From f575c1036baa9b1800f6549bb40a72f3e58faa37 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 3 Jun 2017 14:18:00 +0200 Subject: [PATCH] Finished Python 3.6 migration (#4888) * Add python-3.6 * Merged master. * Do not skip build for bulk updates. * Fix skipping. * Simplify filter logic. * Remove travis_wait, because bioconda-utils now prints a spinner for long-running tasks. * Remove phonenumbers (available in conda-forge). * Skip unnecessary tests in rpy2. * Add libgcc runtime dependency for scoop. * Add zlib to pytabix. Add gcc to python-igraph. * Add bzip2 to libsbml. * add libxml2 as dependency * rebuild flowtools * skip openbabel on py36 * try an other selector * fix the builds a little bit, however this important package needs a some love * fix URL ping @BioNinja, please don't remove tarballs :) * Fix tests for mgf-formatter * That is scary, the checksum changed? * removed in favor of https://github.com/conda-forge/python-magic-feedstock * fix download path * checksum incorrect :( * Fix pybigwig test cases. * Pin conda-build to a newer version. * Revert conda pinning. * Fix merge error. * point to bioconda-utils:enable-build-ids branch * remove dev version from repository * add dependency on pyqt4 * Fix nanosimh source URL. * Add gcc/libgcc to illuminate. * Removed old busco recipe because the source code is not available anymore. * Add automake. Update numpy to 1.12, because 1.10 is not built with Python 3.6 support. * Remove superfluous test case. * Minor. * Fix intarna build string. * Remove old prosic version. * Fix scipy dependency of igdiscover and cosmetic changes. * Add ncurses dependency. * Add pyqt. * Skip zeroc-ice because of segmentation fault. * Try to fix selector. * Add pyqt4 dependency. * Remove old version of bx-python. * Skip python 3.6 * Skip Python 3.6 because it is unsupported. * Use bioconda-utils master again (after the merge). Suppress warnings in intarna build. * Remove llvm dependency of whatshap. * Use debian container image in case of recipes depending on click. The reason is that click requires full unicode support, which is not present in the busybox image used for mulled. * Fixes and blacklisting. Temporarily use a fixed branch of bioconda-utils. * Fix merge conflict in openbabel recipe. * Skip py36 because pysamstats relies on old pysam which does not build on py36. * Use debian container for ggplot. * Revert skipping because of encoding errors. These should be fixed by bioconda/bioconda-utils#116. * Temporarily use fixed branch of bioconda-utils. * Bioconda-utils fix has been merged, use master again. * Add missing library. * Skip whole section outside of osx. * Add missing dependency. * Show test results of last. * Fix hmmlearn dependencies. * Relax setuptools dependency. * Update viral-ngs dependency in order to avoid conflict with py36. * Fix fsnviz dependency. * New garnet version. The old one was removed from pypi!! * Disable make test for intarna. * Add pyqt as build requirement. * Relax bowtie dependency. * Skip osx. * Pyqt is not a dependency of gseapy. * Skip viral-ngs for py36. * Relax matplotlib pinning for qiime. * Fix url. * Skip ig-flowtools until R dependencies have been updated. * Omit futures in python 3k. Add missing dependency. * Try simplifying osx setup for whatshap. The stdlib argument did not work anymore. * Relax snakemake dependency. * Use debian container for samsifter