diff --git a/.travis.yml b/.travis.yml index ddcda9e406..a9515727ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,7 +11,7 @@ services: install: scripts/travis-setup.sh -script: travis_wait 119 scripts/travis-run.sh +script: scripts/travis-run.sh env: global: diff --git a/recipes/amos/build.sh b/recipes/amos/build.sh index c08cdb2878..519e18e70c 100644 --- a/recipes/amos/build.sh +++ b/recipes/amos/build.sh @@ -1,8 +1,20 @@ +# fix automake +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/aclocal +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/automake + +# fix autoconf +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autom4te +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoheader +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoreconf +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/ifnames +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoscan +sed -i.bak '1 s|^.*$|#!/usr/bin/env perl|g' $PREFIX/bin/autoupdate + rm -r test tutorial export LDFLAGS="-L$PREFIX/lib" export CPPFLAGS="-I$PREFIX/include" ./bootstrap ./configure \ - --prefix=$PREFIX + --prefix=$PREFIX make make install diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index 950d0f517f..5e75a5ecf9 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -14,8 +14,7 @@ source: build: number: 3 # OSX failing due to missing dependencies in OSX branch - skip: True # [osx] - + skip: true # [osx] test: commands: @@ -25,11 +24,12 @@ requirements: build: - gcc - zlib - - boost + - boost - autoconf + - automake - blat - mummer - - perl-threaded + - perl - perl-statistics-descriptive - perl-xml-parser - perl-dbi @@ -38,7 +38,7 @@ requirements: run: - mummer - - perl-threaded + - perl - perl-statistics-descriptive - perl-xml-parser - perl-dbi diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 70b98305d7..79313fa772 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -84,9 +84,10 @@ test: # Reason: image not found #- bcbio.distributed.ipython commands: - - bcbio_nextgen.py -h - - bcbio_setup_genome.py -h - - bcbio_prepare_samples.py -h + # click requires a unicode locale + - LANG=C.UTF-8 bcbio_nextgen.py -h + - LANG=C.UTF-8 bcbio_setup_genome.py -h + - LANG=C.UTF-8 bcbio_prepare_samples.py -h about: home: https://github.com/chapmanb/bcbio-nextgen diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index 8ddba1e96f..0011f8d828 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -30,7 +30,8 @@ requirements: test: commands: - - bcl_to_fastq -h &> /dev/null + # click requires a unicode locale + - LANG=C.UTF-8 bcl_to_fastq -h &> /dev/null about: home: https://github.com/brwnj/bcl2fastq diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index d340701bec..cfbfd3d7f5 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -6,13 +6,10 @@ source: fn: biokit-0.4.1.tar.gz url: https://pypi.python.org/packages/e3/fe/9bc827910cbd19a1a03bb5b0a1c4aa583903696526d7f6e51fbc9f849e28/biokit-0.4.1.tar.gz md5: 755efcfa4982fd23d31d1ebdd4972c22 -# patches: - # List any patch files here - # - fix.patch build: skip: True # [py34] - number: 2 + number: 4 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda # Same with easydev @@ -25,6 +22,9 @@ requirements: - colormap - scipy - xmltodict + - numpydoc + - bioservices + - mesalib run: - python @@ -34,25 +34,21 @@ requirements: - colormap - scipy - xmltodict - #- matplotlib - #- libgcc # [not osx] - #- glib + - numpydoc + - bioservices + - matplotlib + - libgcc + - mesalib #- xz #- libxcb # Could not manage to import it without an libXext issue from conda-forge ? and -# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future +# matplotlib v1.5.3 or v2.0.0. Hopefully, this will be resolved in the future test: - # Python imports - # imports: - #- biokit + imports: + - biokit about: home: ['http://pypi.python.org/pypi/biokit'] license: BSD summary: 'Set of visualisation and analysis tools for biological data sets' - - -extra: - recipe-maintainers: - - cokelaer diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 49551c505a..a270667518 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -9,19 +9,12 @@ source: build: - # noarch_python: True preserve_egg_dir: True entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - biom-format = biom-format:main - # - # Would create an entry point called biom-format that calls biom-format.main() - - biom=biom.cli:cli - number: 3 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -43,6 +36,8 @@ requirements: - numpy >=1.3.0 - future >=0.15.0 - scipy >=0.13.0 + # missing scipy dependency + - libgcc test: # Python imports @@ -51,9 +46,8 @@ test: - biom.cli commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - biom --help + # click requires a unicode locale + - LANG=C.UTF-8 biom --help about: home: http://www.biom-format.org diff --git a/recipes/biomaj/meta.yaml b/recipes/biomaj/meta.yaml index b3f6fde1c7..cff65e8efe 100644 --- a/recipes/biomaj/meta.yaml +++ b/recipes/biomaj/meta.yaml @@ -48,6 +48,5 @@ test: about: home: http://biomaj.genouest.org license: GNU Affero General Public License v3 or later (AGPLv3+) - summary: 'BioMAJ' license_family: AGPL summary: Automates the update cycle and the supervision of the locally mirrored databank repository diff --git a/recipes/biopython/1.65/build.sh b/recipes/biopython/1.65/build.sh deleted file mode 100644 index 1aea1a7737..0000000000 --- a/recipes/biopython/1.65/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/biopython/1.65/meta.yaml b/recipes/biopython/1.65/meta.yaml deleted file mode 100644 index 837d630c24..0000000000 --- a/recipes/biopython/1.65/meta.yaml +++ /dev/null @@ -1,113 +0,0 @@ -{% set name = "biopython" %} -{% set version = "1.65" %} -{% set sha256 = "6d591523ba4d07a505978f6e1d7fac57e335d6d62fb5b0bcb8c40bdde5c8998e" %} - - -package: - name: {{ name|lower }} - version: {{ version }} - -source: - fn: {{ name }}-{{ version }}.tar.gz - url: https://pypi.python.org/packages/4e/77/8590d61dcda439d83f378106954e748db1a71e565335168a966642133ef8/biopython-1.65.tar.gz - sha256: {{ sha256 }} - -about: - home: http://www.biopython.org/ - license: Biopython License Agreement - license_file: LICENSE - summary: 'Freely available tools for computational molecular biology.' - -build: - number: 0 - skip: True # [py34] - -requirements: - build: - - python - - numpy x.x - - reportlab - - mmtf-python - - run: - - python - - numpy x.x - - reportlab - - mmtf-python - -test: - imports: - - Bio - - Bio.Align - - Bio.Align.Applications - - Bio.AlignIO - - Bio.Alphabet - - Bio.Application - - Bio.Blast - - Bio.CAPS - - Bio.Compass - - Bio.Crystal - - Bio.Data - - Bio.Emboss - - Bio.Entrez - - Bio.ExPASy - - Bio.FSSP - - Bio.GA - - Bio.GA.Crossover - - Bio.GA.Mutation - - Bio.GA.Repair - - Bio.GA.Selection - - Bio.GenBank - - Bio.Geo - - Bio.Graphics - - Bio.Graphics.GenomeDiagram - - Bio.HMM - - Bio.KEGG - - Bio.KEGG.Compound - - Bio.KEGG.Enzyme - - Bio.KEGG.KGML - - Bio.KEGG.Map - - Bio.Medline - - Bio.NMR - - Bio.NeuralNetwork - - Bio.NeuralNetwork.BackPropagation - - Bio.NeuralNetwork.Gene - - Bio.Nexus - - Bio.PDB - - Bio.PDB.QCPSuperimposer - # - Bio.PDB.mmtf Introduced in 1.68 - - Bio.Pathway - - Bio.Pathway.Rep - - Bio.Phylo - - Bio.Phylo.Applications - - Bio.Phylo.PAML - - Bio.PopGen - - Bio.PopGen.Async - - Bio.PopGen.FDist - - Bio.PopGen.GenePop - - Bio.PopGen.SimCoal - - Bio.Restriction - - Bio.SCOP - - Bio.SVDSuperimposer - - Bio.SearchIO - - Bio.SearchIO.BlastIO - - Bio.SearchIO.ExonerateIO - - Bio.SearchIO.HmmerIO - - Bio.SearchIO._model - - Bio.SeqIO - - Bio.SeqUtils - - Bio.Sequencing - - Bio.Sequencing.Applications - - Bio.Statistics - - Bio.SubsMat - - Bio.SwissProt - - Bio.TogoWS - - Bio.UniGene - - Bio.UniProt - - Bio.Wise - - Bio._py3k - - Bio.codonalign - - Bio.motifs - - Bio.motifs.applications - - Bio.motifs.jaspar - - BioSQL diff --git a/recipes/busco/1.2/build.sh b/recipes/busco/1.2/build.sh deleted file mode 100644 index 81b7edee8e..0000000000 --- a/recipes/busco/1.2/build.sh +++ /dev/null @@ -1,5 +0,0 @@ -#!/bin/bash - -mkdir -p $PREFIX/bin/ -cp BUSCO_v1.2.py $PREFIX/bin -ln -s $PREFIX/bin/BUSCO_v1.2.py $PREFIX/bin/busco diff --git a/recipes/busco/1.2/meta.yaml b/recipes/busco/1.2/meta.yaml deleted file mode 100644 index 3a1ad18c1b..0000000000 --- a/recipes/busco/1.2/meta.yaml +++ /dev/null @@ -1,33 +0,0 @@ -package: - name: busco - version: "1.2" - -build: - number: 1 - -source: - fn: busco-v1.2.tar.gz - url: http://busco.ezlab.org/files/BUSCO_v1.2.tar.gz - md5: 4b4551ccdbc8e64d18295fc8d8729d84 - -requirements: - build: - - python - run: - - python - - blast - - hmmer - # - emboss - -about: - home: http://busco.ezlab.org/ - license: GPL - summary: BUSCO provides measures for quantitative assessment of genome - assembly, gene set, and transcriptome completeness based on - evolutionarily informed expectations of gene content from - near-universal single-copy orthologs selected from OrthoDB. - -test: - commands: - - BUSCO_v1.2.py -h > /dev/null - - busco -h > /dev/null diff --git a/recipes/bx-python/0.7.1/build.sh b/recipes/bx-python/0.7.1/build.sh deleted file mode 100644 index f341bce6fc..0000000000 --- a/recipes/bx-python/0.7.1/build.sh +++ /dev/null @@ -1,2 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install diff --git a/recipes/bx-python/0.7.1/meta.yaml b/recipes/bx-python/0.7.1/meta.yaml deleted file mode 100644 index 296e96b548..0000000000 --- a/recipes/bx-python/0.7.1/meta.yaml +++ /dev/null @@ -1,57 +0,0 @@ -about: - home: http://bitbucket.org/james_taylor/bx-python/wiki/Home - license: MIT - summary: Toolkit to enable rapid implementation of genome scale analyses. - -build: - number: 1 - skip: True # [py3k] - -package: - name: bx-python - version: 0.7.1 - -requirements: - build: - - python - - setuptools - - cython - - nose - - numpy x.x - - run: - - python - - setuptools - - numpy x.x -source: - fn: bx-python-0.7.1.tar.gz - sha256: 9ff7b5354de03c463da6d245d3256a41966e718a16f4021b7f8d4861305c9ea1 - url: https://pypi.python.org/packages/source/b/bx-python/bx-python-0.7.1.tar.gz - -test: - imports: - - bx.align.sitemask - - bx.tabular - - bx.intervals - - bx.align - - bx.bbi - - bx.bbi.bigwig_file - - bx.cookbook - - bx.arrays - - bx.motif.io - - bx.seq - - bx.intervals.operations - - bx.pwm - - bx.misc - - bx.motif - - bx.phylo - - bx.motif.logo - - bx_extras - - bx.align.tools - - bx - - bx.intseq - - requires: - # Put any additional test requirements here. For example - - nose - diff --git a/recipes/bx-python/0.7.2/build.sh b/recipes/bx-python/0.7.2/build.sh deleted file mode 100644 index c150abdaa9..0000000000 --- a/recipes/bx-python/0.7.2/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/sh -$PYTHON setup.py install - diff --git a/recipes/bx-python/0.7.2/meta.yaml b/recipes/bx-python/0.7.2/meta.yaml deleted file mode 100644 index cff8c4d5ef..0000000000 --- a/recipes/bx-python/0.7.2/meta.yaml +++ /dev/null @@ -1,58 +0,0 @@ -about: - home: http://bitbucket.org/james_taylor/bx-python/wiki/Home - license: MIT - summary: Toolkit to enable rapid implementation of genome scale analyses. - -build: - number: 1 - skip: True # [py3k] - -package: - name: bx-python - version: 0.7.2 - -requirements: - build: - - python - - setuptools - - cython - - nose - - numpy x.x - - run: - - python - - setuptools - - numpy x.x - -source: - fn: bx-python-0.7.2.tar.gz - sha256: b083b2c87807bbfa5b11196754768147ca5bb15001cb0dd76ef217065b4ca451 - url: https://pypi.python.org/packages/source/b/bx-python/bx-python-0.7.2.tar.gz - -test: - imports: - - bx.align.sitemask - - bx.tabular - - bx.intervals - - bx.align - - bx.bbi - - bx.bbi.bigwig_file - - bx.cookbook - - bx.arrays - - bx.motif.io - - bx.seq - - bx.intervals.operations - - bx.pwm - - bx.misc - - bx.motif - - bx.phylo - - bx.motif.logo - - bx_extras - - bx.align.tools - - bx - - bx.intseq - - requires: - # Put any additional test requirements here. For example - - nose - diff --git a/recipes/bx-python/build.sh b/recipes/bx-python/build.sh index 4d7fc032b8..b028003b48 100644 --- a/recipes/bx-python/build.sh +++ b/recipes/bx-python/build.sh @@ -1,9 +1,6 @@ #!/bin/bash +ls $PREFIX/bin +which python $PYTHON setup.py install -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index d051e5317b..bc8b7a55b4 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -3,14 +3,17 @@ package: version: '0.7.3' source: - #hg_url: https://bitbucket.org/james_taylor/bx-python fn: bx-python-0.7.3.tar.gz url: https://pypi.python.org/packages/source/b/bx-python/bx-python-0.7.3.tar.gz md5: d8c50c01c9e421bae0bbdbfa00fef6e4 build: number: 1 - skip: True # [not py27] + # On Python 2.7, setuptools import currently fails. + # It is unclear whether this is a bug in the setuptools package or the python package. + # I suggest to fix this when releasing the next bx-python version. + skip: True + # skip: True # [not py27] requirements: build: @@ -19,11 +22,13 @@ requirements: - cython - nose - numpy x.x + - gcc run: - python - setuptools - numpy x.x + - libgcc test: imports: @@ -48,10 +53,6 @@ test: - bx - bx.intseq - requires: - # Put any additional test requirements here. For example - - nose - about: home: http://bitbucket.org/james_taylor/bx-python/wiki/Home license: MIT diff --git a/recipes/cgat-pipelines-nosetests/meta.yaml b/recipes/cgat-pipelines-nosetests/meta.yaml index 2915582b21..fdb582ce17 100644 --- a/recipes/cgat-pipelines-nosetests/meta.yaml +++ b/recipes/cgat-pipelines-nosetests/meta.yaml @@ -70,4 +70,3 @@ about: home: https://www.cgat.org/downloads/public/cgatpipelines/documentation license: MIT summary: "Metapackage to test CGAT Pipelines" - diff --git a/recipes/cgat-report/meta.yaml b/recipes/cgat-report/meta.yaml index ea70cbe2e0..dc9f05aad9 100644 --- a/recipes/cgat-report/meta.yaml +++ b/recipes/cgat-report/meta.yaml @@ -25,7 +25,7 @@ requirements: - seaborn - six - sphinx - - sqlalchemy + - sqlalchemy - python - matplotlib-venn - seaborn @@ -69,4 +69,3 @@ about: home: https://github.com/AndreasHeger/CGATReport license: BSD summary: "A report generator in python based on sphinx" - diff --git a/recipes/cgat-scripts-devel/meta.yaml b/recipes/cgat-scripts-devel/meta.yaml index fb7ef772eb..bb1b249517 100644 --- a/recipes/cgat-scripts-devel/meta.yaml +++ b/recipes/cgat-scripts-devel/meta.yaml @@ -4,7 +4,8 @@ package: version: 0.2.6 build: - skip: True # [osx] + # TODO remove py36 skip once all dependencies are available + skip: True # [osx or (not py27 and not py35)] number: 0 requirements: @@ -87,6 +88,7 @@ requirements: - bioconductor-qvalue - bioconductor-rtracklayer - bioconductor-siggenes + - libglu test: imports: @@ -106,4 +108,3 @@ about: home: https://www.cgat.org/downloads/public/cgat/documentation license: BSD summary: "Computational Genomics Analysis Toolkit" - diff --git a/recipes/cgat-scripts-nosetests/meta.yaml b/recipes/cgat-scripts-nosetests/meta.yaml index 8274cac6c5..5438aebd97 100644 --- a/recipes/cgat-scripts-nosetests/meta.yaml +++ b/recipes/cgat-scripts-nosetests/meta.yaml @@ -68,4 +68,3 @@ about: home: https://www.cgat.org/downloads/public/cgat/documentation/ license: BSD summary: "Computational Genomics Analysis Toolkit" - diff --git a/recipes/cgat-scripts/meta.yaml b/recipes/cgat-scripts/meta.yaml index 9977e3bde5..312b90e7b5 100644 --- a/recipes/cgat-scripts/meta.yaml +++ b/recipes/cgat-scripts/meta.yaml @@ -205,4 +205,3 @@ about: home: https://www.cgat.org/downloads/public/cgat/documentation license: BSD summary: "Computational Genomics Analysis Toolkit" - diff --git a/recipes/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 6ca08f775e..25fe5bc9ab 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -11,29 +11,20 @@ source: # - fix.patch build: - # noarch_python: True + number: 0 preserve_egg_dir: True entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - chanjo = chanjo:main - # - # Would create an entry point called chanjo that calls chanjo.main() - - chanjo = chanjo.__main__:root_command - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - skip: False + # path.py in the default channel is broken + # it does not contain an egg-info and hence setup.py cannot find it. + # Once bioconda can directly depend on conda-forge, we can enable this again. + skip: true requirements: build: - python - setuptools - click - - setuptools - toolz - path.py - pyyaml @@ -41,9 +32,7 @@ requirements: run: - python - - setuptools - click - - setuptools - toolz - path.py - pyyaml @@ -68,22 +57,10 @@ test: - chanjo.store commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - chanjo --help - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - requires: - - pytest + # click requires a unicode locale + - LANG=C.UTF-8 chanjo --help about: home: http://www.chanjo.co/ license: MIT License summary: 'Coverage analysis tool for clinical sequencing' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/checkm-genome/meta.yaml b/recipes/checkm-genome/meta.yaml index 56429cccff..b6e2a827d5 100644 --- a/recipes/checkm-genome/meta.yaml +++ b/recipes/checkm-genome/meta.yaml @@ -6,26 +6,9 @@ source: fn: checkm-genome-1.0.5.tar.gz url: https://pypi.python.org/packages/source/c/checkm-genome/checkm-genome-1.0.5.tar.gz md5: 5b45f196f1741bc8ed6668d1e42f5b80 -# patches: - # List any patch files here - # - fix.patch build: skip: True # [not py27] - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - checkm-genome = checkm-genome:main - # - # Would create an entry point called checkm-genome that calls checkm-genome.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 requirements: build: @@ -47,30 +30,13 @@ requirements: - screamingbackpack >=0.2.333 test: - # Python imports imports: - checkm - checkm.plot - checkm.test - checkm.util - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://pypi.python.org/pypi/checkm/ license: GPL3 summary: 'Assess the quality of putative genome bins.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml index 95600c5872..87850dc4e9 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -11,9 +11,7 @@ source: md5: ee3e12b06673a3f64a019c05e35c4993 build: - number: 1 - # Requires futures which is not available in conda for 3.6 - skip: true # [not py27 and not py35] + number: 2 requirements: build: @@ -34,7 +32,7 @@ requirements: - r-cghflasso - pyfaidx >=0.4.7 - future >=0.15.2 - - futures >=3.0 + - futures >=3.0 # [py27] test: imports: diff --git a/recipes/colormap/meta.yaml b/recipes/colormap/meta.yaml index 9367c59f5a..11497f64e1 100644 --- a/recipes/colormap/meta.yaml +++ b/recipes/colormap/meta.yaml @@ -6,13 +6,6 @@ source: fn: colormap-0.9.8.tar.gz url: https://pypi.python.org/packages/source/c/colormap/colormap-0.9.8.tar.gz md5: da5b29974981d53c498dab83d9687324 -# patches: - # List any patch files here - # - fix.patch - -build: - skip: False - # number: 1 requirements: build: @@ -25,27 +18,10 @@ requirements: - easydev test: - # Python imports imports: - colormap - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: ['http://packages.python.org/colormap/'] license: GNU Library or Lesser General Public License (LGPL) summary: 'Utilities to ease manipulation of matplotlib colormaps and color codecs (e.g., hex2rgb)' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index 5b30dd2015..facbe3524a 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -11,9 +11,10 @@ source: build: number: 0 - #noarch: python # not supported by bioconda yet entry_points: - cooler = cooler.cli:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -44,10 +45,10 @@ test: - cooler.contrib commands: - - cooler --help + # click requires a unicode locale + - LANG=C.UTF-8 cooler --help about: home: https://github.com/mirnylab/cooler license: BSD summary: 'Sparse binary format for genomic interaction matrices' - diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 50b6c90d91..e1d6dbeb74 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -11,6 +11,8 @@ build: number: 0 entry_points: - crimson=crimson.main:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -30,7 +32,8 @@ test: - crimson commands: - - crimson --help + # click requires a unicode locale + - LANG=C.UTF-8 crimson --help about: home: https://github.com/bow/crimson diff --git a/recipes/crispresso/meta.yaml b/recipes/crispresso/meta.yaml index 5878d6ca11..e712dea997 100644 --- a/recipes/crispresso/meta.yaml +++ b/recipes/crispresso/meta.yaml @@ -38,7 +38,7 @@ requirements: - pandas >=0.15 - matplotlib >=1.3.1 - biopython >=1.6.5 - - argparse + - argparse - setuptools - trimmomatic - flash diff --git a/recipes/dr-disco/meta.yaml b/recipes/dr-disco/meta.yaml index ca3cd80d42..4f621ba094 100644 --- a/recipes/dr-disco/meta.yaml +++ b/recipes/dr-disco/meta.yaml @@ -8,9 +8,9 @@ source: sha256: 9ada777754aea147524ab958102cb52d8531cd44d4a84377906a81d5ff424969 build: - preserve_egg_dir: True + preserve_egg_dir: true number: 0 - skip: True # [not py27] + skip: true # [not py27] requirements: build: @@ -30,14 +30,13 @@ requirements: - fuma ==3.0.5 test: - # Python imports imports: - drdisco commands: - - dr-disco --help - - dr-disco --version - + # click requires a unicode locale + - LANG=C.UTF-8 dr-disco --version + # This also tests appropriate loading of libs ~ small functional test # - conda create -n curl curl && source activate curl && curl -L -o test_01.bam http://github.com/yhoogstrate/dr-disco/raw/master/tests/detect-intronic/test_01.bam && dr-disco detect detect.test.bam test_01.bam # - conda create -n curl curl && source activate curl && curl -L -o test_terg_01.filtered.bam http://github.com/yhoogstrate/dr-disco/raw/master/tests/fix-chimeric/test_terg_01.filtered.bam && dr-disco fix fix.test.bam test_terg_01.filtered.bam diff --git a/recipes/dr-disco/v0.3.4/meta.yaml b/recipes/dr-disco/v0.3.4/meta.yaml index 03f054510b..8914ab9d15 100644 --- a/recipes/dr-disco/v0.3.4/meta.yaml +++ b/recipes/dr-disco/v0.3.4/meta.yaml @@ -8,9 +8,9 @@ source: sha256: b5894bf3b932df9a63affc4b353e24c262949fc0ab62542a8303e00748bae75e build: - preserve_egg_dir: True + preserve_egg_dir: true number: 0 - skip: True # [not py27] + skip: true # [not py27] requirements: build: @@ -33,9 +33,9 @@ test: - drdisco commands: - - dr-disco --help - - dr-disco --version - + # click requires a unicode locale + - LANG=C.UTF-8 dr-disco --version + # This also tests appropriate loading of libs ~ small functional test # - conda create -n curl curl && source activate curl && curl -L -o test_01.bam http://github.com/yhoogstrate/dr-disco/raw/master/tests/detect-intronic/test_01.bam && dr-disco detect detect.test.bam test_01.bam # - conda create -n curl curl && source activate curl && curl -L -o test_terg_01.filtered.bam http://github.com/yhoogstrate/dr-disco/raw/master/tests/fix-chimeric/test_terg_01.filtered.bam && dr-disco fix fix.test.bam test_terg_01.filtered.bam diff --git a/recipes/dreamtools/meta.yaml b/recipes/dreamtools/meta.yaml index bc1911e208..132b5f8e03 100644 --- a/recipes/dreamtools/meta.yaml +++ b/recipes/dreamtools/meta.yaml @@ -44,6 +44,7 @@ requirements: - xlrd - tabulate - fitter + - libgcc test: # Python imports @@ -64,6 +65,7 @@ about: license: BSD License summary: 'Scoring functions for the DREAM / SAGE challenges' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + container: + # fitter depends on libGl.so.1 + extended-base: true diff --git a/recipes/ecmwfapi/meta.yaml b/recipes/ecmwfapi/meta.yaml index a5efb06cc6..a3781e94b9 100644 --- a/recipes/ecmwfapi/meta.yaml +++ b/recipes/ecmwfapi/meta.yaml @@ -5,16 +5,14 @@ package: source: fn: ecmwf-api-client-python.tgz url: https://software.ecmwf.int/wiki/download/attachments/56664858/ecmwf-api-client-python.tgz - md5: 3e946b1ffc45ee54a6bc49d540737756 + sha256: 3606f466531b34adca79b25b08a6ff401af80c991a337640490118918a637d1b build: - number: 0 - skip: False + number: 1 requirements: build: - python - run: - python diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index a25562060d..45c82d03ea 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -6,24 +6,13 @@ source: fn: extract_genome_region_0.0.3.tar.gz md5: 3d45e601ff036ebf62405ce7fa482bd8 url: https://github.com/xguse/extract-genome-region/archive/v0.0.3.tar.gz -# patches: - # List any patch files here - # - fix.patch build: - # noarch_python: True - # preserve_egg_dir: True entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - extract_genome_region = extract_genome_region.__main__:main - - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. number: 0 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -38,25 +27,11 @@ requirements: - pyfaidx test: - # Python imports - # imports: - commands: - - "extract_genome_region --help > /dev/null" - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + # click requires a unicode locale + - LANG=C.UTF-8 extract_genome_region --help about: home: https://github.com/xguse/extract-genome-region license: BSD License summary: 'Given a CSV file of variable information defining the regions of interest, return a file that contains a fasta-formatted representation of these regions.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/fitter/meta.yaml b/recipes/fitter/meta.yaml index a680941af5..3bd3dbad69 100644 --- a/recipes/fitter/meta.yaml +++ b/recipes/fitter/meta.yaml @@ -6,13 +6,9 @@ source: fn: fitter-1.0.4.tar.gz url: https://pypi.python.org/packages/source/f/fitter/fitter-1.0.4.tar.gz md5: f9a5b0dea365750168ad08c94cf7ce10 -# patches: - # List any patch files here - # - fix.patch build: skip: False - # number: 1 requirements: build: @@ -31,27 +27,15 @@ requirements: - pandas test: - # Python imports imports: - fitter - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: ['http://github.com/cokelaer/fitter'] license: GNU Library or Lesser General Public License (LGPL) summary: 'A tool to fit data to many distributions and best one(s)' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + container: + # matplotlib depends on libGL.so.1 from the system + extended-base: true diff --git a/recipes/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml index d158a2ec23..a69082ede5 100644 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ b/recipes/fsnviz/0.1.0/meta.yaml @@ -8,7 +8,8 @@ source: md5: 79ba80aeef411b89802e2b3e597b3c37 build: - skip: True # [py2k or py34] + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py2k or py3k] number: 0 entry_points: - fsnviz=fsnviz.main:cli @@ -17,18 +18,23 @@ requirements: build: - python - setuptools - - click >=6.6 + - click ==6.6 - crimson >=0.3.0 - jinja2 ==2.8 - circos ==0.69.2 run: - python - - click >=6.6 + - click ==6.6 - crimson >=0.3.0 - jinja2 ==2.8 - circos ==0.69.2 +test: + commands: + # click requires a unicode locale + - LANG=C.UTF-8 fsnviz --help + about: home: https://github.com/bow/fsnviz license: BSD diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index 4d8eb673d2..d6f918c92e 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -10,7 +10,8 @@ source: md5: 20a051a88d1631e76536828b8b69cac4 build: - skip: True # [py2k or py34] + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py2k or py3k] number: 0 entry_points: - fsnviz=fsnviz.cli:main @@ -31,6 +32,12 @@ requirements: - jinja2 ==2.9.5 - circos >=0.69.2 + +test: + commands: + # click requires a unicode locale + - LANG=C.UTF-8 fsnviz --help + about: home: https://github.com/bow/fsnviz license: BSD diff --git a/recipes/fwdpy/meta.yaml b/recipes/fwdpy/meta.yaml index 60eb6d95e5..da7330db18 100644 --- a/recipes/fwdpy/meta.yaml +++ b/recipes/fwdpy/meta.yaml @@ -10,6 +10,8 @@ source: build: number: 0 string: "py{{CONDA_PY}}_gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" + # does not build currently: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L416 + skip: true requirements: build: @@ -27,6 +29,7 @@ requirements: - pandas >=0.18 - libsequence - gsl {{CONDA_GSL}}* + - libgcc test: # Python imports diff --git a/recipes/garnet/meta.yaml b/recipes/garnet/meta.yaml index c2abda5032..0af66916ec 100644 --- a/recipes/garnet/meta.yaml +++ b/recipes/garnet/meta.yaml @@ -1,31 +1,16 @@ +{% set version = "0.2.20" %} + package: name: garnet - version: "0.2.17" + version: {{ version }} source: - fn: GarNet-0.2.17.tar.gz - url: https://pypi.python.org/packages/c5/06/8a5d8ab7e9c488e12e4ad451ad7dee575fdc229f1e51130ad24de34274bf/GarNet-0.2.17.tar.gz - md5: 1739293585e35c4f552aaf446a6eaf9e -# patches: - # List any patch files here - # - fix.patch + fn: GarNet-{{ version }}.tar.gz + url: https://pypi.io/packages/source/g/garnet/GarNet-{{ version }}.tar.gz + md5: 53eaec2493856d8324ee1c630ce323dd build: skip: True # [py2k or py34] - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - garnet = garnet:main - # - # Would create an entry point called garnet that calls garnet.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 requirements: build: @@ -47,28 +32,12 @@ requirements: - jinja2 test: - # Python imports imports: - GarNet - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - + about: home: https://github.com/fraenkel-lab/GarNet license: GNU General Public License summary: 'UNKNOWN' license_family: GPL -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/genomebaser/meta.yaml b/recipes/genomebaser/meta.yaml index e230047283..ff26d99847 100644 --- a/recipes/genomebaser/meta.yaml +++ b/recipes/genomebaser/meta.yaml @@ -6,26 +6,10 @@ source: fn: GenomeBaser-0.1.2.tar.gz url: https://pypi.python.org/packages/source/G/GenomeBaser/GenomeBaser-0.1.2.tar.gz md5: 11bbc12de57eda659ea93f9fcfe92029 -# patches: - # List any patch files here - # - fix.patch build: skip: True # [not py27 or osx] - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - genomebaser = genomebaser:main - # - # Would create an entry point called genomebaser that calls genomebaser.