15a7e12edaec1bb5f24b87498b599 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was X\_tropicalis\_probe\_tab.' + diff --git a/recipes/bioconductor-xtropicalisprobe/post-link.sh b/recipes/bioconductor-xtropicalisprobe/post-link.sh new file mode 100644 index 0000000000000..55085965cfc1c --- /dev/null +++ b/recipes/bioconductor-xtropicalisprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="xtropicalisprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/xtropicalisprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/xtropicalisprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-xtropicalisprobe/bioconductor-xtropicalisprobe_2.18.0_src_all.tar.gz" +) +MD5="43d15a7e12edaec1bb5f24b87498b599" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-xtropicalisprobe/pre-unlink.sh b/recipes/bioconductor-xtropicalisprobe/pre-unlink.sh new file mode 100644 index 0000000000000..e641def76d762 --- /dev/null +++ b/recipes/bioconductor-xtropicalisprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ xtropicalisprobe diff --git a/recipes/bioconductor-xvector/build.sh b/recipes/bioconductor-xvector/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-xvector/build.sh +++ b/recipes/bioconductor-xvector/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-xvector/meta.yaml b/recipes/bioconductor-xvector/meta.yaml index f383693a09647..419fce739b6e7 100644 --- a/recipes/bioconductor-xvector/meta.yaml +++ b/recipes/bioconductor-xvector/meta.yaml @@ -1,33 +1,34 @@ -{% set version = "0.20.0" %} +{% set version = "0.22.0" %} {% set name = "XVector" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 6e5c1a3b9f5ff1319082165bdc7e5e33a121b8d70c1514b4040f7a4d138454fe + md5: 464c4abd6b6134b894a885f7f42e2ff8 build: number: 0 rpaths: - lib/R/lib/ - lib/ +# Suggests: Biostrings, drosophila2probe, RUnit requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-zlibbioc >=1.26.0,<1.28.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-zlibbioc >=1.28.0,<1.29.0' - r-base build: - {{ compiler('c') }} @@ -36,10 +37,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Memory efficient S4 classes for storing sequences "externally" (behind an R external pointer, or on disk).' extra: identifiers: - biotools:xvector - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-xvector + path: recipes/bioconductor-xvector + version: 0.20.0 + diff --git a/recipes/bioconductor-yamss/build.sh b/recipes/bioconductor-yamss/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-yamss/build.sh +++ b/recipes/bioconductor-yamss/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-yamss/meta.yaml b/recipes/bioconductor-yamss/meta.yaml index 3df1a082d05a5..2896211255177 100644 --- a/recipes/bioconductor-yamss/meta.yaml +++ b/recipes/bioconductor-yamss/meta.yaml @@ -1,41 +1,43 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.1" %} {% set name = "yamss" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 0ed9549260a45ad3063d4ff19186c744de7c3279c8666aa1fa692ea9cfceff61 + md5: 2eae19bf5906a912a04d9fb0c2a31445 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BiocStyle, knitr, rmarkdown, digest, mtbls2, testthat requirements: host: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-matrix run: - - 'bioconductor-biocgenerics >=0.26.0,<0.28.0' - - 'bioconductor-ebimage >=4.22.1,<4.24.0' - - 'bioconductor-iranges >=2.14.12,<2.16.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-mzr >=2.17.0,<2.19.0' - - 'bioconductor-s4vectors >=0.18.3,<0.20.0' - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-biocgenerics >=0.28.0,<0.29.0' + - 'bioconductor-ebimage >=4.24.0,<4.25.0' + - 'bioconductor-iranges >=2.16.0,<2.17.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-mzr >=2.16.0,<2.17.0' + - 'bioconductor-s4vectors >=0.20.0,<0.21.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-data.table - r-matrix @@ -43,9 +45,14 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Tools to analyze and visualize high-throughput metabolomics data aquired using chromatography-mass spectrometry. These tools preprocess data in a way that enables reliable and powerful differential analysis.' extra: identifiers: - biotools:yamss + parent_recipe: + name: bioconductor-yamss + path: recipes/bioconductor-yamss + version: 1.6.0 + diff --git a/recipes/bioconductor-yapsa/build.sh b/recipes/bioconductor-yapsa/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-yapsa/build.sh +++ b/recipes/bioconductor-yapsa/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-yapsa/conda_build_config.yaml b/recipes/bioconductor-yapsa/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-yapsa/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-yapsa/meta.yaml b/recipes/bioconductor-yapsa/meta.yaml index 8a08240bdc742..f6efdc3694201 100644 --- a/recipes/bioconductor-yapsa/meta.yaml +++ b/recipes/bioconductor-yapsa/meta.yaml @@ -1,30 +1,32 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "YAPSA" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 85fb250a2badf2975347257691b2371000ab12476525bdf196c3a090a40a7042 + md5: 09ee5f1de2127297df5914ec0082103b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: BSgenome.Hsapiens.UCSC.hg19, testthat, BiocStyle, knitr, rmarkdown requirements: host: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gtrellis >=1.12.1,<1.14.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gtrellis >=1.14.0,<1.15.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-circlize - r-corrplot @@ -36,13 +38,13 @@ requirements: - r-pmcmr - r-reshape2 run: - - 'bioconductor-complexheatmap >=1.18.1,<1.20.0' - - 'bioconductor-genomeinfodb >=1.16.0,<1.18.0' - - 'bioconductor-genomicranges >=1.32.7,<1.34.0' - - 'bioconductor-gtrellis >=1.12.1,<1.14.0' - - 'bioconductor-keggrest >=1.20.2,<1.22.0' - - 'bioconductor-somaticsignatures >=2.16.0,<2.18.0' - - 'bioconductor-variantannotation >=1.26.1,<1.28.0' + - 'bioconductor-complexheatmap >=1.20.0,<1.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-gtrellis >=1.14.0,<1.15.0' + - 'bioconductor-keggrest >=1.22.0,<1.23.0' + - 'bioconductor-somaticsignatures >=2.18.0,<2.19.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' - r-base - r-circlize - r-corrplot @@ -57,10 +59,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: GPL-3 summary: 'This package provides functions and routines useful in the analysis of somatic signatures (cf. L. Alexandrov et al., Nature 2013). In particular, functions to perform a signature analysis with known signatures (LCD = linear combination decomposition) and a signature analysis on stratified mutational catalogue (SMC = stratify mutational catalogue) are provided.' extra: identifiers: - biotools:yapsa - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-yapsa + path: recipes/bioconductor-yapsa + version: 1.6.0 + diff --git a/recipes/bioconductor-yaqcaffy/build.sh b/recipes/bioconductor-yaqcaffy/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-yaqcaffy/build.sh +++ b/recipes/bioconductor-yaqcaffy/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-yaqcaffy/conda_build_config.yaml b/recipes/bioconductor-yaqcaffy/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-yaqcaffy/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-yaqcaffy/meta.yaml b/recipes/bioconductor-yaqcaffy/meta.yaml index fb26cdb8ad613..b2ed4ce81dc39 100644 --- a/recipes/bioconductor-yaqcaffy/meta.yaml +++ b/recipes/bioconductor-yaqcaffy/meta.yaml @@ -1,36 +1,43 @@ -{% set version = "1.40.0" %} +{% set version = "1.42.0" %} {% set name = "yaqcaffy" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ebb25aba1d352aedc41c94267536d6914d2107a753e426e58cb0f4c27956a7a2 + md5: 0ac961004e53ff216bcfa89616c92b56 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: MAQCsubsetAFX, affydata, xtable, tcltk2, tcltk requirements: host: - - 'bioconductor-simpleaffy >=2.56.0,<2.58.