From 16b0b30af1d5c8a4d3abc26faa988f149e136da4 Mon Sep 17 00:00:00 2001 From: Devon Ryan Date: Mon, 13 May 2019 20:34:44 +0200 Subject: [PATCH] more from #15196 (#15326) * more from #15196 * bump build numbers * updates * updates * old bedtools versions won't build, fix bcftools/1.3.1 * group blacklist items a bit * Try to fix braker and bowtie2 * a few updates * Update meta.yaml --- build-fail-blacklist | 35 ++++++++++++------------------- recipes/bcftools/1.3.1/build.sh | 3 ++- recipes/bcftools/1.3.1/meta.yaml | 35 ++++++++++++++++--------------- recipes/bcftools/meta.yaml | 33 ++++++++++++++++------------- recipes/bedtools/2.19.1/build.sh | 2 +- recipes/bedtools/2.19.1/meta.yaml | 25 +++++++++++----------- recipes/bedtools/2.20.1/build.sh | 6 +++--- recipes/bedtools/2.20.1/meta.yaml | 25 +++++++++++----------- recipes/bedtools/2.22/build.sh | 2 +- recipes/bedtools/2.22/meta.yaml | 26 ++++++++++++----------- recipes/bedtools/2.23.0/build.sh | 2 +- recipes/bedtools/2.23.0/meta.yaml | 24 +++++++++++++-------- recipes/bowtie2/2.2.1/build.sh | 4 +--- recipes/bowtie2/2.2.1/meta.yaml | 24 ++++++++++----------- recipes/bowtie2/2.2.4/build.sh | 2 +- recipes/bowtie2/2.2.4/meta.yaml | 24 ++++++++++----------- recipes/bowtie2/2.2.5/build.sh | 4 +--- recipes/bowtie2/2.2.5/meta.yaml | 31 +++++++++++++-------------- recipes/braker/meta.yaml | 27 ++++++++++++------------ 19 files changed, 168 insertions(+), 166 deletions(-) diff --git a/build-fail-blacklist b/build-fail-blacklist index c58937125e635..1ba7848bdcbd4 100644 --- a/build-fail-blacklist +++ b/build-fail-blacklist @@ -1,3 +1,7 @@ +# ../../utils//fileType/FileRecordTypeChecker.h:120:21: error: 'constexpr' needed for in-class initialization of static data member 'const float FileRecordTypeChecker::PERCENTAGE_PRINTABLE' of non-integral type [-fpermissive] +recipes/bedtools/2.20.1 +recipes/bedtools/2.19.1 + # last-pair-probs.cc:501:10: error: cannot convert 'std::istream {aka std::basic_istream}' to 'bool' in return recipes/last/638 @@ -168,6 +172,14 @@ recipes/soapaligner # missing tarball recipes/metagene_annotator recipes/sloika +recipes/genometools +recipes/nanonet +recipes/knot +recipes/moreutils +recipes/jali +recipes/intervalstats +recipes/mrbayes +recipes/igvtools # missing dep recipes/oligotyping @@ -209,6 +221,7 @@ recipes/libmuscle # compilation error recipes/osra/2.0.1 +recipes/lightning # unable to access jarfile recipes/effectivet3 @@ -222,9 +235,6 @@ recipes/discovar-denovo # seqan errors recipes/bowtie/1.0.0 -# tarball missing -recipes/mrbayes - # depends on perl-pcap recipes/brass @@ -243,10 +253,6 @@ recipes/qiime/1.9.1 # requires wgs-assembler, which has a build fail recipes/sprai -# missing tarballs -recipes/genometools -recipes/nanonet - # missing dependency recipes/genomebaser recipes/garnet @@ -329,9 +335,6 @@ recipes/primerprospector # missing URL recipes/intemap -# compilation error -recipes/lightning - # zlib missing recipes/polymutt recipes/prophyle/0.2.1 @@ -504,9 +507,6 @@ recipes/perl-bio-db-sam recipes/krona/2.6 recipes/krona/2.5 -# tarball missing -recipes/igvtools - # /opt/conda/conda-bld/pash_1531691261758/_test_env_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_placehold_place/lib/ruby/2.4.0/rubygems/core_ext/kernel_require.rb:55:in `require': cannot load such file -- brl/util/textFileUtil (LoadError) recipes/pash @@ -546,17 +546,9 @@ recipes/ghc/6.8.3 # missing python dep recipes/hurry.filesize -# missing tarball -recipes/knot -recipes/moreutils - # compilation error, missing boost header recipes/k-slam -# missing tarball -recipes/jali -recipes/intervalstats - # failing recipes/igblast/1.4.0 @@ -732,7 +724,6 @@ recipes/bioconductor-org.mm.eg.db/3.3.0 