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 1 requirements: build: @@ -40,27 +24,10 @@ requirements: - click test: - # Python imports imports: - GenomeBaser - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://github.com/mscook/GenomeBaser license: ECL 2.0 summary: 'GenomeBaser manages complete (bacterial) genomes from NCBI' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/genomepy/meta.yaml b/recipes/genomepy/meta.yaml index 97eaac1a72..b107702fa2 100644 --- a/recipes/genomepy/meta.yaml +++ b/recipes/genomepy/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -21,7 +23,7 @@ requirements: - xmltodict - bucketcache - msgpack-python - - requests + - requests run: - python diff --git a/recipes/ggplot/meta.yaml b/recipes/ggplot/meta.yaml index 7d7f98b554..8f9076cb45 100644 --- a/recipes/ggplot/meta.yaml +++ b/recipes/ggplot/meta.yaml @@ -43,3 +43,7 @@ about: license: BSD summary: "An extremely un-pythonic package for doing exactly what ggplot2 does" +extra: + container: + # ggplot depends on libGL.so.1 from the system + extended-base: true diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 54110db1ad..832f63f7e9 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -4,28 +4,13 @@ package: source: fn: gseapy-0.7.4.tar.gz - url: https://pypi.python.org/packages/c9/ab/e0128dc2b7aec12732bd5e58841cffe56e70d822fa3789d5a050c086bb6c/gseapy-0.7.4.tar.gz - md5: fe8e5a3a7e559ae66abcfd65bb33a0db -# patches: - # List any patch files here - # - fix.patch + url: https://depot.galaxyproject.org/software/gseapy/gseapy_0.7.4_src_all.tar.gz + sha256: c4e3311a050b86296d0d1a3ef32d153e76745b7efb4c05fd90952b3f1e37ffc0 build: - # noarch_python: True - # preserve_egg_dir: True entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - gseapy = gseapy:main - # - # Would create an entry point called gseapy that calls gseapy.main() - - gseapy = gseapy.__main__:main - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + number: 3 requirements: build: @@ -50,29 +35,18 @@ requirements: - html5lib test: - # Python imports imports: - gseapy - commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - gseapy --help - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: https://github.com/BioNinja/gseapy license: MIT License summary: 'Gene Set Enrichment Analysis in Python' license_family: MIT -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + container: + # matplotlib needs opengl support + extended-base: true diff --git a/recipes/hisat2/meta.yaml b/recipes/hisat2/meta.yaml index a15c4669b8..e4f4a0f46d 100644 --- a/recipes/hisat2/meta.yaml +++ b/recipes/hisat2/meta.yaml @@ -25,6 +25,7 @@ requirements: run: - python - perl + test: commands: - hisat2 --version diff --git a/recipes/hlama/meta.yaml b/recipes/hlama/meta.yaml index 565f53109c..04de94a2f4 100644 --- a/recipes/hlama/meta.yaml +++ b/recipes/hlama/meta.yaml @@ -3,8 +3,10 @@ package: version: "0.3.1" build: - number: 0 - skip: True # [py27 or osx] + number: 1 + # snakemake 3.7.1 is not available for python 3.6 + # the snakemake dependency should be relaxed to allow for a newer version + skip: True # [not py35 or osx] entry_points: - hlama = hlama.app:main diff --git a/recipes/hmmlearn/meta.yaml b/recipes/hmmlearn/meta.yaml index 63ca968f1e..a0c6e642ed 100644 --- a/recipes/hmmlearn/meta.yaml +++ b/recipes/hmmlearn/meta.yaml @@ -7,7 +7,7 @@ source: url: https://github.com/hmmlearn/hmmlearn/archive/dd67a47.tar.gz build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -25,6 +25,8 @@ requirements: - numpy - scipy - scikit-learn + # missing dependency of scipy + - libgcc test: imports: diff --git a/recipes/ig-flowtools/meta.yaml b/recipes/ig-flowtools/meta.yaml index 6ab014deb7..e7b233c1b1 100644 --- a/recipes/ig-flowtools/meta.yaml +++ b/recipes/ig-flowtools/meta.yaml @@ -4,8 +4,13 @@ package: source: fn: immport-galaxy-tools.v1.4.1.tar.gz - md5: afae644d819433c732824ae4f71ef20e url: https://github.com/ImmPortDB/ig-flowtools/archive/immport-galaxy-tools.v1.4.1.tar.gz + md5: afae644d819433c732824ae4f71ef20e + +build: + number: 1 + # TODO reenable once R packages have been updated/rebuild with conda-build > 2.0 + skip: true requirements: build: @@ -15,7 +20,7 @@ requirements: - scipy - jinja2 - matplotlib - - r + - r-base - bioconductor-flowcore - bioconductor-flowcl - bioconductor-flowai @@ -28,7 +33,7 @@ requirements: - scipy - jinja2 - matplotlib - - r + - r-base - bioconductor-flowcore - bioconductor-flowcl - bioconductor-flowai diff --git a/recipes/igdiscover/meta.yaml b/recipes/igdiscover/meta.yaml index 7df8b60975..6b402b2a31 100644 --- a/recipes/igdiscover/meta.yaml +++ b/recipes/igdiscover/meta.yaml @@ -1,14 +1,19 @@ +{% set version = "0.7.0" %} + about: home: https://igdiscover.se/ license: 'MIT' summary: 'Analyze antibody repertoires and discover new V genes' + package: name: igdiscover - version: "0.7.0" + version: {{ version }} + source: - fn: igdiscover-0.7.0.tar.gz - url: https://pypi.python.org/packages/45/14/5bee6932605af2c9068b4137b53267334b8302a2eb866c80d90bd27963ce/igdiscover-0.7.0.tar.gz + fn: igdiscover-{{ version }}.tar.gz + url: https://pypi.io/packages/source/i/igdiscover/igdiscover-{{ version }}.tar.gz md5: 05d2459538c4aa52522105a42ad58312 + requirements: run: - python @@ -20,7 +25,7 @@ requirements: - cutadapt - xopen >=0.1.1 - seaborn >=0.6.0 - - scipy ==0.16.1 + - scipy >=0.16.1 - ruamel.yaml - muscle - pear @@ -38,12 +43,14 @@ requirements: - cutadapt - xopen >=0.1.1 - seaborn >=0.6.0 - - scipy ==0.16.1 + - scipy >=0.16.1 - ruamel.yaml + build: number: 0 skip: True # [py27] script: python3 setup.py install + test: commands: - igdiscover --help > /dev/null diff --git a/recipes/illuminate/meta.yaml b/recipes/illuminate/meta.yaml index f45febde2c..f8c0387b3f 100644 --- a/recipes/illuminate/meta.yaml +++ b/recipes/illuminate/meta.yaml @@ -37,6 +37,7 @@ requirements: - pandas >=0.14 - openpyxl ==1.8.6 - xmltodict + - gcc run: - python @@ -46,6 +47,7 @@ requirements: - pandas >=0.14 - openpyxl ==1.8.6 - xmltodict + - libgcc test: # Python imports diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index 8c34f67c6b..db9d6cca96 100644 --- a/recipes/intarna/build.sh +++ b/recipes/intarna/build.sh @@ -3,7 +3,7 @@ ## Choose extra configure options depending on the operating system ## (mac or linux) ## -CXXFLAGS="$CXXFLAGS"; +CXXFLAGS="$CXXFLAGS -w"; # suppress warnings LDFLAGS="$LDFLAGS -Wl,-rpath ${PREFIX}/lib"; CXX=g++; CC=gcc; @@ -28,6 +28,5 @@ export LDFLAGS=${LDFLAGS} --disable-multithreading \ ${extra_config_options} \ -make -j ${CPU_COUNT} && \ -make tests && \ +make make install diff --git a/recipes/intarna/meta.yaml b/recipes/intarna/meta.yaml index 7bb20a873a..ab017d5a1a 100644 --- a/recipes/intarna/meta.yaml +++ b/recipes/intarna/meta.yaml @@ -8,8 +8,8 @@ about: summary: Efficient target prediction incorporating seeding and accessibility of interaction sites build: - number: 0 - string: {{PKG_BUILDNUM}} + number: 1 + string: boost{{CONDA_BOOST}}_{{PKG_BUILDNUM}} source: fn: intarna-2.0.3.tar.gz diff --git a/recipes/joblib/meta.yaml b/recipes/joblib/meta.yaml index cfefae2c9f..37f8b87178 100644 --- a/recipes/joblib/meta.yaml +++ b/recipes/joblib/meta.yaml @@ -22,9 +22,6 @@ requirements: test: imports: - joblib - - joblib.test - requires: - - nose about: home: http://packages.python.org/joblib/ diff --git a/recipes/last/490/meta.yaml b/recipes/last/490/meta.yaml index 93f2c365d1..d0fe204d15 100644 --- a/recipes/last/490/meta.yaml +++ b/recipes/last/490/meta.yaml @@ -2,9 +2,11 @@ about: home: 'http://last.cbrc.jp/' license: GPLv3 summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + package: name: last version: '490' + source: fn: last-490.zip md5: c4d600c373e5f15dc10fb87b1f9b2d37 @@ -12,18 +14,23 @@ source: patches: - maf-convert.23patch - last-pair-probs.23patch + build: - number: 1 + number: 2 + requirements: build: - python + - gcc run: - python + - libgcc + test: commands: - - "lastal -h &> /dev/null" - - "lastdb -h &> /dev/null" - - "last-split -V &> /dev/null" - - "last-pair-probs -h &> /dev/null" - - "last-merge-batches -V &> /dev/null" - - "maf-convert -h &> /dev/null" + - "lastal -h" + - "lastdb -h" + - "last-split -V" + - "last-pair-probs -h" + - "last-merge-batches -V" + - "maf-convert -h" diff --git a/recipes/last/638/meta.yaml b/recipes/last/638/meta.yaml index df76109a4d..d732d4fac6 100644 --- a/recipes/last/638/meta.yaml +++ b/recipes/last/638/meta.yaml @@ -2,27 +2,34 @@ about: home: 'http://last.cbrc.jp/' license: GPLv3 summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + package: name: last version: '638' + source: fn: last-638.zip md5: 6c5edd2706934bfe7b3224073b79463b url: http://last.cbrc.jp/last-638.zip patches: - maf-convert.23patch + build: number: 5 + requirements: build: - python + - gcc run: - python + - libgcc + test: commands: - - "lastal -V &> /dev/null" - - "lastdb -V &> /dev/null" - - "last-split -V &> /dev/null" - - "last-pair-probs -V &> /dev/null" - - "last-merge-batches -V &> /dev/null" - - "maf-convert -h &> /dev/null" + - "lastal -V" + - "lastdb -V" + - "last-split -V" + - "last-pair-probs -V" + - "last-merge-batches -V" + - "maf-convert -h" diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index dc2aec9128..a50e1c5f67 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -2,9 +2,11 @@ about: home: 'http://last.cbrc.jp/' license: GPLv3 summary: "LAST finds similar regions between sequences, and aligns them. It is designed for comparing large datasets to each other (e.g. vertebrate genomes and/or large numbers of DNA reads)." + package: name: last version: '847' + source: fn: last-847.zip md5: 45c49cd2ce271ec0ef9cc7119feb2c9f @@ -24,11 +26,12 @@ requirements: - python - libgcc - future + test: - commands: - - "lastal -V &> /dev/null" - - "lastdb -V &> /dev/null" - - "last-split -V &> /dev/null" - - "last-pair-probs -V &> /dev/null" - - "last-merge-batches -V &> /dev/null" - - "maf-convert -h &> /dev/null" + commands: + - "lastal -V" + - "lastdb -V" + - "last-split -V" + - "last-pair-probs -V" + - "last-merge-batches -V" + - "maf-convert -h" diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index fe1266a32b..bf2e0c4c3b 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -6,12 +6,11 @@ source: fn: python-libsbml_5.12.0.tar.gz url: https://pypi.python.org/packages/source/p/python-libsbml/python-libsbml_5.12.0.tar.gz md5: f05ed071b48702295a5ea44e52723247 - patches: - fix_path.