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' - r-base run: - - 'bioconductor-simpleaffy >=2.56.0,<2.58.0' + - 'bioconductor-simpleaffy >=2.58.0,<2.59.0' - r-base test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.' extra: identifiers: - biotools:yaqcaffy - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-yaqcaffy + path: recipes/bioconductor-yaqcaffy + version: 1.40.0 + diff --git a/recipes/bioconductor-yarn/build.sh b/recipes/bioconductor-yarn/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-yarn/build.sh +++ b/recipes/bioconductor-yarn/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-yarn/meta.yaml b/recipes/bioconductor-yarn/meta.yaml index 2cb61bab40931..7f2548e2397e5 100644 --- a/recipes/bioconductor-yarn/meta.yaml +++ b/recipes/bioconductor-yarn/meta.yaml @@ -1,29 +1,31 @@ -{% set version = "1.6.0" %} +{% set version = "1.8.0" %} {% set name = "yarn" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: 10760732a1437ca8e94773e452fbc49ed96a44ac6ff1a5c71b0e751136b39e3b + md5: 9c0b6f644acc014874a723bd1e69115b build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat (>= 0.8) requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-quantro >=1.14.0,<1.16.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-quantro >=1.16.0,<1.17.0' - r-base - r-downloader - r-gplots @@ -31,12 +33,12 @@ requirements: - r-rcolorbrewer - r-readr run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' - - 'bioconductor-biomart >=2.36.1,<2.38.0' - - 'bioconductor-edger >=3.22.4,<3.24.0' - - 'bioconductor-limma >=3.36.5,<3.38.0' - - 'bioconductor-preprocesscore >=1.42.0,<1.44.0' - - 'bioconductor-quantro >=1.14.0,<1.16.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-biomart >=2.38.0,<2.39.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-limma >=3.38.0,<3.39.0' + - 'bioconductor-preprocesscore >=1.44.0,<1.45.0' + - 'bioconductor-quantro >=1.16.0,<1.17.0' - r-base - r-downloader - r-gplots @@ -47,10 +49,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: Artistic-2.0 summary: 'Expedite large RNA-Seq analyses using a combination of previously developed tools. YARN is meant to make it easier for the user in performing basic mis-annotation quality control, filtering, and condition-aware normalization. YARN leverages many Bioconductor tools and statistical techniques to account for the large heterogeneity and sparsity found in very large RNA-seq experiments.' extra: identifiers: - biotools:yarn - doi:10.1101/086587 + parent_recipe: + name: bioconductor-yarn + path: recipes/bioconductor-yarn + version: 1.6.0 + diff --git a/recipes/bioconductor-ye6100subacdf/meta.yaml b/recipes/bioconductor-ye6100subacdf/meta.yaml new file mode 100644 index 0000000000000..65cdc89eb304a --- /dev/null +++ b/recipes/bioconductor-ye6100subacdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ye6100subacdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 27bd71410956bfe8bffc8de14b85bdb0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ye6100subA.CDF file.' + diff --git a/recipes/bioconductor-ye6100subacdf/post-link.sh b/recipes/bioconductor-ye6100subacdf/post-link.sh new file mode 100644 index 0000000000000..2618040a506ee --- /dev/null +++ b/recipes/bioconductor-ye6100subacdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ye6100subacdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subacdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ye6100subacdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subacdf/bioconductor-ye6100subacdf_2.18.0_src_all.tar.gz" +) +MD5="27bd71410956bfe8bffc8de14b85bdb0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ye6100subacdf/pre-unlink.sh b/recipes/bioconductor-ye6100subacdf/pre-unlink.sh new file mode 100644 index 0000000000000..18c84f1e2be07 --- /dev/null +++ b/recipes/bioconductor-ye6100subacdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ye6100subacdf diff --git a/recipes/bioconductor-ye6100subbcdf/meta.yaml b/recipes/bioconductor-ye6100subbcdf/meta.yaml new file mode 100644 index 0000000000000..6e21f36d705c2 --- /dev/null +++ b/recipes/bioconductor-ye6100subbcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ye6100subbcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ee9ec4bd941940745bad538d79bfeab4 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ye6100subB.CDF file.' + diff --git a/recipes/bioconductor-ye6100subbcdf/post-link.sh b/recipes/bioconductor-ye6100subbcdf/post-link.sh new file mode 100644 index 0000000000000..5cdf064d86bfb --- /dev/null +++ b/recipes/bioconductor-ye6100subbcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ye6100subbcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subbcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ye6100subbcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subbcdf/bioconductor-ye6100subbcdf_2.18.0_src_all.tar.gz" +) +MD5="ee9ec4bd941940745bad538d79bfeab4" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ye6100subbcdf/pre-unlink.sh b/recipes/bioconductor-ye6100subbcdf/pre-unlink.sh new file mode 100644 index 0000000000000..ab741db63157f --- /dev/null +++ b/recipes/bioconductor-ye6100subbcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ye6100subbcdf diff --git a/recipes/bioconductor-ye6100subccdf/meta.yaml b/recipes/bioconductor-ye6100subccdf/meta.yaml new file mode 100644 index 0000000000000..62399d9de555d --- /dev/null +++ b/recipes/bioconductor-ye6100subccdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ye6100subccdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: fcdfed29a695fe53b62bacfe13dfe0c1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ye6100subC.CDF file.' + diff --git a/recipes/bioconductor-ye6100subccdf/post-link.sh b/recipes/bioconductor-ye6100subccdf/post-link.sh new file mode 100644 index 0000000000000..c7287c2554bd0 --- /dev/null +++ b/recipes/bioconductor-ye6100subccdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ye6100subccdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subccdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ye6100subccdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subccdf/bioconductor-ye6100subccdf_2.18.0_src_all.tar.gz" +) +MD5="fcdfed29a695fe53b62bacfe13dfe0c1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ye6100subccdf/pre-unlink.sh b/recipes/bioconductor-ye6100subccdf/pre-unlink.sh new file mode 100644 index 0000000000000..b62ad3dac5d02 --- /dev/null +++ b/recipes/bioconductor-ye6100subccdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ye6100subccdf diff --git a/recipes/bioconductor-ye6100subdcdf/meta.yaml b/recipes/bioconductor-ye6100subdcdf/meta.yaml new file mode 100644 index 0000000000000..3a9dd0b43eb16 --- /dev/null +++ b/recipes/bioconductor-ye6100subdcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ye6100subdcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 521b501ddbcdc680c3d27b5b201029b1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Ye6100subD.CDF file.' + diff --git a/recipes/bioconductor-ye6100subdcdf/post-link.sh b/recipes/bioconductor-ye6100subdcdf/post-link.sh new file mode 100644 index 0000000000000..239e87d187afe --- /dev/null +++ b/recipes/bioconductor-ye6100subdcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ye6100subdcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ye6100subdcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ye6100subdcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ye6100subdcdf/bioconductor-ye6100subdcdf_2.18.0_src_all.tar.gz" +) +MD5="521b501ddbcdc680c3d27b5b201029b1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ye6100subdcdf/pre-unlink.sh b/recipes/bioconductor-ye6100subdcdf/pre-unlink.sh new file mode 100644 index 0000000000000..6eec710efc438 --- /dev/null +++ b/recipes/bioconductor-ye6100subdcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ye6100subdcdf diff --git a/recipes/bioconductor-yeast.db0/meta.yaml b/recipes/bioconductor-yeast.db0/meta.yaml new file mode 100644 index 0000000000000..d9a923c206e21 --- /dev/null +++ b/recipes/bioconductor-yeast.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "yeast.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: d46ddb0d3ab987389ada054068806531 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for yeast, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-yeast.db0/post-link.sh b/recipes/bioconductor-yeast.db0/post-link.sh new file mode 100644 index 0000000000000..9e448c9dabaf2 --- /dev/null +++ b/recipes/bioconductor-yeast.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeast.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/yeast.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast.db0/bioconductor-yeast.db0_3.7.1_src_all.tar.gz" +) +MD5="d46ddb0d3ab987389ada054068806531" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeast.db0/pre-unlink.sh b/recipes/bioconductor-yeast.db0/pre-unlink.sh new file mode 100644 index 0000000000000..ef120164cf20e --- /dev/null +++ b/recipes/bioconductor-yeast.