recipes/bioconductor-qdnaseq.mm10/1.4.0 recipes/bioconductor-rgraphviz/2.13.0 recipes/bioconductor-ropls/1.2.14 -recipes/r-seurat/1.4.0.16 recipes/r-speaq/1.2.1 recipes/bioconductor-cummerbund/2.8.2 recipes/bioconductor-cummerbund/2.12.1 diff --git a/recipes/bcftools/1.3.1/build.sh b/recipes/bcftools/1.3.1/build.sh index 58a27f3d9bcd5..d1bcbd736b94f 100644 --- a/recipes/bcftools/1.3.1/build.sh +++ b/recipes/bcftools/1.3.1/build.sh @@ -2,4 +2,5 @@ export CPPFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" -make prefix=$PREFIX CPPFLAGS=$CPPFLAGS LDFLAGS=$LDFLAGS plugins install +make all prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS" +make install prefix=${PREFIX} CC=${CC} LDFLAGS="$LDFLAGS" CFLAGS="$CFLAGS" diff --git a/recipes/bcftools/1.3.1/meta.yaml b/recipes/bcftools/1.3.1/meta.yaml index fa4bbee170b8e..0279cb5701dbf 100644 --- a/recipes/bcftools/1.3.1/meta.yaml +++ b/recipes/bcftools/1.3.1/meta.yaml @@ -1,20 +1,14 @@ -about: - home: https://github.com/samtools/bcftools - license: MIT - summary: BCFtools is a set of utilities that manipulate variant calls in the Variant - Call Format (VCF) and its binary counterpart BCF. All commands work transparently - with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands - accept VCF, bgzipped VCF and BCF with filetype detected automatically even when - streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed - VCF and BCF and streams will work in most, but not all situations. - -build: - number: 4 - package: name: bcftools version: '1.3.1' +source: + sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924 + url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 + +build: + number: 5 + requirements: build: - {{ compiler('c') }} @@ -23,16 +17,23 @@ requirements: run: - zlib -source: - sha256: 12c37a4054cbf1980223e2b3a80a7fdb3fd850324a4ba6832e38fdba91f1b924 - url: https://github.com/samtools/bcftools/releases/download/1.3.1/bcftools-1.3.1.tar.bz2 - test: commands: - "bcftools -h > /dev/null" - bcftools --version - bcftools plugin -lv +about: + home: https://github.com/samtools/bcftools + license: MIT + license_file: "LICENSE" + summary: BCFtools is a set of utilities that manipulate variant calls in the Variant + Call Format (VCF) and its binary counterpart BCF. All commands work transparently + with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands + accept VCF, bgzipped VCF and BCF with filetype detected automatically even when + streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed + VCF and BCF and streams will work in most, but not all situations. + extra: identifiers: - biotools:bcftools diff --git a/recipes/bcftools/meta.yaml b/recipes/bcftools/meta.yaml index 7d483559add71..d0de65be7fe4a 100644 --- a/recipes/bcftools/meta.yaml +++ b/recipes/bcftools/meta.yaml @@ -1,19 +1,16 @@ {% set version="1.9" %} -about: - home: https://github.com/samtools/bcftools - license: MIT - summary: BCFtools is a set of utilities that manipulate variant calls in the Variant - Call Format (VCF) and its binary counterpart BCF. All commands work transparently - with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands - accept VCF, bgzipped VCF and BCF with filetype detected automatically even when - streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed - VCF and BCF and streams will work in most, but not all situations. -build: - number: 3 package: name: bcftools version: {{ version }} + +build: + number: 4 + +source: + url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 + sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8 + requirements: build: - {{ compiler('c') }} @@ -33,10 +30,6 @@ requirements: - zlib - libdeflate -source: - url: https://github.com/samtools/bcftools/releases/download/{{ version }}/bcftools-{{ version }}.tar.bz2 - sha256: 6f36d0e6f16ec4acf88649fb1565d443acf0ba40f25a9afd87f14d14d13070c8 - test: commands: - bcftools -h @@ -44,6 +37,16 @@ test: - bcftools plugin -lv #- plot-vcfstats -h 2>&1 | grep -q "Plots output of " +about: + home: https://github.com/samtools/bcftools + license: MIT + summary: BCFtools is a set of utilities that manipulate variant calls in the Variant + Call Format (VCF) and its binary counterpart BCF. All commands work transparently + with both VCFs and BCFs, both uncompressed and BGZF-compressed. Most commands + accept VCF, bgzipped VCF and BCF with filetype detected automatically even when + streaming from a pipe. Indexed VCF and BCF will work in all situations. Un-indexed + VCF and BCF and streams will work in most, but not all situations. + extra: identifiers: - biotools:bcftools diff --git a/recipes/bedtools/2.19.1/build.sh b/recipes/bedtools/2.19.1/build.sh index e829f0c73c5f9..cb1f36a5aba74 100644 --- a/recipes/bedtools/2.19.1/build.sh +++ b/recipes/bedtools/2.19.1/build.sh @@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make +make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" mkdir -p $PREFIX/bin mv bin/* $PREFIX/bin/ diff --git a/recipes/bedtools/2.19.1/meta.yaml b/recipes/bedtools/2.19.1/meta.yaml index 092d51584cd5c..0a8acf5db1abe 100644 --- a/recipes/bedtools/2.19.1/meta.yaml +++ b/recipes/bedtools/2.19.1/meta.yaml @@ -1,31 +1,32 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: 2.19.1 +source: + sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77 + url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz + +build: + number: 3 + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 17253439e8191cb51a8bffba640c580e09ba158d3a0c66649e53d23ee3e50f77 - url: https://github.com/arq5x/bedtools2/releases/download/v2.19.1/bedtools-2.19.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.20.1/build.sh b/recipes/bedtools/2.20.1/build.sh index e829f0c73c5f9..28f488f4b3c86 100644 --- a/recipes/bedtools/2.20.1/build.sh +++ b/recipes/bedtools/2.20.1/build.sh @@ -4,6 +4,6 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make -mkdir -p $PREFIX/bin -mv bin/* $PREFIX/bin/ +make prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" +mkdir -p ${PREFIX}/bin +mv bin/* ${PREFIX}/bin/ diff --git a/recipes/bedtools/2.20.1/meta.yaml b/recipes/bedtools/2.20.1/meta.yaml index 880c9ac171a56..3625c0ae97898 100644 --- a/recipes/bedtools/2.20.1/meta.yaml +++ b/recipes/bedtools/2.20.1/meta.yaml @@ -1,31 +1,32 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: 2.20.1 +source: + sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 + url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz + +build: + number: 3 + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: b5401810f8b12b683575f0119521dda64ff2f0a59faa308357405c4ae4e328d3 - url: https://github.com/arq5x/bedtools2/releases/download/v2.20.1/bedtools-2.20.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.22/build.sh b/recipes/bedtools/2.22/build.sh index 88a14a2ff40fa..69dc51361596b 100644 --- a/recipes/bedtools/2.22/build.sh +++ b/recipes/bedtools/2.22/build.sh @@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make install prefix=$PREFIX +make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/bedtools/2.22/meta.yaml b/recipes/bedtools/2.22/meta.yaml index 89aa6cdb89b2e..66c0a05ec68a1 100644 --- a/recipes/bedtools/2.22/meta.yaml +++ b/recipes/bedtools/2.22/meta.yaml @@ -1,31 +1,33 @@ -about: - home: http://bedtools.readthedocs.org/ - license: GPL v2 - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' - -build: - number: 2 - package: name: bedtools version: '2.22' +source: + sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233 + url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz + +build: + number: 3 + skip: True # [osx] + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 43ab5da6b41350bbef78ea2ee5be0609fb02d76b920a3301b687a39af7017233 - url: https://github.com/arq5x/bedtools2/releases/download/v2.22.1/bedtools-2.22.1.tar.gz - test: commands: - bedtools +about: + home: http://bedtools.readthedocs.org/ + license: GPL v2 + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bedtools/2.23.0/build.sh b/recipes/bedtools/2.23.0/build.sh index 88a14a2ff40fa..69dc51361596b 100644 --- a/recipes/bedtools/2.23.0/build.sh +++ b/recipes/bedtools/2.23.0/build.sh @@ -4,4 +4,4 @@ export CFLAGS="-I$PREFIX/include" export LDFLAGS="-L$PREFIX/lib" export CPATH=${PREFIX}/include -make install prefix=$PREFIX +make install prefix=$PREFIX CXX=$CXX CC=$CC LDFLAGS="-L$PREFIX/lib" diff --git a/recipes/bedtools/2.23.0/meta.yaml b/recipes/bedtools/2.23.0/meta.yaml index 12c60f31d4367..0e617034b90e4 100644 --- a/recipes/bedtools/2.23.0/meta.yaml +++ b/recipes/bedtools/2.23.0/meta.yaml @@ -1,27 +1,33 @@ -about: - home: 'http://bedtools.readthedocs.org/' - license: 'GPL v2' - summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' -build: - number: 2 package: name: bedtools version: '2.23.0' + +source: + sha256: 9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056 + url: https://github.com/arq5x/bedtools2/archive/v2.23.0.tar.gz + +build: + number: 3 + skip: True # [osx] + requirements: build: - {{ compiler('cxx') }} + - {{ compiler('c') }} host: - zlib run: - zlib -source: - sha256: 9dacaa561d11ce9835d1d51e5aeb092bcbe117b7119663ec9a671abac6a36056 - url: https://github.com/arq5x/bedtools2/archive/v2.23.0.tar.gz test: commands: - bedtools +about: + home: 'http://bedtools.readthedocs.org/' + license: 'GPL v2' + summary: 'A swiss army knife for genome arithmetic. https://github.com/arq5x/bedtools2 ' + extra: identifiers: - biotools:bedtools diff --git a/recipes/bowtie2/2.2.1/build.sh b/recipes/bowtie2/2.2.1/build.sh index 41792e491fa35..70faeb3eb6431 100644 --- a/recipes/bowtie2/2.2.1/build.sh +++ b/recipes/bowtie2/2.2.1/build.sh @@ -1,9 +1,7 @@ #!/bin/bash set -eu -o pipefail -if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make -fi +make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -ltbb -ltbbmalloc -lpthread" binaries="\ bowtie2 \ diff --git a/recipes/bowtie2/2.2.1/meta.yaml b/recipes/bowtie2/2.2.1/meta.yaml index 89df12580c6a0..33b8952b8772a 100644 --- a/recipes/bowtie2/2.2.1/meta.yaml +++ b/recipes/bowtie2/2.2.1/meta.yaml @@ -1,14 +1,3 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.1 @@ -18,7 +7,7 @@ source: sha256: 32728b127abf0a8c3aa48e6fb8bf81a9133f54da7e065c2a7bd3410704195f9d build: - number: 1 + number: 2 skip: True # [osx] requirements: @@ -38,6 +27,17 @@ test: - bowtie2-align-s --help - bowtie2_wrapper.sh -h +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/bowtie2/2.2.4/build.sh b/recipes/bowtie2/2.2.4/build.sh index 41792e491fa35..0a6064f83144e 100644 --- a/recipes/bowtie2/2.2.4/build.sh +++ b/recipes/bowtie2/2.2.4/build.sh @@ -2,7 +2,7 @@ set -eu -o pipefail if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make + make CXX=${CXX} fi binaries="\ diff --git a/recipes/bowtie2/2.2.4/meta.yaml b/recipes/bowtie2/2.2.4/meta.yaml index b11303e2a0d12..275006cb62033 100644 --- a/recipes/bowtie2/2.2.4/meta.yaml +++ b/recipes/bowtie2/2.2.4/meta.yaml @@ -1,14 +1,3 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.4 @@ -18,7 +7,7 @@ source: md5: d31294875092e76ebb061eadc7998582 build: - number: 3 + number: 4 skip: True # [osx] requirements: @@ -38,6 +27,17 @@ test: - bowtie2-align-s --help - bowtie2_wrapper.sh -h +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/bowtie2/2.2.5/build.sh b/recipes/bowtie2/2.2.5/build.sh index dd462b4414662..7f4e56c8aaa1f 100644 --- a/recipes/bowtie2/2.2.5/build.sh +++ b/recipes/bowtie2/2.2.5/build.sh @@ -1,9 +1,7 @@ #!