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -19,10 +18,13 @@ requirements: - python - libxml2 - gcc - + - bzip2 + - libxml2 run: - python - libgcc + - bzip2 + - libxml2 test: imports: diff --git a/recipes/mercat/meta.yaml b/recipes/mercat/meta.yaml index cd2b220996..01fa46ed8e 100644 --- a/recipes/mercat/meta.yaml +++ b/recipes/mercat/meta.yaml @@ -51,5 +51,6 @@ extra: recipe-maintainers: - ajaypanyala - raw937 - - + container: + # needs libGL.so.1 + extended-base: true diff --git a/recipes/mgf-formatter/meta.yaml b/recipes/mgf-formatter/meta.yaml index 975c9493bf..615591d0ae 100644 --- a/recipes/mgf-formatter/meta.yaml +++ b/recipes/mgf-formatter/meta.yaml @@ -1,15 +1,9 @@ -about: - home: https://bitbucket.org/galaxyp-applications/mgf-formatter - license: Eclipse Public License - summary: Tools for convert peak lists into MGF files formatted for particular downstream applications - package: name: mgf-formatter version: 1.0.0 build: - number: 0 - skip: False + number: 1 source: fn: d3fdf38.tar.gz @@ -18,11 +12,14 @@ source: requirements: run: - - java-jdk + - openjdk - python test: - files: - - test.mzML commands: - - mgf-formatter --mgf_format "DEFAULT" --output output test.mzML + - mgf-formatter --help + +about: + home: https://bitbucket.org/galaxyp-applications/mgf-formatter + license: Eclipse Public License + summary: Tools for convert peak lists into MGF files formatted for particular downstream applications diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index 4b383bcc89..c964bdc1d8 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -8,9 +8,8 @@ source: md5: 8fc7a56a695bc339cc6b306f52ff6339 build: - # noarch_python: True - skip: True #[not py27] - preserve_egg_dir: True + skip: true #[not py27] + preserve_egg_dir: true entry_points: - moca=scripts.mocacli:cli @@ -119,7 +118,8 @@ test: - scripts commands: - - moca --help + # click requires a unicode locale + - LANG=C.UTF-8 moca --help requires: - pytest diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index f2830c8ac8..535d8425ea 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -10,8 +10,8 @@ source: build: number: 4 preserve_egg_dir: True - # multiqc currently not compatible with py3 due to click locale issues - skip: true # [not py27] + # multiqc does not support py3k because of click + skip: true # [py3k] requirements: build: @@ -32,4 +32,3 @@ about: home: http://multiqc.info license: GNU General Public License v3 (GPLv3) summary: 'MultiQC plugin for bcbio report visualization.' - diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index 5a7a20eb39..9c8f470ba6 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -8,9 +8,10 @@ source: md5: 0ba67f2fcb20c6d42929069a0865731f build: - number: 1 + number: 4 preserve_egg_dir: True - skip: false + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -92,9 +93,12 @@ test: - multiqc.templates.simple - multiqc.utils + commands: + # click requires a unicode locale + - LANG=C.UTF-8 multiqc --version + about: home: http://multiqc.info license: GNU General Public License v3 (GPLv3) summary: 'Create aggregate bioinformatics analysis reports across many samples and tools' license_family: GPL3 - diff --git a/recipes/nglview/meta.yaml b/recipes/nglview/meta.yaml index bda190bb39..3ddb775bb4 100644 --- a/recipes/nglview/meta.yaml +++ b/recipes/nglview/meta.yaml @@ -1,6 +1,6 @@ {% set version = "0.6.3" %} {% set minimum_ipywidgets_version = "5.2.2" %} -{% set md5 = "6e443876a9d6345cde17e52fb7be736f" %} +{% set md5 = "fbad7cc96adf23600909191100c9bd09" %} package: name: nglview diff --git a/recipes/onto2nx/meta.yaml b/recipes/onto2nx/meta.yaml index 76b730002d..136b4b6d67 100644 --- a/recipes/onto2nx/meta.yaml +++ b/recipes/onto2nx/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: diff --git a/recipes/openbabel/2.3.90dev7d621d9/build.sh b/recipes/openbabel/2.3.90dev7d621d9/build.sh deleted file mode 100755 index 6aa1e739f6..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/build.sh +++ /dev/null @@ -1,26 +0,0 @@ -#!/bin/bash -if [ `uname` == Darwin ]; then - SO_EXT='dylib' -else - SO_EXT='so' -fi - -PYTHON_INCLUDE_DIR=$($PYTHON -c 'import distutils.sysconfig, sys; sys.stdout.write(distutils.sysconfig.get_python_inc())') -PYTHON_LIBRARY=$($PYTHON -c 'from distutils.sysconfig import get_config_var; import os, sys; sys.stdout.write(os.path.join(get_config_var("LIBDIR"),get_config_var("LDLIBRARY")))') - -cmake -DCMAKE_INSTALL_PREFIX=$PREFIX \ - -DPYTHON_LIBRARY=$PYTHON_LIBRARY \ - -DPYTHON_EXECUTABLE=$PYTHON \ - -DPYTHON_INCLUDE_DIR=$PYTHON_INCLUDE_DIR \ - -DPYTHON_BINDINGS=ON \ - -DLIBXML2_INCLUDE_DIR=$PREFIX/include \ - -DLIBXML2_LIBRARIES=$PREFIX/lib/libxml2.${SO_EXT} \ - -DZLIB_INCLUDE_DIR=$PREFIX/include \ - -DZLIB_LIBRARY=$PREFIX/lib/libz.${SO_EXT} \ - -DRUN_SWIG=ON - -make -j${CPU_COUNT} -make install - -cd scripts/python -OPENBABEL_INCLUDE_DIRS=$(pwd)/..:$PREFIX/include/openbabel-2.0 python setup.py install diff --git a/recipes/openbabel/2.3.90dev7d621d9/fix_data_path.diff b/recipes/openbabel/2.3.90dev7d621d9/fix_data_path.diff deleted file mode 100644 index a682218a5c..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/fix_data_path.diff +++ /dev/null @@ -1,18 +0,0 @@ -diff --git a/src/tokenst.cpp b/src/tokenst.cpp -index 2ab6454..badfade 100644 ---- src/tokenst.cpp -+++ src/tokenst.cpp -@@ -206,7 +206,13 @@ namespace OpenBabel - string file; - const char* datadir = getenv(envvar.c_str()); - if(!datadir) -+ { - datadir = BABEL_DATADIR; -+ } -+ //puts(datadir); -+ std::string tempstring = string(datadir); -+ datadir = tempstring.c_str(); -+ //puts(datadir); - - // check the subdirectory for this version number - file = datadir; \ No newline at end of file diff --git a/recipes/openbabel/2.3.90dev7d621d9/fix_library_path_search.diff b/recipes/openbabel/2.3.90dev7d621d9/fix_library_path_search.diff deleted file mode 100644 index c40ab86523..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/fix_library_path_search.diff +++ /dev/null @@ -1,30 +0,0 @@ -Devised by Richard West in an attempt to fix the way paths -are manipulated when making anaconda packages. See -https://github.com/conda/conda-recipes/pull/310#issuecomment-106533773 - -diff --git a/openbabel-2.3.2/src/dlhandler_unix.cpp b/openbabel-2.3.2/src/dlhandler_unix.cpp -index 5bffac3..bc66235 100644 ---- src/dlhandler_unix.cpp -+++ src/dlhandler_unix.cpp - -@@ -79,7 +79,19 @@ int DLHandler::findFiles (std::vector & file_list, - char buffer[BUFF_SIZE]; - - if (!path.empty()) -- paths.push_back(path); -+ { -+ strncpy(buffer, path.c_str(), BUFF_SIZE - 1); -+ // add a trailing NULL just in case -+ buffer[BUFF_SIZE - 1] = '\0'; -+ OpenBabel::tokenize(vs, buffer, "\r\n:"); -+ if (!vs.empty()) -+ { -+ for (unsigned int i = 0; i < vs.size(); ++i) { -+ paths.push_back(vs[i]); -+ } -+ } -+ } -+ - - if (getenv("BABEL_LIBDIR") != NULL) - { diff --git a/recipes/openbabel/2.3.90dev7d621d9/include-dirs.patch b/recipes/openbabel/2.3.90dev7d621d9/include-dirs.patch deleted file mode 100644 index a3e53d3df5..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/include-dirs.patch +++ /dev/null @@ -1,25 +0,0 @@ -From 44c0593fa49e1e7281024ae2229e07c11515ead7 Mon Sep 17 00:00:00 2001 -From: Robert McGibbon -Date: Tue, 13 Oct 2015 18:02:09 -0700 -Subject: [PATCH] patch - ---- - setup.py | 2 ++ - 1 file changed, 2 insertions(+) - -diff --git scripts/python/setup.py scripts/python/setup.py -index ae2f5f4..af286d2 100644 ---- scripts/python/setup.py -+++ scripts/python/setup.py -@@ -97,6 +97,8 @@ class CustomBuildExt(build_ext): - include_dirs, library_dirs = locate_ob() - self.include_dirs.append(include_dirs) - self.library_dirs.append(library_dirs) -+ if 'OPENBABEL_INCLUDE_DIRS' in os.environ: -+ self.include_dirs.extend(os.environ['OPENBABEL_INCLUDE_DIRS'].split(':')) - self.swig_opts = ['-c++', '-small', '-O', '-templatereduce', '-naturalvar'] - self.swig_opts += ['-I%s' % i for i in self.include_dirs] - print('- include_dirs: %s\n- library_dirs: %s' % (self.include_dirs, self.library_dirs)) --- -2.3.4 - diff --git a/recipes/openbabel/2.3.90dev7d621d9/meta.yaml b/recipes/openbabel/2.3.90dev7d621d9/meta.yaml deleted file mode 100644 index e4e8a7e66d..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/meta.yaml +++ /dev/null @@ -1,48 +0,0 @@ -package: - name: openbabel - version: 2.3.90dev7d621d9 - -source: - url: https://github.com/openbabel/openbabel/archive/7d621d9c9f2f07a1f105896a765bf2afa22e6028.zip - fn: 7d621d9c9f2f07a1f105896a765bf2afa22e6028.zip - - patches: - - include-dirs.patch - - fix_library_path_search.diff - - fix_data_path.diff - -build: - number: 0 - detect_binary_files_with_prefix: true - skip: - - [win] - -requirements: - build: - - gcc # [linux] - - llvm # [osx] - - cmake - - zlib - - swig - - eigen - - bzip2 - - python - - zlib - - libxml2 - run: - - python - - libgcc # [linux] - - zlib - - libxml2 - -test: - imports: - - openbabel - - pybel - commands: - - obabel --help - -about: - home: http://www.openbabel.org/ - license: GPLv2 - summary: "A chemical toolbox designed to speak the many languages of chemical data" diff --git a/recipes/openbabel/2.3.90dev7d621d9/run_test.py b/recipes/openbabel/2.3.90dev7d621d9/run_test.py deleted file mode 100644 index e7d5a37011..0000000000 --- a/recipes/openbabel/2.3.90dev7d621d9/run_test.py +++ /dev/null @@ -1,15 +0,0 @@ -# tests for openbabel-2.3.2 - -# A test of some smiple SMILES manipulation -# by Richard West -# Three SMILES, first two obviously the same, third one a resonance isomer. -smis=['[CH2]C=CCO', 'C([CH2])=CCO','C=C[CH]CO'] - -import pybel -canonicals = [pybel.readstring("smi", smile).write("can").strip() for smile in smis] -assert len(canonicals) == 3 -assert len(set(canonicals)) == 2 -# go via InChI to recognize resonance isomer -inchis = [pybel.readstring("smi", smile).write("inchi").strip() for smile in smis] -canonicals = [pybel.readstring("inchi", inchi).write("can").strip() for inchi in inchis] -assert len(set(canonicals)) == 1 diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml index 0cdc4deeb2..e20a0f6051 100644 --- a/recipes/openbabel/2.4.1/meta.yaml +++ b/recipes/openbabel/2.4.1/meta.yaml @@ -16,6 +16,8 @@ source: - 372.patch build: + # https://bugs.archlinux.org/task/52409 + skip: true # [not py2k and not py35] number: 1 detect_binary_files_with_prefix: true diff --git a/recipes/peakzilla/meta.yaml b/recipes/peakzilla/meta.yaml index 8f8ee046ee..429e68a131 100644 --- a/recipes/peakzilla/meta.yaml +++ b/recipes/peakzilla/meta.yaml @@ -3,20 +3,18 @@ package: version: 1.0 source: - fn: master.zip - url: https://github.com/steinmann/peakzilla/archive/master.zip - md5: 38944abe797d7d25f7ecf39fa8bd8953 + fn: 0fc94780ee1a8c2b6395b5c7489e21a70eeb5217.tar.gz + url: https://github.com/steinmann/peakzilla/archive/0fc94780ee1a8c2b6395b5c7489e21a70eeb5217.tar.gz + sha256: 982d2bbcde736e4ce7837a7758ce37e8040cd1cc148c64a3856b9ea837f2740c patches: - indent.patch build: - number: 0 - skip: False + number: 1 requirements: build: - python - run: - python diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index a2e26cfd79..689b95c70c 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -1,6 +1,7 @@ build: number: 0 - skip: True # [osx] + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k or osx] package: name: ped_parser @@ -10,25 +11,6 @@ source: fn: ped_parser-1.6.5.tar.gz url: https://pypi.python.org/packages/source/p/ped_parser/ped_parser-1.6.5.tar.gz md5: 1f404e131c3d210d32e6253ac500b200 -# patches: - # List any patch files here - # - fix.patch - -# build: - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - ped_parser = ped_parser:main - # - # Would create an entry point called ped_parser that calls ped_parser.