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeast.db0 diff --git a/recipes/bioconductor-yeast2.db/meta.yaml b/recipes/bioconductor-yeast2.db/meta.yaml new file mode 100644 index 0000000000000..f3f140ed4ef7b --- /dev/null +++ b/recipes/bioconductor-yeast2.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "yeast2.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 818981b9562630e8a219dbe23a316e08 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Yeast Genome 2.0 Array annotation data (chip yeast2) assembled using data from public repositories' + diff --git a/recipes/bioconductor-yeast2.db/post-link.sh b/recipes/bioconductor-yeast2.db/post-link.sh new file mode 100644 index 0000000000000..2c41d332811a0 --- /dev/null +++ b/recipes/bioconductor-yeast2.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeast2.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/yeast2.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2.db/bioconductor-yeast2.db_3.2.3_src_all.tar.gz" +) +MD5="818981b9562630e8a219dbe23a316e08" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeast2.db/pre-unlink.sh b/recipes/bioconductor-yeast2.db/pre-unlink.sh new file mode 100644 index 0000000000000..f65f52bafe0ce --- /dev/null +++ b/recipes/bioconductor-yeast2.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeast2.db diff --git a/recipes/bioconductor-yeast2cdf/meta.yaml b/recipes/bioconductor-yeast2cdf/meta.yaml new file mode 100644 index 0000000000000..bed0e8e0b079d --- /dev/null +++ b/recipes/bioconductor-yeast2cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "yeast2cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 0a718d78ae56bef9bad8168123038ac8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Yeast_2.cdf file.' + diff --git a/recipes/bioconductor-yeast2cdf/post-link.sh b/recipes/bioconductor-yeast2cdf/post-link.sh new file mode 100644 index 0000000000000..01617c9253c56 --- /dev/null +++ b/recipes/bioconductor-yeast2cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeast2cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeast2cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2cdf/bioconductor-yeast2cdf_2.18.0_src_all.tar.gz" +) +MD5="0a718d78ae56bef9bad8168123038ac8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeast2cdf/pre-unlink.sh b/recipes/bioconductor-yeast2cdf/pre-unlink.sh new file mode 100644 index 0000000000000..8f359a8656b79 --- /dev/null +++ b/recipes/bioconductor-yeast2cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeast2cdf diff --git a/recipes/bioconductor-yeast2probe/meta.yaml b/recipes/bioconductor-yeast2probe/meta.yaml new file mode 100644 index 0000000000000..57c0b2267c8bd --- /dev/null +++ b/recipes/bioconductor-yeast2probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "yeast2probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 3f52a2b7bd379624bc2966ca28c9ddf9 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Yeast\_2\_probe\_tab.' + diff --git a/recipes/bioconductor-yeast2probe/post-link.sh b/recipes/bioconductor-yeast2probe/post-link.sh new file mode 100644 index 0000000000000..8dc1b937783f7 --- /dev/null +++ b/recipes/bioconductor-yeast2probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeast2probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/yeast2probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeast2probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeast2probe/bioconductor-yeast2probe_2.18.0_src_all.tar.gz" +) +MD5="3f52a2b7bd379624bc2966ca28c9ddf9" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeast2probe/pre-unlink.sh b/recipes/bioconductor-yeast2probe/pre-unlink.sh new file mode 100644 index 0000000000000..2c02486a8c3db --- /dev/null +++ b/recipes/bioconductor-yeast2probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeast2probe diff --git a/recipes/bioconductor-yeastcc/meta.yaml b/recipes/bioconductor-yeastcc/meta.yaml index 3401987270c8a..f388925709d50 100644 --- a/recipes/bioconductor-yeastcc/meta.yaml +++ b/recipes/bioconductor-yeastcc/meta.yaml @@ -1,35 +1,40 @@ -{% set version = "1.20.0" %} +{% set version = "1.22.0" %} {% set name = "yeastCC" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 1098741155fb624a2a02d1f74874d307882842dfcbb79937bd64f9120ed6602f + md5: 5b31b8fadb3318846770cdd2f6b620a1 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic requirements: host: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base run: - - 'bioconductor-biobase >=2.40.0,<2.42.0' + - 'bioconductor-biobase >=2.42.0,<2.43.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: Artistic-2.0 summary: 'ExpressionSet for Spellman et al. (1998) yeast cell cycle microarray experiment' - +extra: + parent_recipe: + name: bioconductor-yeastcc + path: recipes/bioconductor-yeastcc + version: 1.20.0 diff --git a/recipes/bioconductor-yeastcc/post-link.sh b/recipes/bioconductor-yeastcc/post-link.sh index 0c62ebc7b5b9b..b27cb838f300a 100644 --- a/recipes/bioconductor-yeastcc/post-link.sh +++ b/recipes/bioconductor-yeastcc/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastCC_1.20.0.tar.gz" +FN="yeastCC_1.22.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/yeastCC_1.20.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastCC_1.20.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.20.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastCC_1.22.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastCC_1.22.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastcc/bioconductor-yeastcc_1.22.0_src_all.tar.gz" ) -MD5="01c7f1799dc44282f802e6e05cc6b730" +MD5="5b31b8fadb3318846770cdd2f6b620a1" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-yeastexpdata/meta.yaml b/recipes/bioconductor-yeastexpdata/meta.yaml index 8203b9957f8fb..fc01c6b6a8809 100644 --- a/recipes/bioconductor-yeastexpdata/meta.yaml +++ b/recipes/bioconductor-yeastexpdata/meta.yaml @@ -1,35 +1,41 @@ -{% set version = "0.26.0" %} +{% set version = "0.28.0" %} {% set name = "yeastExpData" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: 07e0e11fbf2c30f393c72e0f0363fa331e616441d39575fa90837b5b52fa45e0 + md5: ab56e8741e012db8ce829bb43673cb35 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: Biobase, GO.db, RBGL, org.Sc.sgd.db requirements: host: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base run: - - 'bioconductor-graph >=1.58.0,<1.60.0' + - 'bioconductor-graph >=1.60.0,<1.61.0' - r-base - wget test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' license: GPL summary: 'A collection of different sets of experimental data from yeast.' - +extra: + parent_recipe: + name: bioconductor-yeastexpdata + path: recipes/bioconductor-yeastexpdata + version: 0.26.0 diff --git a/recipes/bioconductor-yeastexpdata/post-link.sh b/recipes/bioconductor-yeastexpdata/post-link.sh index a5991bfbe185b..3cda6d63cb218 100644 --- a/recipes/bioconductor-yeastexpdata/post-link.sh +++ b/recipes/bioconductor-yeastexpdata/post-link.sh @@ -1,11 +1,11 @@ #!/bin/bash -FN="yeastExpData_0.26.0.tar.gz" +FN="yeastExpData_0.28.0.tar.gz" URLS=( - "http://bioconductor.org/packages/3.7/data/experiment/src/contrib/yeastExpData_0.26.0.tar.gz" - "https://bioarchive.galaxyproject.org/yeastExpData_0.26.0.tar.gz" - "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.26.0_src_all.tar.gz" + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastExpData_0.28.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastExpData_0.28.