From 3f459ca17346a0e3fa1c880c74b62ed7d5207554 Mon Sep 17 00:00:00 2001 From: Dan Fornika Date: Fri, 2 Nov 2018 14:10:12 -0700 Subject: [PATCH] MentaLiST: Remove old versions and pin dependencies in current versions (#10720) * Remove old versions and pin julia in current versions * Pin hdf5 * Pin hdf5=1.8.17 * Pin mpfr=3.1.* * Add build.sh for 0.1.9 * Use global pinning for hdf5 * Pin hdf5 again --- recipes/mentalist/0.1.3/meta.yaml | 36 ------------------ recipes/mentalist/0.1.4/meta.yaml | 36 ------------------ recipes/mentalist/0.1.5/meta.yaml | 40 -------------------- recipes/mentalist/0.1.6/meta.yaml | 40 -------------------- recipes/mentalist/0.1.7/meta.yaml | 41 --------------------- recipes/mentalist/0.1.8/meta.yaml | 41 --------------------- recipes/mentalist/{0.2.2 => 0.1.9}/build.sh | 9 +---- recipes/mentalist/0.1.9/meta.yaml | 14 +++---- recipes/mentalist/0.2.1/meta.yaml | 35 ------------------ recipes/mentalist/0.2.2/meta.yaml | 36 ------------------ recipes/mentalist/meta.yaml | 6 +-- 11 files changed, 11 insertions(+), 323 deletions(-) delete mode 100644 recipes/mentalist/0.1.3/meta.yaml delete mode 100644 recipes/mentalist/0.1.4/meta.yaml delete mode 100644 recipes/mentalist/0.1.5/meta.yaml delete mode 100644 recipes/mentalist/0.1.6/meta.yaml delete mode 100644 recipes/mentalist/0.1.7/meta.yaml delete mode 100644 recipes/mentalist/0.1.8/meta.yaml rename recipes/mentalist/{0.2.2 => 0.1.9}/build.sh (57%) delete mode 100644 recipes/mentalist/0.2.1/meta.yaml delete mode 100644 recipes/mentalist/0.2.2/meta.yaml diff --git a/recipes/mentalist/0.1.3/meta.yaml b/recipes/mentalist/0.1.3/meta.yaml deleted file mode 100644 index e6f4c56af1c67..0000000000000 --- a/recipes/mentalist/0.1.3/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.3" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 57874e2168b48c165fc68c2bab41819259ec828e298bc54cbc3da8f3c904c63e - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia >=0.6.1 - - hdf5 - - mpfr - - libxml2 - run: - - julia >=0.6.1 - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.4/meta.yaml b/recipes/mentalist/0.1.4/meta.yaml deleted file mode 100644 index 747d473d8eb2f..0000000000000 --- a/recipes/mentalist/0.1.4/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.4" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 7dc6bd983156a28d59ad480bea1d7761ebdcd25087db73ef9ce3fb0e59cd224b - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.5/meta.yaml b/recipes/mentalist/0.1.5/meta.yaml deleted file mode 100644 index ebf49838c33af..0000000000000 --- a/recipes/mentalist/0.1.5/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.5" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 7152813c3f8934ffb29413d670c5662098111203305962534a1ffcd7734a8144 - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.6/meta.yaml b/recipes/mentalist/0.1.6/meta.yaml deleted file mode 100644 index 3ebebd1934c1d..0000000000000 --- a/recipes/mentalist/0.1.6/meta.yaml +++ /dev/null @@ -1,40 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.6" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 32518624f81378aae8ba5b7a8a6da077b2489609da00394bad1fca8d3fef2814 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.1.7/meta.yaml b/recipes/mentalist/0.1.7/meta.yaml deleted file mode 100644 index 0d109254345b8..0000000000000 --- a/recipes/mentalist/0.1.7/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.7" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: ba419318f9f8a1184de2d7711966f8debfe99c601f94c231bf3935b0adcd2984 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE - diff --git a/recipes/mentalist/0.1.8/meta.yaml b/recipes/mentalist/0.1.8/meta.yaml deleted file mode 100644 index 3d6b888dc9a31..0000000000000 --- a/recipes/mentalist/0.1.8/meta.yaml +++ /dev/null @@ -1,41 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.1.8" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 