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 requirements: build: @@ -43,27 +25,13 @@ requirements: - click test: - # Python imports imports: - ped_parser - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + commands: + # click requires a unicode locale + - LANG=C.UTF-8 ped_parser --help about: home: https://github.com/moonso/ped_parser license: BSD License summary: 'A ped file parser.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/phizz/meta.yaml b/recipes/phizz/meta.yaml index 77abc47b40..1484e99ee6 100644 --- a/recipes/phizz/meta.yaml +++ b/recipes/phizz/meta.yaml @@ -6,26 +6,13 @@ source: fn: phizz-0.0.1.tar.gz url: https://files.pythonhosted.org/packages/e9/a9/ffdd3c5fa5418b93e29101dd4d2ac84f8143bdd0d34b897bd61b2b8b6208/phizz-0.0.1.tar.gz md5: 29387dba01cd9148e47d2998fa932961 -# patches: - # List any patch files here - # - fix.patch build: - # noarch_python: True - preserve_egg_dir: True + preserve_egg_dir: true entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - phizz = phizz:main - # - # Would create an entry point called phizz that calls phizz.main() - - phizz = phizz.__main__:cli - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -41,30 +28,16 @@ requirements: - configobj test: - # Python imports imports: - phizz - phizz.database - phizz.utils commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - phizz --help - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + # click requires a unicode locale + - LANG=C.UTF-8 phizz --help about: home: https://github.com/moonso/query_hpo license: MIT License summary: 'Tool to query hpo database and some other sources' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/phonenumbers/build.sh b/recipes/phonenumbers/build.sh deleted file mode 100644 index b161f631b7..0000000000 --- a/recipes/phonenumbers/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - diff --git a/recipes/phonenumbers/meta.yaml b/recipes/phonenumbers/meta.yaml deleted file mode 100644 index f0b07645f4..0000000000 --- a/recipes/phonenumbers/meta.yaml +++ /dev/null @@ -1,35 +0,0 @@ -package: - name: phonenumbers - version: "7.2.4" - -source: - fn: phonenumbers-7.2.4.tar.gz - url: https://pypi.python.org/packages/source/p/phonenumbers/phonenumbers-7.2.4.tar.gz - md5: 1a8dfeb4109189a580a17258ec259b4c - -build: - number: 0 - skip: False - -requirements: - build: - - python - - setuptools - - run: - - python - -test: - imports: - - phonenumbers - - phonenumbers.carrierdata - - phonenumbers.data - - phonenumbers.geodata - - phonenumbers.shortdata - - phonenumbers.tzdata - -about: - home: https://github.com/daviddrysdale/python-phonenumbers - license: Apache Software License - summary: "Python version of Google's common library for parsing, formatting, storing and validating international phone numbers." - diff --git a/recipes/planemo/0.23.0/meta.yaml b/recipes/planemo/0.23.0/meta.yaml index f16f99cee3..a7b81e5e45 100644 --- a/recipes/planemo/0.23.0/meta.yaml +++ b/recipes/planemo/0.23.0/meta.yaml @@ -11,7 +11,6 @@ build: preserve_egg_dir: True entry_points: - planemo=planemo.cli:planemo - number: 0 skip: True # [py3k] @@ -53,7 +52,8 @@ test: - planemo.xml commands: - - planemo --help + # click requires a unicode locale + - LANG=C.UTF-8 planemo --help about: home: https://github.com/galaxyproject/planemo diff --git a/recipes/planemo/0.34.1/meta.yaml b/recipes/planemo/0.34.1/meta.yaml index 0045e153b8..a7b2454916 100644 --- a/recipes/planemo/0.34.1/meta.yaml +++ b/recipes/planemo/0.34.1/meta.yaml @@ -8,11 +8,10 @@ source: md5: cdb907816e915acaa873f61522166739 build: - preserve_egg_dir: True - skip: True # [py3k] + preserve_egg_dir: true + skip: true # [py3k] entry_points: - planemo=planemo.cli:planemo - number: 1 requirements: @@ -42,7 +41,6 @@ requirements: - aenum test: - # Python imports imports: - planemo - planemo.commands @@ -59,10 +57,9 @@ test: - planemo.shed2tap - planemo.test - planemo.xml - commands: - - - planemo --help + # click requires a unicode locale + - LANG=C.UTF-8 planemo --help about: home: https://github.com/galaxyproject/planemo diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index f9eea62a06..4427de933f 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -12,11 +12,10 @@ source: md5: {{ md5 }} build: - preserve_egg_dir: True - skip: True # [py3k] + preserve_egg_dir: true + skip: true # [py3k] entry_points: - planemo=planemo.cli:planemo - number: 0 requirements: @@ -46,7 +45,6 @@ requirements: - docutils test: - # Python imports imports: - planemo - planemo.commands @@ -65,8 +63,8 @@ test: - planemo.xml commands: - - - planemo --help + # click requires a unicode locale + - LANG=C.UTF-8 planemo --help about: home: https://github.com/galaxyproject/planemo diff --git a/recipes/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index 7ad81a71ed..4b4c518dde 100644 --- a/recipes/platypus-conquistador/meta.yaml +++ b/recipes/platypus-conquistador/meta.yaml @@ -6,26 +6,9 @@ source: fn: platypus-conquistador-0.9.0.zip url: https://pypi.python.org/packages/source/p/platypus-conquistador/platypus-conquistador-0.9.0.zip md5: 609e38711a1ebc7cb2b54a14c3a258f3 -# patches: - # List any patch files here - # - fix.patch build: - skip: True # [not py27 or osx] - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - platypus-conquistador = platypus-conquistador:main - # - # Would create an entry point called platypus-conquistador that calls platypus-conquistador.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 + skip: true # [not py27 or osx] requirements: build: @@ -39,27 +22,10 @@ requirements: - click test: - # Python imports imports: - platypus - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://github.com/biocore/platypus license: BSD License summary: 'Platypus Conquistador: Confirming specific taxonomic groups within your metagenomic samples.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/pomegranate/meta.yaml b/recipes/pomegranate/meta.yaml index e083aa2f56..6a43edebcc 100644 --- a/recipes/pomegranate/meta.yaml +++ b/recipes/pomegranate/meta.yaml @@ -6,25 +6,9 @@ source: fn: pomegranate-0.3.7.tar.gz url: https://pypi.python.org/packages/source/p/pomegranate/pomegranate-0.3.7.tar.gz md5: 28826d27bde9294478bc468509f5ec9d -# patches: - # List any patch files here - # - fix.patch build: - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - pomegranate = pomegranate:main - # - # Would create an entry point called pomegranate that calls pomegranate.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - number: 1 + number: 2 requirements: build: @@ -42,29 +26,14 @@ requirements: - joblib >=0.9.0b4 - networkx >=1.8.1 - scipy + # missing dependency of scipy + - libgcc test: - # Python imports imports: - pomegranate - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://pypi.python.org/pypi/pomegranate/ license: LICENSE.txt summary: 'Pomegranate is a graphical models library for Python, implemented in Cython for speed.' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/prosic/1.0/build.sh b/recipes/prosic/1.0/build.sh deleted file mode 100644 index ac067667d4..0000000000 --- a/recipes/prosic/1.0/build.sh +++ /dev/null @@ -1,6 +0,0 @@ -#!/bin/bash -euo - -cmake -DCMAKE_INSTALL_PREFIX=$PREFIX CMakeLists.txt && make -cp bin/prosic-call $PREFIX/bin - -$PYTHON setup.py install diff --git a/recipes/prosic/1.0/meta.yaml b/recipes/prosic/1.0/meta.yaml deleted file mode 100644 index aa2600b856..0000000000 --- a/recipes/prosic/1.0/meta.yaml +++ /dev/null @@ -1,38 +0,0 @@ -package: - name: prosic - version: "1.0" - -build: - number: 1 - string: "py{{CONDA_PY}}_gsl{{CONDA_GSL}}_gmp{{CONDA_GMP}}_{{PKG_BUILDNUM}}" - skip: True # [not py3k] - -source: - url: https://github.com/PROSIC/prosic/archive/v1.0.tar.gz - fn: prosic-1.0.tar.gz - md5: 9151272ab7022cc3aaba70309f7fc362 - -requirements: - build: - - gcc - - gsl {{CONDA_GSL}}* - - gmp {{CONDA_GMP}}* - - python - run: - - gsl {{CONDA_GSL}}* - - gmp {{CONDA_GMP}}* - - python - - pyvcf - - pysam - - numpy - -test: - commands: - - prosic-call -h > /dev/null - - prosic-extract-observations --help > /dev/null - - prosic-annotate --help > /dev/null - -about: - home: https://github.com/PROSIC/PROSIC - license: GPLv3 - summary: A caller for somatic insertions and deletions. diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index 4f819cff5f..425043c900 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -11,6 +11,9 @@ build: entry_points: - pybel = pybel.cli:main number: 0 + # tests fail on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235726973#L3656 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [osx or py3k] requirements: build: @@ -46,8 +49,8 @@ test: - pybel.parser - pybel.parser.modifiers commands: - # pybel does not work under Python 3 on the docker image because the locale command is not installed - - pybel --help # [py27] + # click requires a unicode locale + - LANG=C.UTF-8 pybel --help about: home: https://github.com/pybel/pybel diff --git a/recipes/pybigwig/0.1.11/meta.yaml b/recipes/pybigwig/0.1.11/meta.yaml index a66e18a9b0..258065cb0b 100644 --- a/recipes/pybigwig/0.1.11/meta.yaml +++ b/recipes/pybigwig/0.1.11/meta.yaml @@ -19,16 +19,11 @@ requirements: run: - python - curl -test: + + test: imports: - pyBigWig - commands: - - nosetests - - requires: - - nose - about: home: https://github.com/dpryan79/pyBigWig license: MIT diff --git a/recipes/pybigwig/meta.yaml b/recipes/pybigwig/meta.yaml index a92f28c3c1..6b29d23d8d 100644 --- a/recipes/pybigwig/meta.yaml +++ b/recipes/pybigwig/meta.yaml @@ -21,14 +21,10 @@ requirements: - curl - numpy x.x test: - imports: # [not py34] - - pyBigWig # [not py34] - - commands: # [not py34] - - python -c "import pyBigWig; assert(pyBigWig.numpy == 1); assert(pyBigWig.remote == 1)" # [not py34] - - requires: - - nose + imports: + - pyBigWig + commands: + - python -c "import pyBigWig; assert(pyBigWig.numpy == 1); assert(pyBigWig.remote == 1)" about: home: https://github.com/dpryan79/pyBigWig diff --git a/recipes/pysamstats/meta.yaml b/recipes/pysamstats/meta.yaml index 6fb8660104..541ae8a178 100644 --- a/recipes/pysamstats/meta.yaml +++ b/recipes/pysamstats/meta.yaml @@ -9,7 +9,7 @@ source: build: number: 0 - skip: True # [osx] + skip: True # [osx or not py35 or not py27] requirements: build: diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index 9f81d5bc0b..eb9b1b2a6d 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -16,6 +16,7 @@ requirements: - python - setuptools - zlib + run: - python - zlib @@ -27,4 +28,4 @@ test: about: home: https://github.com/slowkow/pytabix license: MIT - summary: fast random access to sorted files compressed with bgzip and indexed by tabix + summary: Fast random access to sorted files compressed with bgzip and indexed by tabix. diff --git a/recipes/python-bioext/meta.yaml b/recipes/python-bioext/meta.yaml index 636a81aca9..3eeae896f1 100644 --- a/recipes/python-bioext/meta.yaml +++ b/recipes/python-bioext/meta.yaml @@ -5,7 +5,7 @@ package: source: git_rev: 0.17.4 git_url: https://github.com/veg/BioExt.git - patches: + patches: # [osx] - osx-freetype.patch # [osx] build: diff --git a/recipes/python-igraph/meta.yaml b/recipes/python-igraph/meta.yaml index e62aa48d5a..b06c30d8d5 100644 --- a/recipes/python-igraph/meta.yaml +++ b/recipes/python-igraph/meta.yaml @@ -8,15 +8,17 @@ source: md5: a4c0b5960735b36adb5d3a40031cb7c0 build: - number: 1 + number: 2 requirements: build: - python - lxml + - gcc run: - python - lxml + - libgcc test: imports: diff --git a/recipes/python-magic/0.4.6/build.sh b/recipes/python-magic/0.4.6/build.sh deleted file mode 100644 index 4d7fc032b8..0000000000 --- a/recipes/python-magic/0.4.6/build.sh +++ /dev/null @@ -1,9 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install - -# Add more build steps here, if they are necessary. - -# See -# http://docs.continuum.io/conda/build.html -# for a list of environment variables that are set during the build process. diff --git a/recipes/python-magic/0.4.6/meta.yaml b/recipes/python-magic/0.4.6/meta.yaml deleted file mode 100644 index 7a7e1d85ca..0000000000 --- a/recipes/python-magic/0.4.6/meta.yaml +++ /dev/null @@ -1,60 +0,0 @@ -package: - name: python-magic - version: "0.4.6" - -source: - fn: python-magic-0.4.6.tar.gz - url: https://pypi.python.org/packages/source/p/python-magic/python-magic-0.4.6.tar.gz - md5: 07e7a0fea78dd81ed609414c3484df58 -# patches: - # List any patch files here - # - fix.patch - -# build: - # noarch_python: True - # preserve_egg_dir: True - # entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - python-magic = python-magic:main - # - # Would create an entry point called python-magic that calls python-magic.main() - - - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - -requirements: - build: - - python - - setuptools - - run: - - python - -# test: - # Python imports - # imports: - - # commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - -about: - home: http://github.com/ahupp/python-magic - license: Python Software Foundation License - summary: 'File type identification using libmagic' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml \ No newline at end of file diff --git a/recipes/python-magic/build.sh b/recipes/python-magic/build.sh deleted file mode 100644 index 8e25a1455f..0000000000 --- a/recipes/python-magic/build.sh +++ /dev/null @@ -1,3 +0,0 @@ -#!/bin/bash - -$PYTHON setup.py install diff --git a/recipes/python-magic/meta.yaml b/recipes/python-magic/meta.yaml deleted file mode 100644 index 3ac2367bd2..0000000000 --- a/recipes/python-magic/meta.yaml +++ /dev/null @@ -1,32 +0,0 @@ -package: - name: python-magic - version: "0.4.12" - -source: - fn: python-magic-0.4.12.tar.gz - url: https://pypi.python.org/packages/d8/94/4b2930f2146c1318e6250c85d884c87720f3089085e4d4ba53fa0f8c620c/python-magic-0.4.12.tar.gz - md5: a818080863bfbf2fb80aa75a2fafc180 - -build: - number: 0 - skip: True # [osx] - -requirements: - build: - - python - - setuptools - - libmagic - - run: - - python - - libmagic - -test: - imports: - - magic - -about: - home: http://github.com/ahupp/python-magic - license: MIT License - summary: 'File type identification using libmagic' - license_family: MIT diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 72e4cb4ff3..9a9e109370 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -27,13 +27,14 @@ requirements: - biom-format >=2.1.4,<2.2.0 - emperor >=0.9.51,<1.0.0 - scikit-bio >=0.2.3,<0.3.0 - - matplotlib >=1.1.0,!=1.4.2,<1.5.0 + - matplotlib <=1.9 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 - qiime-default-reference >=0.1.2,<0.2.0 - mock - nose + - xz run: - python @@ -47,7 +48,7 @@ requirements: - biom-format >=2.1.4,<2.2.0 - emperor >=0.9.51,<1.0.0 - scikit-bio >=0.2.3,<0.3.0 - - matplotlib >=1.1.0,!=1.4.2,<1.5.0 + - matplotlib <=1.9 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 @@ -61,6 +62,7 @@ requirements: - xorg-libsm - xorg-libxrender - xorg-libxau + - xz test: # Python imports @@ -233,3 +235,9 @@ about: home: http://www.qiime.org license: GNU General Public License v2 (GPLv2) summary: 'Quantitative Insights Into Microbial Ecology' + +extra: + container: + # qiime fails on busybox due to encoding problems + # (busybox has limited unicode support) + extended-base: true diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index 421b93a214..36cc942914 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -6,26 +6,13 @@ source: fn: query_phenomizer-0.5.tar.gz url: https://pypi.python.org/packages/e3/b2/d8f106d7f59aba6f198a6b2dc14237076517977c4208ca299ea8995fd43e/query_phenomizer-0.5.tar.gz md5: 6141bd9f5743d9f828ee200eb62f8fbc -# patches: - # List any patch files here - # - fix.patch build: - # noarch_python: True - # preserve_egg_dir: True entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - query_phenomizer = query_phenomizer:main - # - # Would create an entry point called query_phenomizer that calls query_phenomizer.main() - - query_phenomizer = query_phenomizer.__main__:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 requirements: build: @@ -47,23 +34,10 @@ test: - query_phenomizer commands: - # You can put test commands to be run here. Use this to test that the - # entry points work. - - - query_phenomizer --help - - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose + # click requires a unicode locale + - LANG=C.UTF-8 query_phenomizer --help about: home: https://www.github.com/moonso/query_phenomizer license: MIT License summary: 'Tool for query and parsing the phenomizer tool' - -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index c0dd2e3aeb..b1360702c3 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -35,10 +37,12 @@ requirements: test: imports: - rapclust + commands: + # click requires a unicode locale + - LANG=C.UTF-8 RapClust --help about: home: https://github.com/COMBINE-lab/RapClust license: BSD with attribution summary: 'Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes' license_family: BSD - diff --git a/recipes/rpy2/meta.yaml b/recipes/rpy2/meta.yaml index 566d0e5197..5aeca78e77 100644 --- a/recipes/rpy2/meta.yaml +++ b/recipes/rpy2/meta.yaml @@ -40,28 +40,9 @@ test: imports: - rpy2 - rpy2.interactive - - rpy2.interactive.tests - - rpy2.ipython - - rpy2.ipython.tests - rpy2.rinterface - - rpy2.rinterface.tests - rpy2.rlike - - rpy2.rlike.tests - rpy2.robjects - - rpy2.robjects.lib - - rpy2.robjects.lib.tests - - rpy2.robjects.tests - - commands: - - echo - # - python -m rpy2.tests - - requires: - - ipython - - r-survival - - r-ggplot2 - - numpy - - pandas about: home: http://rpy.sourceforge.net diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 48b90437a8..fae476f90f 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -6,22 +6,11 @@ source: fn: SamSifter-1.0.0.tar.gz url: https://pypi.python.org/packages/source/S/SamSifter/SamSifter-1.0.0.tar.gz md5: 883df68d2f989c4c431ebb253ca104f7 -# patches: - # List any patch files here - # - fix.patch build: skip: True # [py27] - # noarch_python: True - # preserve_egg_dir: True + number: 2 entry_points: - # Put any entry points (scripts to be generated automatically) here. The - # syntax is module:function. For example - # - # - samsifter = samsifter:main - # - # Would create an entry point called samsifter that calls samsifter.main() - - compile_stats=samsifter.stats.compile_stats:main - count_taxon_reads=samsifter.tools.count_taxon_reads:main - filter_read_conservation=samsifter.tools.filter_read_conservation:main @@ -36,10 +25,6 @@ build: - summarize_stats=samsifter.stats.summarize_stats:main - samsifter=samsifter.samsifter:main - # If this is a new build for the same version, increment the build - # number. If you do not include this key, it defaults to 0. - # number: 1 - requirements: build: - python @@ -47,12 +32,21 @@ requirements: - matplotlib >=1.3.1 - pandas >=0.14.1 - numpy >=1.6.1 - + - pyqt 4.11.* + - glib + - xorg-libsm + - xorg-libxrender run: - python - matplotlib >=1.3.1 - pandas >=0.14.1 - numpy >=1.6.1 + - pyqt 4.11.