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastexpdata/bioconductor-yeastexpdata_0.28.0_src_all.tar.gz" ) -MD5="43d0c9935427e1b2d7c35ff5fbb3d5fc" +MD5="ab56e8741e012db8ce829bb43673cb35" # Use a staging area in the conda dir rather than temp dirs, both to avoid # permission issues as well as to have things downloaded in a predictable diff --git a/recipes/bioconductor-yeastgsdata/meta.yaml b/recipes/bioconductor-yeastgsdata/meta.yaml new file mode 100644 index 0000000000000..cbe32f8bb6c07 --- /dev/null +++ b/recipes/bioconductor-yeastgsdata/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "0.20.0" %} +{% set name = "yeastGSData" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: 16b3bf8e7fbdcabb099a801c9076f5e8 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'A collection of so-called gold (and other) standard data sets' + diff --git a/recipes/bioconductor-yeastgsdata/post-link.sh b/recipes/bioconductor-yeastgsdata/post-link.sh new file mode 100644 index 0000000000000..ec8ec8c753cd6 --- /dev/null +++ b/recipes/bioconductor-yeastgsdata/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeastGSData_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastGSData_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastGSData_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastgsdata/bioconductor-yeastgsdata_0.20.0_src_all.tar.gz" +) +MD5="16b3bf8e7fbdcabb099a801c9076f5e8" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeastgsdata/pre-unlink.sh b/recipes/bioconductor-yeastgsdata/pre-unlink.sh new file mode 100644 index 0000000000000..9c3d047c87ca5 --- /dev/null +++ b/recipes/bioconductor-yeastgsdata/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeastGSData diff --git a/recipes/bioconductor-yeastnagalakshmi/meta.yaml b/recipes/bioconductor-yeastnagalakshmi/meta.yaml new file mode 100644 index 0000000000000..b25b3c9ad9866 --- /dev/null +++ b/recipes/bioconductor-yeastnagalakshmi/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.18.0" %} +{% set name = "yeastNagalakshmi" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: c3f3493454c6d90bb79f06fa54021ee1 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'The yeast genome data was retrieved from the sequence read archive, aligned with bwa, and converted to BAM format with samtools.' + diff --git a/recipes/bioconductor-yeastnagalakshmi/post-link.sh b/recipes/bioconductor-yeastnagalakshmi/post-link.sh new file mode 100644 index 0000000000000..661216218f98b --- /dev/null +++ b/recipes/bioconductor-yeastnagalakshmi/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeastNagalakshmi_1.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastNagalakshmi_1.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastNagalakshmi_1.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastnagalakshmi/bioconductor-yeastnagalakshmi_1.18.0_src_all.tar.gz" +) +MD5="c3f3493454c6d90bb79f06fa54021ee1" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeastnagalakshmi/pre-unlink.sh b/recipes/bioconductor-yeastnagalakshmi/pre-unlink.sh new file mode 100644 index 0000000000000..b40c483cd1c23 --- /dev/null +++ b/recipes/bioconductor-yeastnagalakshmi/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeastNagalakshmi diff --git a/recipes/bioconductor-yeastrnaseq/meta.yaml b/recipes/bioconductor-yeastrnaseq/meta.yaml new file mode 100644 index 0000000000000..7ceaa51265d2a --- /dev/null +++ b/recipes/bioconductor-yeastrnaseq/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "0.20.0" %} +{% set name = "yeastRNASeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a642a1c83917e78e156bc3841e609f7b +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: Biobase, ShortRead, IRanges +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'A selection of RNA-Seq data from a yeast transcriptome experiment.' + diff --git a/recipes/bioconductor-yeastrnaseq/post-link.sh b/recipes/bioconductor-yeastrnaseq/post-link.sh new file mode 100644 index 0000000000000..4dcd6dc9e6b4b --- /dev/null +++ b/recipes/bioconductor-yeastrnaseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yeastRNASeq_0.20.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yeastRNASeq_0.20.0.tar.gz" + "https://bioarchive.galaxyproject.org/yeastRNASeq_0.20.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yeastrnaseq/bioconductor-yeastrnaseq_0.20.0_src_all.tar.gz" +) +MD5="a642a1c83917e78e156bc3841e609f7b" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yeastrnaseq/pre-unlink.sh b/recipes/bioconductor-yeastrnaseq/pre-unlink.sh new file mode 100644 index 0000000000000..527c9a67591b8 --- /dev/null +++ b/recipes/bioconductor-yeastrnaseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yeastRNASeq diff --git a/recipes/bioconductor-ygs98.db/meta.yaml b/recipes/bioconductor-ygs98.db/meta.yaml new file mode 100644 index 0000000000000..b6ddb4d4fad59 --- /dev/null +++ b/recipes/bioconductor-ygs98.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "ygs98.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ddbf44a3db85a114be4477f917f3a724 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.sc.sgd.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix Yeast Genome S98 Array annotation data (chip ygs98) assembled using data from public repositories' + diff --git a/recipes/bioconductor-ygs98.db/post-link.sh b/recipes/bioconductor-ygs98.db/post-link.sh new file mode 100644 index 0000000000000..376c52aee9af4 --- /dev/null +++ b/recipes/bioconductor-ygs98.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ygs98.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/ygs98.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98.db/bioconductor-ygs98.db_3.2.3_src_all.tar.gz" +) +MD5="ddbf44a3db85a114be4477f917f3a724" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ygs98.db/pre-unlink.sh b/recipes/bioconductor-ygs98.db/pre-unlink.sh new file mode 100644 index 0000000000000..4e397f9633143 --- /dev/null +++ b/recipes/bioconductor-ygs98.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ygs98.db diff --git a/recipes/bioconductor-ygs98cdf/meta.yaml b/recipes/bioconductor-ygs98cdf/meta.yaml new file mode 100644 index 0000000000000..2416c8ea0c6c5 --- /dev/null +++ b/recipes/bioconductor-ygs98cdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ygs98cdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: ec7df7564cf28e093646325ec55baf1e +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the YG_S98.cdf file.' + diff --git a/recipes/bioconductor-ygs98cdf/post-link.sh b/recipes/bioconductor-ygs98cdf/post-link.sh new file mode 100644 index 0000000000000..2a69683f8e061 --- /dev/null +++ b/recipes/bioconductor-ygs98cdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ygs98cdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98cdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ygs98cdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98cdf/bioconductor-ygs98cdf_2.18.0_src_all.tar.gz" +) +MD5="ec7df7564cf28e093646325ec55baf1e" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ygs98cdf/pre-unlink.sh b/recipes/bioconductor-ygs98cdf/pre-unlink.sh new file mode 100644 index 0000000000000..ee1a7be8a6cdc --- /dev/null +++ b/recipes/bioconductor-ygs98cdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ygs98cdf diff --git a/recipes/bioconductor-ygs98frmavecs/meta.yaml b/recipes/bioconductor-ygs98frmavecs/meta.yaml new file mode 100644 index 0000000000000..ae3b79580552b --- /dev/null +++ b/recipes/bioconductor-ygs98frmavecs/meta.yaml @@ -0,0 +1,33 @@ +{% set version = "1.3.0" %} +{% set name = "ygs98frmavecs" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: e78c8447eb381b91dafb2f9688da39dc +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: 'GPL (>= 2)' + summary: 'This package was created by frmaTools version 1.19.3 and hgu133ahsentrezgcdf version 19.0.0.' + diff --git a/recipes/bioconductor-ygs98frmavecs/post-link.sh b/recipes/bioconductor-ygs98frmavecs/post-link.sh new file mode 100644 index 0000000000000..4adc28aa1f698 --- /dev/null +++ b/recipes/bioconductor-ygs98frmavecs/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ygs98frmavecs_1.3.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98frmavecs_1.3.0.tar.gz" + "https://bioarchive.galaxyproject.org/ygs98frmavecs_1.3.