15a56b979f31aafbbb3c9512983568d62f9d8dada60dda15b6ff53a91f652ba7 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - - libxml2 - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - - test -f $PREFIX/scripts/ESCwgMLST.txt - - test -f $PREFIX/scripts/SALwgMLST.txt - - test -f $PREFIX/scripts/YERwgMLST.txt - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE - diff --git a/recipes/mentalist/0.2.2/build.sh b/recipes/mentalist/0.1.9/build.sh similarity index 57% rename from recipes/mentalist/0.2.2/build.sh rename to recipes/mentalist/0.1.9/build.sh index b35fa88516929..3a44013cd6f91 100644 --- a/recipes/mentalist/0.2.2/build.sh +++ b/recipes/mentalist/0.1.9/build.sh @@ -1,24 +1,17 @@ #!/bin/sh -# circumvent a bug in conda-build >=2.1.18,<3.0.10 -# https://github.com/conda/conda-build/issues/2255 -[[ -z $REQUESTS_CA_BUNDLE && ${REQUESTS_CA_BUNDLE+x} ]] && unset REQUESTS_CA_BUNDLE -[[ -z $SSL_CERT_FILE && ${SSL_CERT_FILE+x} ]] && unset SSL_CERT_FILE - cp -r $SRC_DIR/src/*.jl $PREFIX/bin cp -r $SRC_DIR/scripts $PREFIX ln -s $PREFIX/bin/MentaLiST.jl $PREFIX/bin/mentalist chmod +x $PREFIX/bin/mentalist julia -e 'Pkg.init()' +julia -e 'Pkg.add("Suppressor")' julia -e 'Pkg.add("ArgParse")' julia -e 'Pkg.add("Bio")' julia -e 'Pkg.add("OpenGene")' julia -e 'Pkg.add("Logging")' julia -e 'Pkg.add("Lumberjack")' -julia -e 'Pkg.add("FastaIO")' -julia -e 'Pkg.add("JLD")' -julia -e 'Pkg.add("DataStructures")' rm -f "$PREFIX"/share/julia/site/lib/v*/*.ji rm -rf "$PREFIX"/share/julia/site/v*/METADATA diff --git a/recipes/mentalist/0.1.9/meta.yaml b/recipes/mentalist/0.1.9/meta.yaml index 1af4b75b7623c..5e5e513cc83b4 100644 --- a/recipes/mentalist/0.1.9/meta.yaml +++ b/recipes/mentalist/0.1.9/meta.yaml @@ -10,19 +10,19 @@ source: sha256: 44f6718c7d64d952e439fbddba6a413558c95b00de6f3daf0c0807b850914c3e build: - number: 2 + number: 3 skip: True # [osx] requirements: host: - - julia - - hdf5 - - mpfr + - julia 0.5.2 + - hdf5 1.8.17 + - mpfr 3.1.* - libxml2 run: - - julia - - hdf5 - - mpfr + - julia 0.5.2 + - hdf5 1.8.17 + - mpfr 3.1.* - libxml2 - unzip diff --git a/recipes/mentalist/0.2.1/meta.yaml b/recipes/mentalist/0.2.1/meta.yaml deleted file mode 100644 index 051a0ec50666d..0000000000000 --- a/recipes/mentalist/0.2.1/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.2.1" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: a148fcd552c9ce4964dd7cc88d7771fc5bde7d94ed46e8145ba61c8a88804c92 - -build: - number: 3 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - run: - - julia - - hdf5 - - mpfr - - libxml2 - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/0.2.2/meta.yaml b/recipes/mentalist/0.2.2/meta.yaml deleted file mode 100644 index a74ff17a72073..0000000000000 --- a/recipes/mentalist/0.2.2/meta.yaml +++ /dev/null @@ -1,36 +0,0 @@ -{% set name = "MentaLiST" %} -{% set version = "0.2.2" %} - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - url: https://github.com/WGS-TB/MentaLiST/archive/v{{ version }}.tar.gz - sha256: 1bf9cd79b3c2fee652bcef2d7e6b867fc4be172a59bcdf4258c4aeed8a929322 - -build: - number: 2 - skip: True # [osx] - -requirements: - host: - - julia - - hdf5 - - mpfr - run: - - julia - - hdf5 - - mpfr - - libxml2 - - unzip - -test: - commands: - - mentalist -h - -about: - home: https://github.com/WGS-TB/MentaLiST - summary: The MLST pipeline developed by the PathOGiST research group. - license: MIT - license_file: LICENSE diff --git a/recipes/mentalist/meta.yaml b/recipes/mentalist/meta.yaml index 702b8d63bc337..227c65c883b5c 100644 --- a/recipes/mentalist/meta.yaml +++ b/recipes/mentalist/meta.yaml @@ -10,16 +10,16 @@ source: sha256: d456615fb9228737aff735d58b272d5bcefd241db6593ece218f2c26c27f165a build: - number: 0 + number: 1 skip: True # [osx] requirements: host: - - julia + - julia 0.6.1 - hdf5 - mpfr run: - - julia + - julia 0.6.1 - hdf5 - mpfr - libxml2