/bin/bash set -eu -o pipefail -if [ "$(expr substr $(uname -s) 1 5)" == "Linux" ]; then - make -fi +make CXX=$CXX CPP=$CXX CC=$CC LDLIBS="-L$PREFIX/lib -lz -ltbb -ltbbmalloc -lpthread" binaries="\ bowtie2 \ diff --git a/recipes/bowtie2/2.2.5/meta.yaml b/recipes/bowtie2/2.2.5/meta.yaml index 3c62150955be9..6801333f67d84 100644 --- a/recipes/bowtie2/2.2.5/meta.yaml +++ b/recipes/bowtie2/2.2.5/meta.yaml @@ -1,26 +1,14 @@ -about: - home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' - license: GPLv3 - summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing - reads to long reference sequences. It is particularly good at aligning reads of - about 50 up to 100s or 1,000s of characters, and particularly good at aligning - to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with - an FM Index to keep its memory footprint small: for the human genome, its memory - footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end - alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' - package: name: bowtie2 version: 2.2.5 source: - url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip # [linux] - sha256: e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 # [linux] - url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-macos-x86_64.zip # [osx] - sha256: 0f142477738accc73276f3e47877d54a64b6f7ac7911d0609b662adcd15374a0 # [osx] + url: http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip + sha256: e22766dd9421c10e82a3e207ee1f0eb924c025b909ad5fffa36633cd7978d3b0 build: - number: 4 + number: 5 + skip: True # [osx] requirements: build: @@ -38,6 +26,17 @@ test: - bowtie2-inspect-l --help - bowtie2-align-s --help +about: + home: 'http://bowtie-bio.sourceforge.net/bowtie2/index.shtml' + license: GPLv3 + summary: 'Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing + reads to long reference sequences. It is particularly good at aligning reads of + about 50 up to 100s or 1,000s of characters, and particularly good at aligning + to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with + an FM Index to keep its memory footprint small: for the human genome, its memory + footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end + alignment modes. http://bowtie-bio.sourceforge.net/bowtie2/index.shtml ' + extra: identifiers: - biotools:bowtie2 diff --git a/recipes/braker/meta.yaml b/recipes/braker/meta.yaml index e263f8fde2c3d..4c60b9e0f6bd4 100644 --- a/recipes/braker/meta.yaml +++ b/recipes/braker/meta.yaml @@ -1,16 +1,15 @@ -about: - home: http://bioinf.uni-greifswald.de/augustus/ - license: ' ' - summary: 'BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS' - -build: - number: 2 - skip: True # [osx] - package: name: braker version: '1.9' +source: + url: http://exon.gatech.edu/genemark/Braker/BRAKER1.tar.gz + sha256: 9e959984f739208d2a0aab4cc978e7b11db11a86a25fcc5b8f71c9a31e9239f2 + +build: + number: 3 + skip: True # [osx] + requirements: build: - perl-module-build @@ -20,11 +19,13 @@ requirements: - perl-pathtools - perl-scalar-util-numeric -source: - url: http://exon.gatech.edu/genemark/Braker/BRAKER1.tar.gz - sha256: 9e959984f739208d2a0aab4cc978e7b11db11a86a25fcc5b8f71c9a31e9239f2 - test: commands: - filterGenemark.pl --help - filterIntronsFindStrand.pl --help + +about: + home: http://bioinf.uni-greifswald.de/augustus/ + license: 'Artistic license' + license_file: 'licence.txt' + summary: 'BRAKER1: Unsupervised RNA-Seq-based genome annotation with GeneMark-ET and AUGUSTUS'