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98frmavecs/bioconductor-ygs98frmavecs_1.3.0_src_all.tar.gz" +) +MD5="e78c8447eb381b91dafb2f9688da39dc" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ygs98frmavecs/pre-unlink.sh b/recipes/bioconductor-ygs98frmavecs/pre-unlink.sh new file mode 100644 index 0000000000000..a67a370e0797c --- /dev/null +++ b/recipes/bioconductor-ygs98frmavecs/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ygs98frmavecs diff --git a/recipes/bioconductor-ygs98probe/meta.yaml b/recipes/bioconductor-ygs98probe/meta.yaml new file mode 100644 index 0000000000000..3953d966a2ce2 --- /dev/null +++ b/recipes/bioconductor-ygs98probe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "ygs98probe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: f40f21d7074818a4ee74a45b5533e89d +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was YG-S98\_probe\_tab.' + diff --git a/recipes/bioconductor-ygs98probe/post-link.sh b/recipes/bioconductor-ygs98probe/post-link.sh new file mode 100644 index 0000000000000..1b11221cbd2ed --- /dev/null +++ b/recipes/bioconductor-ygs98probe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="ygs98probe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/ygs98probe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/ygs98probe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-ygs98probe/bioconductor-ygs98probe_2.18.0_src_all.tar.gz" +) +MD5="f40f21d7074818a4ee74a45b5533e89d" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-ygs98probe/pre-unlink.sh b/recipes/bioconductor-ygs98probe/pre-unlink.sh new file mode 100644 index 0000000000000..922f5387831ee --- /dev/null +++ b/recipes/bioconductor-ygs98probe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ ygs98probe diff --git a/recipes/bioconductor-yri1kgv/meta.yaml b/recipes/bioconductor-yri1kgv/meta.yaml new file mode 100644 index 0000000000000..5f7978263a80e --- /dev/null +++ b/recipes/bioconductor-yri1kgv/meta.yaml @@ -0,0 +1,37 @@ +{% set version = "0.24.0" %} +{% set name = "yri1kgv" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 6b8aff46adfa18440787125c32b2eac5 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + run: + - 'bioconductor-biobase >=2.42.0,<2.43.0' + - 'bioconductor-ggbase >=3.44.0,<3.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'expression + genotype on 79 unrelated YRI individuals' + diff --git a/recipes/bioconductor-yri1kgv/post-link.sh b/recipes/bioconductor-yri1kgv/post-link.sh new file mode 100644 index 0000000000000..66e82306e37cb --- /dev/null +++ b/recipes/bioconductor-yri1kgv/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yri1kgv_0.24.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yri1kgv_0.24.0.tar.gz" + "https://bioarchive.galaxyproject.org/yri1kgv_0.24.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yri1kgv/bioconductor-yri1kgv_0.24.0_src_all.tar.gz" +) +MD5="6b8aff46adfa18440787125c32b2eac5" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yri1kgv/pre-unlink.sh b/recipes/bioconductor-yri1kgv/pre-unlink.sh new file mode 100644 index 0000000000000..06d381c76b983 --- /dev/null +++ b/recipes/bioconductor-yri1kgv/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yri1kgv diff --git a/recipes/bioconductor-yrimulti/meta.yaml b/recipes/bioconductor-yrimulti/meta.yaml new file mode 100644 index 0000000000000..f2172519b1f22 --- /dev/null +++ b/recipes/bioconductor-yrimulti/meta.yaml @@ -0,0 +1,54 @@ +{% set version = "0.12.0" %} +{% set name = "yriMulti" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: a5ac85ebbea7b116ab9a5200658fbab6 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: erma, BiocStyle, knitr, rmarkdown, gQTLstats (>= 1.9.2), doParallel, geuvPack, knitcitations, bibtex +requirements: + host: + - 'bioconductor-dsqtl >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geuvpack >=1.14.0,<1.15.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + run: + - 'bioconductor-dsqtl >=0.20.0,<0.21.0' + - 'bioconductor-genomeinfodb >=1.18.0,<1.19.0' + - 'bioconductor-genomicfiles >=1.18.0,<1.19.0' + - 'bioconductor-genomicranges >=1.34.0,<1.35.0' + - 'bioconductor-geuvpack >=1.14.0,<1.15.0' + - 'bioconductor-gqtlbase >=1.14.0,<1.15.0' + - 'bioconductor-homo.sapiens >=1.3.0,<1.4.0' + - 'bioconductor-multiassayexperiment >=1.8.0,<1.9.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' + - 'bioconductor-variantannotation >=1.28.0,<1.29.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'expression, methylation, DHS for YRI' + diff --git a/recipes/bioconductor-yrimulti/post-link.sh b/recipes/bioconductor-yrimulti/post-link.sh new file mode 100644 index 0000000000000..8e656e8758c42 --- /dev/null +++ b/recipes/bioconductor-yrimulti/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="yriMulti_0.12.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/yriMulti_0.12.0.tar.gz" + "https://bioarchive.galaxyproject.org/yriMulti_0.12.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-yrimulti/bioconductor-yrimulti_0.12.0_src_all.tar.gz" +) +MD5="a5ac85ebbea7b116ab9a5200658fbab6" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-yrimulti/pre-unlink.sh b/recipes/bioconductor-yrimulti/pre-unlink.sh new file mode 100644 index 0000000000000..bb8fe1ff95431 --- /dev/null +++ b/recipes/bioconductor-yrimulti/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ yriMulti diff --git a/recipes/bioconductor-zebrafish.db/meta.yaml b/recipes/bioconductor-zebrafish.db/meta.yaml new file mode 100644 index 0000000000000..e692f4e0e659d --- /dev/null +++ b/recipes/bioconductor-zebrafish.db/meta.yaml @@ -0,0 +1,38 @@ +{% set version = "3.2.3" %} +{% set name = "zebrafish.db" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: bd3924751e782a01b08d82b0aae07579 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: DBI, annotate, RUnit +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - 'bioconductor-org.dr.eg.db >=3.7.0,<3.8.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Affymetrix zebrafish annotation data (chip zebrafish) assembled using data from public repositories' + diff --git a/recipes/bioconductor-zebrafish.db/post-link.sh b/recipes/bioconductor-zebrafish.db/post-link.sh new file mode 100644 index 0000000000000..316ee83efeb54 --- /dev/null +++ b/recipes/bioconductor-zebrafish.db/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="zebrafish.db_3.2.3.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafish.db_3.2.3.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafish.db_3.2.3.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db/bioconductor-zebrafish.db_3.2.3_src_all.tar.gz" +) +MD5="bd3924751e782a01b08d82b0aae07579" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-zebrafish.db/pre-unlink.sh b/recipes/bioconductor-zebrafish.db/pre-unlink.sh new file mode 100644 index 0000000000000..921752fe7f5b5 --- /dev/null +++ b/recipes/bioconductor-zebrafish.db/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ zebrafish.db diff --git a/recipes/bioconductor-zebrafish.db0/meta.yaml b/recipes/bioconductor-zebrafish.db0/meta.yaml new file mode 100644 index 0000000000000..7058fe55e0482 --- /dev/null +++ b/recipes/bioconductor-zebrafish.db0/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "3.7.1" %} +{% set name = "zebrafish.db0" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: a8cb94655507b3640f4c2cd59816597a +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: Artistic-2.0 + summary: 'Base annotation databases for zebrafish, intended ONLY to be used by AnnotationDbi to produce regular annotation packages.' + diff --git a/recipes/bioconductor-zebrafish.db0/post-link.sh b/recipes/bioconductor-zebrafish.db0/post-link.sh new file mode 100644 index 0000000000000..94cc8207d9082 --- /dev/null +++ b/recipes/bioconductor-zebrafish.db0/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="zebrafish.db0_3.7.1.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafish.db0_3.7.1.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafish.db0_3.7.1.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafish.db0/bioconductor-zebrafish.db0_3.7.1_src_all.tar.gz" +) +MD5="a8cb94655507b3640f4c2cd59816597a" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-zebrafish.db0/pre-unlink.sh b/recipes/bioconductor-zebrafish.db0/pre-unlink.sh new file mode 100644 index 0000000000000..753cdf527ae34 --- /dev/null +++ b/recipes/bioconductor-zebrafish.db0/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ zebrafish.db0 diff --git a/recipes/bioconductor-zebrafishcdf/meta.yaml b/recipes/bioconductor-zebrafishcdf/meta.yaml new file mode 100644 index 0000000000000..952e178d258b8 --- /dev/null +++ b/recipes/bioconductor-zebrafishcdf/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "zebrafishcdf" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: 04edbb632600c97610b86423c2d850e7 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'A package containing an environment representing the Zebrafish.cdf file.' + diff --git a/recipes/bioconductor-zebrafishcdf/post-link.sh b/recipes/bioconductor-zebrafishcdf/post-link.sh new file mode 100644 index 0000000000000..5040b0d7752d0 --- /dev/null +++ b/recipes/bioconductor-zebrafishcdf/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="zebrafishcdf_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafishcdf_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafishcdf_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishcdf/bioconductor-zebrafishcdf_2.18.0_src_all.tar.gz" +) +MD5="04edbb632600c97610b86423c2d850e7" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-zebrafishcdf/pre-unlink.sh b/recipes/bioconductor-zebrafishcdf/pre-unlink.sh new file mode 100644 index 0000000000000..620b190540d6c --- /dev/null +++ b/recipes/bioconductor-zebrafishcdf/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ zebrafishcdf diff --git a/recipes/bioconductor-zebrafishprobe/meta.yaml b/recipes/bioconductor-zebrafishprobe/meta.yaml new file mode 100644 index 0000000000000..130a70a554fd7 --- /dev/null +++ b/recipes/bioconductor-zebrafishprobe/meta.yaml @@ -0,0 +1,35 @@ +{% set version = "2.18.0" %} +{% set name = "zebrafishprobe" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' + md5: eea2747859afa763addc7313ab0a2452 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +requirements: + host: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + run: + - 'bioconductor-annotationdbi >=1.44.0,<1.45.0' + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/annotation/html/{{ name }}.html' + license: LGPL + summary: 'This package was automatically created by package AnnotationForge version 1.11.21. The probe sequence data was obtained from http://www.affymetrix.com. The file name was Zebrafish\_probe\_tab.' + diff --git a/recipes/bioconductor-zebrafishprobe/post-link.sh b/recipes/bioconductor-zebrafishprobe/post-link.sh new file mode 100644 index 0000000000000..8a5ba85263e7b --- /dev/null +++ b/recipes/bioconductor-zebrafishprobe/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="zebrafishprobe_2.18.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/annotation/src/contrib/zebrafishprobe_2.18.0.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafishprobe_2.18.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishprobe/bioconductor-zebrafishprobe_2.18.0_src_all.tar.gz" +) +MD5="eea2747859afa763addc7313ab0a2452" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-zebrafishprobe/pre-unlink.sh b/recipes/bioconductor-zebrafishprobe/pre-unlink.sh new file mode 100644 index 0000000000000..fd8b2e6524f7b --- /dev/null +++ b/recipes/bioconductor-zebrafishprobe/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ zebrafishprobe diff --git a/recipes/bioconductor-zebrafishrnaseq/meta.yaml b/recipes/bioconductor-zebrafishrnaseq/meta.yaml new file mode 100644 index 0000000000000..b6f0a7bdee44c --- /dev/null +++ b/recipes/bioconductor-zebrafishrnaseq/meta.yaml @@ -0,0 +1,34 @@ +{% set version = "1.2.0" %} +{% set name = "zebrafishRNASeq" %} +{% set bioc = "3.8" %} + +package: + name: 'bioconductor-{{ name|lower }}' + version: '{{ version }}' +source: + url: + - 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' + - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' + md5: f29dab65186b6775efb0a5e5eaeae5e0 +build: + number: 0 + rpaths: + - lib/R/lib/ + - lib/ + noarch: generic +# Suggests: BiocStyle, knitr +requirements: + host: + - r-base + run: + - r-base + - wget +test: + commands: + - '$R -e "library(''{{ name }}'')"' +about: + home: 'https://bioconductor.org/packages/{{ bioc }}/data/experiment/html/{{ name }}.html' + license: GPL + summary: 'Gene-level read counts from RNA-Seq for gallein-treated and control zebrafish.' + diff --git a/recipes/bioconductor-zebrafishrnaseq/post-link.sh b/recipes/bioconductor-zebrafishrnaseq/post-link.sh new file mode 100644 index 0000000000000..3ea10eaab419a --- /dev/null +++ b/recipes/bioconductor-zebrafishrnaseq/post-link.sh @@ -0,0 +1,46 @@ +#!/bin/bash +FN="zebrafishRNASeq_1.2.0.tar.gz" +URLS=( + "https://bioconductor.org/packages/3.8/data/experiment/src/contrib/zebrafishRNASeq_1.2.0.tar.gz" + "https://bioarchive.galaxyproject.org/zebrafishRNASeq_1.2.0.tar.gz" + "https://depot.galaxyproject.org/software/bioconductor-zebrafishrnaseq/bioconductor-zebrafishrnaseq_1.2.0_src_all.tar.gz" +) +MD5="f29dab65186b6775efb0a5e5eaeae5e0" + +# Use a staging area in the conda dir rather than temp dirs, both to avoid +# permission issues as well as to have things downloaded in a predictable +# manner. +STAGING=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM +mkdir -p $STAGING +TARBALL=$STAGING/$FN + +SUCCESS=0 +for URL in ${URLS[@]}; do + wget -O- -q $URL > $TARBALL + [[ $? == 0 ]] || continue + + # Platform-specific md5sum checks. + if [[ $(uname -s) == "Linux" ]]; then + if md5sum -c <<<"$MD5 $TARBALL"; then + SUCCESS=1 + break + fi + else if [[ $(uname -s) == "Darwin" ]]; then + if [[ $(md5 $TARBALL | cut -f4 -d " ") == "$MD5" ]]; then + SUCCESS=1 + break + fi + fi +fi +done + +if [[ $SUCCESS != 1 ]]; then + echo "ERROR: post-link.sh was unable to download any of the following URLs with the md5sum $MD5:" + printf '%s\n' "${URLS[@]}" + exit 1 +fi + +# Install and clean up +R CMD INSTALL --library=$PREFIX/lib/R/library $TARBALL +rm $TARBALL +rmdir $STAGING diff --git a/recipes/bioconductor-zebrafishrnaseq/pre-unlink.sh b/recipes/bioconductor-zebrafishrnaseq/pre-unlink.sh new file mode 100644 index 0000000000000..b20b298f19972 --- /dev/null +++ b/recipes/bioconductor-zebrafishrnaseq/pre-unlink.sh @@ -0,0 +1 @@ +R CMD REMOVE --library=$PREFIX/lib/R/library/ zebrafishRNASeq diff --git a/recipes/bioconductor-zfpkm/build.sh b/recipes/bioconductor-zfpkm/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-zfpkm/build.sh +++ b/recipes/bioconductor-zfpkm/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-zfpkm/meta.yaml b/recipes/bioconductor-zfpkm/meta.yaml index b4ae1d7a49a2d..311eafd497285 100644 --- a/recipes/bioconductor-zfpkm/meta.yaml +++ b/recipes/bioconductor-zfpkm/meta.yaml @@ -1,31 +1,33 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "zFPKM" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name|lower }}/bioconductor-{{ name|lower }}_{{ version }}_src_all.tar.gz' - sha256: e96ab54765a5198bb135eed7d31ac835f62aa1dfbd5167e089d579fab37571da + md5: 563d34bd16b73596c886bf427f11fab4 build: number: 0 rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, limma, edgeR, GEOquery, stringr, printr requirements: host: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-checkmate - r-dplyr - r-ggplot2 - r-tidyr run: - - 'bioconductor-summarizedexperiment >=1.10.1,<1.12.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-checkmate - r-dplyr @@ -35,8 +37,12 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'GPL-3 | file LICENSE' summary: 'Perform the zFPKM transform on RNA-seq FPKM data. This algorithm is based on the publication by Hart et al., 2013 (Pubmed ID 24215113). Reference recommends using zFPKM > -3 to select expressed genes. Validated with encode open/closed chromosome data. Works well for gene level data using FPKM or TPM. Does not appear to calibrate well for transcript level data.' - +extra: + parent_recipe: + name: bioconductor-zfpkm + path: recipes/bioconductor-zfpkm + version: 1.2.0 diff --git a/recipes/bioconductor-zinbwave/build.sh b/recipes/bioconductor-zinbwave/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-zinbwave/build.sh +++ b/recipes/bioconductor-zinbwave/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-zinbwave/conda_build_config.yaml b/recipes/bioconductor-zinbwave/conda_build_config.yaml deleted file mode 100644 index d3da287204f8d..0000000000000 --- a/recipes/bioconductor-zinbwave/conda_build_config.yaml +++ /dev/null @@ -1,2 +0,0 @@ -r_base: - - 3.5.1 diff --git a/recipes/bioconductor-zinbwave/meta.yaml b/recipes/bioconductor-zinbwave/meta.yaml index 5dbf4df5aa581..d0984a31a87a7 100644 --- a/recipes/bioconductor-zinbwave/meta.yaml +++ b/recipes/bioconductor-zinbwave/meta.yaml @@ -1,54 +1,59 @@ -{% set version = "1.2.0" %} +{% set version = "1.4.0" %} {% set name = "zinbwave" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: a01299397b8cd8bc4d1e6818b3006f25cf9da2a4a482703e703ee63159ab819a + md5: 06892200948d0ebe42ae058931695366 build: number: 0 - skip: true # [osx] rpaths: - lib/R/lib/ - lib/ + noarch: generic +# Suggests: knitr, rmarkdown, testthat, matrixStats, magrittr, scRNAseq, ggplot2, biomaRt, BiocStyle, Rtsne, DESeq2, Seurat requirements: - build: - - 'bioconductor-biocparallel >=1.14.0,<1.16.0' - - 'bioconductor-edger >=3.22.0,<3.24.