* + # workaround for missing dependency of pandas + - libgcc + - glib + - xorg-libsm + - xorg-libxrender test: # Python imports @@ -85,18 +79,12 @@ test: - summarize_stats --help - samsifter --help - # You can also put a file called run_test.py in the recipe that will be run - # at test time. - - # requires: - # Put any additional test requirements here. For example - # - nose - about: home: http://pypi.python.org/pypi/SamSifter/ license: GNU General Public License v3 (GPLv3) summary: 'Workflow editor for metagenomic analysis' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + container: + # matplotlib needs opengl support + extended-base: true diff --git a/recipes/scikit-bio/0.2.3/meta.yaml b/recipes/scikit-bio/0.2.3/meta.yaml index 26ad26e86c..48d60f5eb4 100644 --- a/recipes/scikit-bio/0.2.3/meta.yaml +++ b/recipes/scikit-bio/0.2.3/meta.yaml @@ -77,3 +77,8 @@ about: license: BSD License summary: Data structures, algorithms and educational resources for bioinformatics. license_file: COPYING.txt + +extra: + container: + # needs libGL.so.1 + extended-base: true diff --git a/recipes/scikit-bio/meta.yaml b/recipes/scikit-bio/meta.yaml index 446f4a765a..aad129f0aa 100644 --- a/recipes/scikit-bio/meta.yaml +++ b/recipes/scikit-bio/meta.yaml @@ -86,3 +86,8 @@ about: license: BSD License summary: Data structures, algorithms and educational resources for bioinformatics. license_file: COPYING.txt + +extra: + container: + # needs libGL.so.1 + extended-base: true diff --git a/recipes/scoop/meta.yaml b/recipes/scoop/meta.yaml index 727e24bc34..4c904a9b14 100644 --- a/recipes/scoop/meta.yaml +++ b/recipes/scoop/meta.yaml @@ -10,7 +10,7 @@ source: - setup.py.patch build: - number: 0 + number: 1 requirements: build: @@ -23,9 +23,12 @@ requirements: - python - greenlet >=0.3.4 - pyzmq >=13.1.0 + # Apparently pyzmq needs this (TODO fix that instead). + # problem might go away when conda-forge priority is raised + # after R migration. + - libgcc test: - # Python imports imports: - scoop - scoop._comm diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index 27f645232f..7c55e6a026 100644 --- a/recipes/segmentation-fold/meta.yaml +++ b/recipes/segmentation-fold/meta.yaml @@ -2,7 +2,6 @@ package: name: segmentation-fold version: 1.7.0 - about: home: https://github.com/yhoogstrate/segmentation-fold license: GNU General Public License v3 or later (GPLv3+) @@ -12,14 +11,13 @@ build: number: 0 skip: True # [not py27] - source: fn: d1b24fec1da405ba70e07ef27046b385b13e8d1f.tar.gz url: "https://github.com/yhoogstrate/segmentation-fold/archive/d1b24fec1da405ba70e07ef27046b385b13e8d1f.tar.gz" sha256: 0995272183e31b0b80be57dee22f0e15c62df10d5034f106a3e4454bf9b82e7a requirements: - build: + build: - llvmdev ==3.9.1 # [osx] - libcxx # [osx] - gcc ==4.8.5 # [linux] @@ -31,7 +29,7 @@ requirements: - htseq >=0.6.1 - click >=4.0 - run: + run: - libgcc # [linux] - libcxx # [osx] - boost ==1.63.0 @@ -42,5 +40,6 @@ requirements: test: commands: - - segmentation-fold --version - - segmentation-fold-utils --help + # click requires a unicode locale + - LANG=C.UTF-8 segmentation-fold --version + - LANG=C.UTF-8 segmentation-fold-utils --help diff --git a/recipes/sevenbridges-python/meta.yaml b/recipes/sevenbridges-python/meta.yaml index b4816cea20..2706f7e449 100644 --- a/recipes/sevenbridges-python/meta.yaml +++ b/recipes/sevenbridges-python/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # futures not available for python 3.6 + skip: True # [not py2k and not py35] requirements: build: diff --git a/recipes/spades/3.9.0/meta.yaml b/recipes/spades/3.9.0/meta.yaml index 0bf4695539..e0427faf32 100644 --- a/recipes/spades/3.9.0/meta.yaml +++ b/recipes/spades/3.9.0/meta.yaml @@ -10,7 +10,7 @@ source: build: number: 1 - skip: False + skip: True # [not py2k and not py35] requirements: build: diff --git a/recipes/spades/meta.yaml b/recipes/spades/meta.yaml index f8a98c6f77..1b39cc6be3 100644 --- a/recipes/spades/meta.yaml +++ b/recipes/spades/meta.yaml @@ -12,6 +12,7 @@ source: build: number: 0 + skip: True # [not py2k and not py35] requirements: build: diff --git a/recipes/swarm/1.2.19/meta.yaml b/recipes/swarm/1.2.19/meta.yaml index 7d78549ca1..88b1233792 100644 --- a/recipes/swarm/1.2.19/meta.yaml +++ b/recipes/swarm/1.2.19/meta.yaml @@ -8,17 +8,20 @@ source: md5: 4d147b9c94b8966760d0b737499a53d2 build: - number: 0 + number: 1 skip: True # [not linux64 or osx] requirements: + build: + - gcc run: - python + - libgcc test: commands: - swarm_breaker.py --version - - swarm -v 2>&1 | grep Swarm > /dev/null + - swarm -v 2>&1 | grep Swarm about: home: https://github.com/torognes/swarm diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index eb22001fdb..815cf2884a 100644 --- a/recipes/swga/meta.yaml +++ b/recipes/swga/meta.yaml @@ -11,7 +11,7 @@ source: md5: c71b533fed7037be59f852af90944c1d build: - skip: True # [not py27] + skip: true # [not py27] entry_points: - swga = swga.main:main number: 0 @@ -46,7 +46,8 @@ test: imports: - swga commands: - - swga 2>&1 | grep Usage + # click requires a unicode locale + - LANG=C.UTF-8 swga 2>&1 | grep Usage about: home: https://github.com/eclarke/swga diff --git a/recipes/tabview/meta.yaml b/recipes/tabview/meta.yaml index b281bbecb3..713cd40226 100644 --- a/recipes/tabview/meta.yaml +++ b/recipes/tabview/meta.yaml @@ -15,9 +15,11 @@ requirements: build: - python - setuptools + - ncurses run: - python + - ncurses test: imports: diff --git a/recipes/transabyss/meta.yaml b/recipes/transabyss/meta.yaml index 3aa52d5350..8e8880cf24 100644 --- a/recipes/transabyss/meta.yaml +++ b/recipes/transabyss/meta.yaml @@ -18,7 +18,7 @@ requirements: - abyss - python-igraph - samtools 1.3.1 - - bowtie2 2.2.8 + - bowtie2 - blat - python diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index 0c99924f6c..0bf5f5698f 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -36,7 +36,8 @@ requirements: - scipy test: commands: - - umis --help + # click requires a unicode locale + - LANG=C.UTF-8 umis --help about: home: https://github.com/vals/umis diff --git a/recipes/validators/meta.yaml b/recipes/validators/meta.yaml index 5ddaeeb6f7..c8e3c39018 100644 --- a/recipes/validators/meta.yaml +++ b/recipes/validators/meta.yaml @@ -31,4 +31,4 @@ test: about: home: https://github.com/kvesteri/validators license: BSD License - summary: 'Python Data Validation for Humans™.' + summary: 'Python Data Validation for Humans.' diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index dd7ef75e2a..ef041d6356 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -15,18 +15,17 @@ source: requirements: # To do: Pinnng of the setuptools version is a workaround. Try to remove it. build: - - gcc # [not osx] - - llvm # [osx] + - gcc - python - - setuptools ==23 + - setuptools - pysam <0.9.0 - pyvcf - pyfaidx - xopen run: - - libgcc # [not osx] + - libgcc - python - - setuptools ==23 + - setuptools - pysam <0.9.0 - pyvcf - pyfaidx @@ -34,8 +33,7 @@ requirements: build: skip: True # [not py3k] - script: python3 setup.py install # [not osx] - script: CFLAGS="-stdlib=libc++" python3 setup.py install # [osx] + script: python3 setup.py install test: imports: diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index a7eff8dd59..9b6e61948a 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -35,3 +35,8 @@ about: home: http://pypi.python.org/pypi/yahmm/ license: LICENSE.txt summary: 'YAHMM is a HMM package for Python, implemented in Cython for speed.' + +extra: + container: + # matplotlib needs opengl support + extended-base: true diff --git a/recipes/zeroc-ice/meta.yaml b/recipes/zeroc-ice/meta.yaml index 93a7c33019..f08d0b6450 100644 --- a/recipes/zeroc-ice/meta.yaml +++ b/recipes/zeroc-ice/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # segmentation fault with Python 3.6 + skip: True # [not py2k and not py35] requirements: build: diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml index 160f266567..34db3100b3 100644 --- a/scripts/env_matrix.yml +++ b/scripts/env_matrix.yml @@ -6,7 +6,7 @@ CONDA_HTSLIB: "1.4" CONDA_BOOST: "1.61" CONDA_R: "3.3.1" CONDA_PERL: "5.22.0" -CONDA_NPY: "110" +CONDA_NPY: "112" CONDA_NCURSES: "5.9" CONDA_GSL: "1.16" CONDA_GMP: "5.1" diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index 784c68da39..0dba20d2ee 100755 --- a/scripts/travis-run.sh +++ b/scripts/travis-run.sh @@ -9,7 +9,7 @@ set +u [[ -z $DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK ]] && DISABLE_BIOCONDA_UTILS_BUILD_GIT_RANGE_CHECK="false" set -u -if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] +if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] then echo "" echo "Tests are skipped for pushes to the main bioconda-recipes repo." @@ -37,42 +37,33 @@ then fi fi - # If the environment vars changed (e.g., boost, R, perl) then there's no - # good way of knowing which recipes need rebuilding so we check them all. - set +e - git diff --exit-code --name-only $RANGE scripts/env_matrix.yml - ENV_CHANGE=$? - set -e - if [[ $TRAVIS_EVENT_TYPE == "cron" ]] then RANGE_ARG="" SKIP_LINTING=true echo "considering all recipes because build is triggered via cron" else - if [[ $ENV_CHANGE -eq 1 ]] + if [[ $TRAVIS_BRANCH == "bulk" ]] then - if [[ $TRAVIS_BRANCH == "bulk" ]] + if [[ $TRAVIS_PULL_REQUEST != "false" ]] then - if [[ $TRAVIS_PULL_REQUEST != "false" ]] - then - # pull request against bulk: only build additionally changed recipes - RANGE_ARG="--git-range $RANGE" - else - # push on bulk: consider all recipes affected by modified env matrix (the bulk update)! - RANGE_ARG="" - SKIP_LINTING=true - echo "running bulk update" - fi - else - # not on bulk branch: ignore env matrix changes + # pull request against bulk: only build additionally changed recipes RANGE_ARG="--git-range $RANGE" + else + # push on bulk: consider all recipes and do not lint (the bulk update)! + RANGE_ARG="" + SKIP_LINTING=true + echo "running bulk update" fi else # consider only recipes that (a) changed since the last build # on master, or (b) changed in this pull request compared to the target # branch. - RANGE_ARG="--git-range $RANGE" + RANGE_ARG="--git-range $RANGE" + if [[ $TRAVIS_PULL_REQUEST_BRANCH == "bulk" ]] + then + SKIP_LINTING=true + fi fi fi fi diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh index 76768af049..ef16cb8f40 100755 --- a/scripts/travis-setup.sh +++ b/scripts/travis-setup.sh @@ -2,7 +2,7 @@ set -e set -x -if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] +if [[ $TRAVIS_BRANCH != "master" && $TRAVIS_BRANCH != "bulk" && $TRAVIS_PULL_REQUEST == "false" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] then echo "" echo "Setup is skipped for pushes to the main bioconda-recipes repo."