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + host: + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-copula - r-glmnet + - r-matrix - r-softimpute - - gsl >=2.4 run: - - 'bioconductor-biocparallel >=1.14.0,<1.16.0' - - 'bioconductor-edger >=3.22.0,<3.24.0' - - 'bioconductor-genefilter >=1.62.0,<1.64.0' - - 'bioconductor-singlecellexperiment >=1.2.0,<1.4.0' - - 'bioconductor-summarizedexperiment >=1.10.0,<1.12.0' + - 'bioconductor-biocparallel >=1.16.0,<1.17.0' + - 'bioconductor-edger >=3.24.0,<3.25.0' + - 'bioconductor-genefilter >=1.64.0,<1.65.0' + - 'bioconductor-singlecellexperiment >=1.4.0,<1.5.0' + - 'bioconductor-summarizedexperiment >=1.12.0,<1.13.0' - r-base - r-copula - r-glmnet + - r-matrix - r-softimpute - - gsl >=2.4 test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' - license: 'Artistic-2.0' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + license: Artistic-2.0 summary: 'Implements a general and flexible zero-inflated negative binomial model that can be used to provide a low-dimensional representations of single-cell RNA-seq data. The model accounts for zero inflation (dropouts), over-dispersion, and the count nature of the data. The model also accounts for the difference in library sizes and optionally for batch effects and/or other covariates, avoiding the need for pre-normalize the data.' - extra: identifiers: - biotools:zinbwave - doi:10.1038/s41467-017-02554-5 + parent_recipe: + name: bioconductor-zinbwave + path: recipes/bioconductor-zinbwave + version: 1.2.0 + diff --git a/recipes/bioconductor-zlibbioc/build.sh b/recipes/bioconductor-zlibbioc/build.sh index da43ce2168312..c1d13421f5f1e 100644 --- a/recipes/bioconductor-zlibbioc/build.sh +++ b/recipes/bioconductor-zlibbioc/build.sh @@ -1,4 +1,11 @@ #!/bin/bash mv DESCRIPTION DESCRIPTION.old grep -v '^Priority: ' DESCRIPTION.old > DESCRIPTION +mkdir -p ~/.R +echo -e "CC=$CC +FC=$FC +CXX=$CXX +CXX98=$CXX +CXX11=$CXX +CXX14=$CXX" > ~/.R/Makevars $R CMD INSTALL --build . \ No newline at end of file diff --git a/recipes/bioconductor-zlibbioc/meta.yaml b/recipes/bioconductor-zlibbioc/meta.yaml index 95d1e203c029d..60e46f4f69f4c 100644 --- a/recipes/bioconductor-zlibbioc/meta.yaml +++ b/recipes/bioconductor-zlibbioc/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "1.26.0" %} +{% set version = "1.28.0" %} {% set name = "zlibbioc" %} -{% set bioc = "3.7" %} +{% set bioc = "3.8" %} package: name: 'bioconductor-{{ name|lower }}' version: '{{ version }}' source: url: - - 'http://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' + - 'https://bioconductor.org/packages/{{ bioc }}/bioc/src/contrib/{{ name }}_{{ version }}.tar.gz' - 'https://bioarchive.galaxyproject.org/{{ name }}_{{ version }}.tar.gz' - 'https://depot.galaxyproject.org/software/bioconductor-{{ name }}/bioconductor-{{ name }}_{{ version }}_src_all.tar.gz' - sha256: ff9d472e7505f049f291285bc276e48fa40aab24712b1d0116e12814590599e7 + md5: a92d411b500d3f88434653351a8e9aea build: number: 0 rpaths: @@ -29,10 +29,15 @@ test: commands: - '$R -e "library(''{{ name }}'')"' about: - home: 'http://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' + home: 'https://bioconductor.org/packages/{{ bioc }}/bioc/html/{{ name }}.html' license: 'Artistic-2.0 + file LICENSE' summary: 'This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means (most Linux and Mac users should have system-level access to zlib, and no direct need for this package). See the vignette for instructions on use.' extra: identifiers: - biotools:zlibbioc - doi:10.1038/nmeth.3252 + parent_recipe: + name: bioconductor-zlibbioc + path: recipes/bioconductor-zlibbioc + version: 1.26.0 + diff --git a/recipes/biolite/meta.yaml b/recipes/biolite/meta.yaml index 8bc2532e4480d..2a174e9b755ba 100644 --- a/recipes/biolite/meta.yaml +++ b/recipes/biolite/meta.yaml @@ -1,13 +1,13 @@ package: name: biolite - version: 1.2.0 + version: 1.1.0 source: - url: https://bitbucket.org/caseywdunn/biolite/get/release-1.2.0.zip - sha256: 61d9268278a50b3ea03b7a4e1a5424beeff2482634ab570d6c66925dac26d9e2 + url: https://bitbucket.org/caseywdunn/biolite/get/release-1.1.0.zip + sha256: dbfb9cce029098c476d930af179ab0e33c8e9f459c62bb007c0fd9c33fa7b30a build: - number: 0 + number: 2 skip: True # [not py27] requirements: diff --git a/recipes/kneaddata/meta.yaml b/recipes/kneaddata/meta.yaml index 25b3c845713ea..4ec0c24f538a4 100644 --- a/recipes/kneaddata/meta.yaml +++ b/recipes/kneaddata/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "0.7.2" %} +{% set version = "0.7.0" %} package: name: kneaddata @@ -6,7 +6,7 @@ package: source: url: https://bitbucket.org/biobakery/kneaddata/get/{{ version }}.tar.gz - sha256: 87f74c5f94a28d61384a11544f23bd6bdbca0fb4477ac29727929024e140bacb + sha256: ec097857b3354e0e03d5043905d3f95afb5b763063c8bf27dda529d1dbf9bdee build: number: 0 diff --git a/recipes/microhapdb/meta.yaml b/recipes/microhapdb/meta.yaml deleted file mode 100644 index c1cb8b54bfe7c..0000000000000 --- a/recipes/microhapdb/meta.yaml +++ /dev/null @@ -1,39 +0,0 @@ -{% set version = "0.2" %} -{% set sha256 = "450faabc3420fc7ed9107c0de3a0643b82352a592bde487c4afc6dc064bc8f7a" %} - -package: - name: microhapdb - version: '{{version}}' - -source: - url: https://github.com/bioforensics/microhapdb/archive/{{ version }}.tar.gz - sha256: '{{sha256}}' - -build: - noarch: python - entry_points: - - microhapdb = microhapdb.cli:main - script: python -m pip install --no-deps --ignore-installed . - number: 0 - -requirements: - host: - - python >=3 - - pip - run: - - python >=3 - - pandas - -test: - imports: - - microhapdb - requires: - - pytest - - pytest-cov - -about: - home: https://github.com/bioforensics/MicroHapDB/ - license: BSD License - license_family: BSD - summary: Data package providing convenient programmatic access to published microhaplotype data. - dev_url: https://github.com/bioforensics/MicroHapDB/ diff --git a/recipes/moff/meta.yaml b/recipes/moff/meta.yaml index b0cdff246d06e..d0bd424099135 100644 --- a/recipes/moff/meta.yaml +++ b/recipes/moff/meta.yaml @@ -1,4 +1,4 @@ -{% set version = "2.0.2" %} +{% set version = "2.0.1" %} package: name: moff @@ -6,7 +6,7 @@ package: source: url: https://github.com/compomics/moFF/archive/{{ version }}.tar.gz - sha256: 42ded39204b4ffd536d2ea9f0b22350ec7a228c6d497d3f3028d3cf6af6810d9 + md5: cd8176137643087622554efb2ef265ed build: number: 0 diff --git a/recipes/msstitch/meta.yaml b/recipes/msstitch/meta.yaml index 76addaa82f4ea..d83ab10facf05 100644 --- a/recipes/msstitch/meta.yaml +++ b/recipes/msstitch/meta.yaml @@ -1,10 +1,10 @@ package: name: msstitch - version: "2.10" + version: "2.9" source: - url: https://files.pythonhosted.org/packages/af/4e/6a98b424697b6bdf43e089ea0446cddb2e8500cd13a70e439f840c4f500f/msstitch-2.10.tar.gz - sha256: b85c2791484ecd61e8c5832c2c3359921680bbc414f3c6feccd3c82ec4b77cdb + url: https://files.pythonhosted.org/packages/e9/c2/a6f965f8e4dbfd2e819126b96110940903215df1a4d5cad5d84c821eb484/msstitch-2.9.tar.gz + sha256: 0096958917e597cbe998b8eefab6be7c3af5d490a2e4a0f722311cb6bdeb07b8 build: skip: True # [py2k or osx] diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index dbb225c7455ba..501f27d8a42f2 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -1,4 +1,4 @@ -{% set tag="66c7e1d" %} +{% set tag="374afb6" %} package: name: multiqc-bcbio @@ -6,11 +6,11 @@ package: source: url: https://github.com/MultiQC/MultiQC_bcbio/archive/{{ tag }}.tar.gz - sha256: 31d4efbd574d61255b0638b29ccad396066c4aeebfc2a6ca323a207857eabf3b + md5: c29e4fce85472b858d74cd829f0add1e build: noarch: python - number: 4 + number: 3 preserve_egg_dir: True requirements: diff --git a/recipes/nextflow/meta.yaml b/recipes/nextflow/meta.yaml index 6bff6d7912a22..1a86ab4e5865f 100644 --- a/recipes/nextflow/meta.yaml +++ b/recipes/nextflow/meta.yaml @@ -5,7 +5,7 @@ package: version: {{ version }} build: - number: 3 + number: 2 noarch: generic source: @@ -14,11 +14,11 @@ source: requirements: host: - - openjdk >=8,<=9 + - openjdk >=8,<=11 - coreutils - curl run: - - openjdk >=8,<=9 + - openjdk >=8,<=11 - coreutils - curl diff --git a/recipes/popdel/Makefile.patch b/recipes/popdel/Makefile.patch new file mode 100644 index 0000000000000..a31ec8c115409 --- /dev/null +++ b/recipes/popdel/Makefile.patch @@ -0,0 +1,45 @@ +--- Makefile 2018-10-18 15:23:37.903614000 +0200 ++++ MakefileConda 2018-10-18 15:53:03.215652075 +0200 +@@ -1,10 +1,3 @@ +-# Use version 4.9 of g++ +- +-# Set dependencies, s.t. make detects changes in header files. +-%.o: %.cc %.h +- g++ -c $^ +- +-CXX=g++ + CC=$(CXX) + + # Set this to include SeqAn libraries, either system wide +@@ -14,14 +7,13 @@ + CXXFLAGS+=-I$(SEQAN_LIB) -DSEQAN_HAS_ZLIB=1 -std=c++14 -DSEQAN_DISABLE_VERSION_CHECK + LDLIBS=-lz -lpthread + +-DATE=on $(shell git log --pretty=format:"%cd" --date=iso | cut -f 1,2 -d " " | head -n 1) +-VERSION=1.0.4-$(shell git log --pretty=format:"%h" --date=iso | head -n 1) ++DATE=on 2018-11-09 ++VERSION=1.0.4 + CXXFLAGS+=-DDATE=\""$(DATE)"\" -DVERSION=\""$(VERSION)"\" + + # Enable warnings + CXXFLAGS+=-W -Wall -Wno-long-long -pedantic -Wno-variadic-macros -Wno-unused-result + +- + HEADERS=parse_popdel.h insert_histogram_popdel.h workflow_popdel.h utils_popdel.h popdel_view_parameter_parsing.h + HEADERS+=popdel_profile/*.h + HEADERS+=popdel_call/*.h +@@ -30,14 +22,6 @@ + all: CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 + all: popdel + +-.PHONY: profiling +-profiling: CXXFLAGS+=-g -O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=1 +-profiling: popdel +- +-.PHONY: debug +-debug: CXXFLAGS+=-g -O0 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=1 +-debug: popdel +- + PREFIX = /usr/local + .PHONY: install + install: CXXFLAGS+=-O3 -DSEQAN_ENABLE_TESTING=0 -DSEQAN_ENABLE_DEBUG=0 diff --git a/recipes/popdel/build.sh b/recipes/popdel/build.sh index 36448bcdcdb41..dc77fe956bee6 100644 --- a/recipes/popdel/build.sh +++ b/recipes/popdel/build.sh @@ -1,6 +1,4 @@ #!/bin/sh -DATE=2018-12-06 - -make CXX=${CXX} VERSION=${PKG_VERSION} DATE=${DATE} +make all mkdir -p ${PREFIX}/bin cp popdel ${PREFIX}/bin diff --git a/recipes/popdel/meta.yaml b/recipes/popdel/meta.yaml index d9ed54e867f39..f015eadc03948 100644 --- a/recipes/popdel/meta.yaml +++ b/recipes/popdel/meta.yaml @@ -1,10 +1,12 @@ package: name: popdel - version: "1.0.5" + version: "1.0.4" source: - url: https://github.com/kehrlab/PopDel/archive/v1.0.5.tar.gz - sha256: 7ab33573780b0f373787cfd9014b7a60d0451049956e072521670708b401109c + url: https://github.com/kehrlab/PopDel/archive/v1.0.4.tar.gz + sha256: eb611363a5279b5d7db0dcc8de9b086f73fd34e1516c762425ea655917e55041 + patches: + - Makefile.patch build: number: 0 diff --git a/recipes/seq2c/build.sh b/recipes/seq2c/build.sh index f0b89ab7a5e2b..161c67a79661b 100644 --- a/recipes/seq2c/build.sh +++ b/recipes/seq2c/build.sh @@ -4,6 +4,10 @@ target=$PREFIX/share/$PKG_NAME-$PKG_VERSION-$PKG_BUILDNUM mkdir -p $target mkdir -p $PREFIX/bin +# fix references to handle symlinks +sed -i.bak 's/FindBin::Bin/FindBin::RealBin/' cov2lr.pl +sed -i.bak 's/FindBin::Bin/FindBin::RealBin/' lr2gene.pl + cp -r * $target ln -s $target/seq2cov.pl $PREFIX/bin ln -s $target/cov2lr.pl $PREFIX/bin diff --git a/recipes/seq2c/meta.yaml b/recipes/seq2c/meta.yaml index 68ea7324520bf..d22e06c330b57 100644 --- a/recipes/seq2c/meta.yaml +++ b/recipes/seq2c/meta.yaml @@ -1,14 +1,13 @@ package: name: seq2c - version: '2018.12.05' + version: '2016.03.23' source: - url: https://github.com/chapmanb/Seq2C/archive/dd69de2.tar.gz - #url: https://github.com/AstraZeneca-NGS/Seq2C/archive/7b33abe.tar.gz - sha256: 1d181da8433c088dee5b5b133915efc7140633e5cb0136a0bd87e6a8c1f7cc2c + url: https://github.com/AstraZeneca-NGS/Seq2C/archive/8e62a3f.tar.gz + sha256: 0b50b6f14a3feed233956a72a631d321e3c8f6328521444886f1b0a8c7f24a5b build: - number: 0 + number: 1 skip: False requirements: @@ -16,7 +15,6 @@ requirements: - perl run: - perl - - perl-statistics-ttest test: commands: diff --git a/recipes/snakemake-minimal/meta.yaml b/recipes/snakemake-minimal/meta.yaml index 9d4f61e555959..0d72f355a726a 100644 --- a/recipes/snakemake-minimal/meta.yaml +++ b/recipes/snakemake-minimal/meta.yaml @@ -1,15 +1,15 @@ -{% set version = "5.3.1" %} +{% set version = "5.3.0" %} package: name: snakemake-minimal - version: {{ version }} + version: "5.3.0" source: - url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ version }}.tar.gz - sha256: a43d66d80d7bf83b0429cf03ab5500b2775bbe78a53eee9622c1a2cb802eac5f + url: https://pypi.io/packages/source/s/snakemake/snakemake-{{ PKG_VERSION }}.tar.gz + sha256: 612a16f2bba580c47183e4f752ed40b034852541ca3e96e480d01fb30ad9570c build: - number: 0 + number: 2 noarch: python script: python -m pip install --no-deps --ignore-installed . entry_points: @@ -41,7 +41,6 @@ test: imports: - snakemake commands: - - export GIT\_PYTHON_REFRESH=warn - snakemake --version - snakemake --version | grep "{{ version }}" diff --git a/recipes/snakemake/meta.yaml b/recipes/snakemake/meta.yaml index c03010d193ab7..3f38f91fbf699 100644 --- a/recipes/snakemake/meta.yaml +++ b/recipes/snakemake/meta.yaml @@ -1,16 +1,16 @@ -{% set version = "5.3.1" %} +{% set version = "5.3.0" %} package: name: snakemake - version: {{ version }} + version: "5.3.0" build: - number: 0 + number: 2 noarch: generic requirements: run: - - snakemake-minimal ={{ version }} + - snakemake-minimal ={{ PKG_VERSION }} # optional dependencies needed for the full experience # require this dropbox version to ensure that a conda doesn't pick up the # outdated version available @@ -34,7 +34,6 @@ test: imports: - snakemake commands: - - export GIT\_PYTHON_REFRESH=warn - snakemake --version - snakemake --version | grep "{{ version }}" diff --git a/recipes/teloclip/meta.yaml b/recipes/teloclip/meta.yaml index 9532ae99ec7b8..d385f33e54ef1 100644 --- a/recipes/teloclip/meta.yaml +++ b/recipes/teloclip/meta.yaml @@ -1,8 +1,8 @@ {% set name = "teloclip" %} -{% set version = "0.0.3" %} +{% set version = "0.0.2" %} {% set file_ext = "tar.gz" %} {% set hash_type = "sha256" %} -{% set hash_value = "48b25ce0a3dce9f44bc2703ccbcb9738861c260568a9ce1f3687c4aca054b14d" %} +{% set hash_value = "bee069ec44dec8fd0aff171ddfa146da66a750dea8fa41903cd846f2bdab3ebb" %} package: name: '{{ name|lower }}' @@ -13,11 +13,10 @@ source: '{{ hash_type }}': '{{ hash_value }}' build: - skip: True # [py27] + noarch: python number: 0 entry_points: - teloclip=teloclip.run_self:main - - teloclip-extract=teloclip.run_extract:main script: python setup.py install --single-version-externally-managed --record=record.txt requirements: @@ -32,17 +31,16 @@ test: - teloclip commands: - teloclip --help - - teloclip-extract --help about: home: https://github.com/Adamtaranto/teloclip license: MIT License license_family: MIT license_file: '' - summary: A tool for the recovery of unassembled telomeres from soft-clipped read alignments. + summary: Filter SAM file for soft-clipped alignments containing unassembled telomeric repeats. description: '' doc_url: '' dev_url: '' extra: - recipe-maintainers: 'Adam Taranto' + recipe-maintainers: '' diff --git a/recipes/tracy/meta.yaml b/recipes/tracy/meta.yaml index bf24a6408be0b..fb36eaf480cb3 100644 --- a/recipes/tracy/meta.yaml +++ b/recipes/tracy/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "0.3.7" %} -{% set sha256 = "1b7582809595d1a8c6821c84807b839828387f9c01d63f4694a3225fada7e7b4" %} +{% set version = "0.3.6" %} +{% set sha256 = "e00f42d0d052941117f678f9ede99ab4da897606b4fa89134c0b2c60ea6798a1" %} package: name: tracy @@ -12,7 +12,7 @@ source: - Makefile.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -21,13 +21,13 @@ requirements: host: - zlib - bzip2 - - boost + - boost ==1.61.0 - htslib - sdsl-lite run: - zlib - bzip2 - - boost + - boost ==1.61.0 - htslib - sdsl-lite diff --git a/recipes/ucsc-cell-browser/meta.yaml b/recipes/ucsc-cell-browser/meta.yaml index 8c151af7ddfd0..b5c2b94d53d5f 100644 --- a/recipes/ucsc-cell-browser/meta.yaml +++ b/recipes/ucsc-cell-browser/meta.yaml @@ -9,7 +9,7 @@ source: sha256: e2a019f8bb150f8d115b0dd1f75a76831c9e96898c42d70b42f37ff61f01641e build: - number: 1 + number: 0 noarch: python requirements: @@ -19,8 +19,6 @@ requirements: - python >=3.6 - numpy - r-data.table - - r-argparser - - r-matrix - anndata test: diff --git a/recipes/vsearch/meta.yaml b/recipes/vsearch/meta.yaml index 4eb9eb4fe8667..e55d4e21cebc0 100644 --- a/recipes/vsearch/meta.yaml +++ b/recipes/vsearch/meta.yaml @@ -1,5 +1,5 @@ -{% set version = "2.10.1" %} -{% set sha256 = "fd0726bd0604c00ed8e90d1b5bfe9a1afa42786acb01389e0255c2b418f1bc99" %} +{% set version = "2.10.0" %} +{% set sha256 = "a1ca14a6aaa96d4734572a224624af802973b38bbd3f12a95df1ed4cf918c7d4" %} package: name: vsearch