because it depends on X11 libs. * Skip rapclust. * Fix matplotlib version. * Skip chanjo * Fix perl dependency. * Fix last dependencies. * Use extended container for fitter. * Fix args. * Fix gseapy. * Handle locale in test cases of click-related recipes. Fix swarm tests. * Fixes. * Remove unnecessary dependencies. * Use our own extended base image. * Use master branch of bioconda-utils. * Documentation and base image. * Fix swarm dependencies. * Skip until we have completely switched to conda-forge. * Use extended base image for dreamtools. * Skip fwdpy (missing headers in own source). * Fixes and formatting. * Skipping hlama for anything except py35. @holtgrewe this is because for py36, you would need to depend on a current Snakemake version. I suggest to relax this dependency since Snakemake is backwards compatible anyway. * Fixes * Adapt container image definition to new syntax. Skip click-based recipes on py3k. * Add zlib to bx-python. * Fixes. * Add missing dependency. * Add gcc. * Add missing dependency xz. * Remove bx-python 0.7.1 because it does not build even on python 2.7 * Use extended base image. * Add missing lib. * Use UTF-8 in test cases. * Debug bx-python. * Fix qiime. Use test branch of bioconda-utils. * Fix qiime. Use test branch of bioconda-utils. * Skip cgat-scripts-devel on py36. Use master branch of bioconda-utils again after PR has been merged. * Skip linting when PR comes from the special bulk branch. --- .travis.yml | 2 +- recipes/amos/build.sh | 14 ++- recipes/amos/meta.yaml | 10 +- recipes/bcbio-nextgen/meta.yaml | 7 +- recipes/bcl2fastq-nextseq/meta.yaml | 3 +- recipes/biokit/meta.yaml | 28 +++-- recipes/biom-format/2.1.5/meta.yaml | 18 ++-- recipes/biomaj/meta.yaml | 1 - recipes/biopython/1.65/build.sh | 3 - recipes/biopython/1.65/meta.yaml | 113 --------------------- recipes/busco/1.2/build.sh | 5 - recipes/busco/1.2/meta.yaml | 33 ------ recipes/bx-python/0.7.1/build.sh | 2 - recipes/bx-python/0.7.1/meta.yaml | 57 ----------- recipes/bx-python/0.7.2/build.sh | 3 - recipes/bx-python/0.7.2/meta.yaml | 58 ----------- recipes/bx-python/build.sh | 7 +- recipes/bx-python/meta.yaml | 13 +-- recipes/cgat-pipelines-nosetests/meta.yaml | 1 - recipes/cgat-report/meta.yaml | 3 +- recipes/cgat-scripts-devel/meta.yaml | 5 +- recipes/cgat-scripts-nosetests/meta.yaml | 1 - recipes/cgat-scripts/meta.yaml | 1 - recipes/chanjo/meta.yaml | 37 ++----- recipes/checkm-genome/meta.yaml | 34 ------- recipes/cnvkit/meta.yaml | 6 +- recipes/colormap/meta.yaml | 24 ----- recipes/cooler/meta.yaml | 7 +- recipes/crimson/meta.yaml | 5 +- recipes/crispresso/meta.yaml | 2 +- recipes/dr-disco/meta.yaml | 11 +- recipes/dr-disco/v0.3.4/meta.yaml | 10 +- recipes/dreamtools/meta.yaml | 8 +- recipes/ecmwfapi/meta.yaml | 6 +- recipes/extract_genome_region/meta.yaml | 33 +----- recipes/fitter/meta.yaml | 24 +---- recipes/fsnviz/0.1.0/meta.yaml | 12 ++- recipes/fsnviz/meta.yaml | 9 +- recipes/fwdpy/meta.yaml | 3 + recipes/garnet/meta.yaml | 45 ++------ recipes/genomebaser/meta.yaml | 35 +------ recipes/genomepy/meta.yaml | 4 +- recipes/ggplot/meta.yaml | 4 + recipes/gseapy/meta.yaml | 40 ++------ recipes/hisat2/meta.yaml | 1 + recipes/hlama/meta.yaml | 6 +- recipes/hmmlearn/meta.yaml | 4 +- recipes/ig-flowtools/meta.yaml | 11 +- recipes/igdiscover/meta.yaml | 17 +++- recipes/illuminate/meta.yaml | 2 + recipes/intarna/build.sh | 5 +- recipes/intarna/meta.yaml | 4 +- recipes/joblib/meta.yaml | 3 - recipes/last/490/meta.yaml | 21 ++-- recipes/last/638/meta.yaml | 19 ++-- recipes/last/meta.yaml | 17 ++-- recipes/libsbml/meta.yaml | 8 +- recipes/mercat/meta.yaml | 5 +- recipes/mgf-formatter/meta.yaml | 19 ++-- recipes/moca/meta.yaml | 8 +- recipes/multiqc-bcbio/meta.yaml | 5 +- recipes/multiqc/meta.yaml | 10 +- recipes/nglview/meta.yaml | 2 +- recipes/onto2nx/meta.yaml | 2 + recipes/openbabel/2.3.90dev7d621d9/build.sh | 26 ----- .../openbabel/2.3.90dev7d621d9/fix_data_path.diff | 18 ---- .../2.3.90dev7d621d9/fix_library_path_search.diff | 30 ------ .../openbabel/2.3.90dev7d621d9/include-dirs.patch | 25 ----- recipes/openbabel/2.3.90dev7d621d9/meta.yaml | 48 --------- recipes/openbabel/2.3.90dev7d621d9/run_test.py | 15 --- recipes/openbabel/2.4.1/meta.yaml | 2 + recipes/peakzilla/meta.yaml | 10 +- recipes/ped_parser/meta.yaml | 42 +------- recipes/phizz/meta.yaml | 37 +------ recipes/phonenumbers/build.sh | 4 - recipes/phonenumbers/meta.yaml | 35 ------- recipes/planemo/0.23.0/meta.yaml | 4 +- recipes/planemo/0.34.1/meta.yaml | 11 +- recipes/planemo/meta.yaml | 10 +- recipes/platypus-conquistador/meta.yaml | 36 +------ recipes/pomegranate/meta.yaml | 37 +------ recipes/prosic/1.0/build.sh | 6 -- recipes/prosic/1.0/meta.yaml | 38 ------- recipes/pybel/meta.yaml | 7 +- recipes/pybigwig/0.1.11/meta.yaml | 9 +- recipes/pybigwig/meta.yaml | 12 +-- recipes/pysamstats/meta.yaml | 2 +- recipes/pytabix/meta.yaml | 3 +- recipes/python-bioext/meta.yaml | 2 +- recipes/python-igraph/meta.yaml | 4 +- recipes/python-magic/0.4.6/build.sh | 9 -- recipes/python-magic/0.4.6/meta.yaml | 60 ----------- recipes/python-magic/build.sh | 3 - recipes/python-magic/meta.yaml | 32 ------ recipes/qiime/1.9.1/meta.yaml | 12 ++- recipes/query_phenomizer/meta.yaml | 34 +------ recipes/rapclust/meta.yaml | 6 +- recipes/rpy2/meta.yaml | 19 ---- recipes/samsifter/meta.yaml | 42 +++----- recipes/scikit-bio/0.2.3/meta.yaml | 5 + recipes/scikit-bio/meta.yaml | 5 + recipes/scoop/meta.yaml | 7 +- recipes/segmentation-fold/meta.yaml | 11 +- recipes/sevenbridges-python/meta.yaml | 2 + recipes/spades/3.9.0/meta.yaml | 2 +- recipes/spades/meta.yaml | 1 + recipes/swarm/1.2.19/meta.yaml | 7 +- recipes/swga/meta.yaml | 5 +- recipes/tabview/meta.yaml | 2 + recipes/transabyss/meta.yaml | 2 +- recipes/umis/meta.yaml | 3 +- recipes/validators/meta.yaml | 2 +- recipes/whatshap/meta.yaml | 12 +-- recipes/yahmm/meta.yaml | 5 + recipes/zeroc-ice/meta.yaml | 2 + scripts/env_matrix.yml | 2 +- scripts/travis-run.sh | 37 +++---- scripts/travis-setup.sh | 2 +- 118 files changed, 392 insertions(+), 1328 deletions(-) delete mode 100644 recipes/biopython/1.65/build.sh delete mode 100644 recipes/biopython/1.65/meta.yaml delete mode 100644 recipes/busco/1.2/build.sh delete mode 100644 recipes/busco/1.2/meta.yaml delete mode 100644 recipes/bx-python/0.7.1/build.sh delete mode 100644 recipes/bx-python/0.7.1/meta.yaml delete mode 100644 recipes/bx-python/0.7.2/build.sh delete mode 100644 recipes/bx-python/0.7.2/meta.yaml delete mode 100755 recipes/openbabel/2.3.90dev7d621d9/build.sh delete mode 100644 recipes/openbabel/2.3.90dev7d621d9/fix_data_path.diff delete mode 100644 recipes/openbabel/2.3.90dev7d621d9/fix_library_path_search.diff delete mode 100644 recipes/openbabel/2.3.90dev7d621d9/include-dirs.patch delete mode 100644 recipes/openbabel/2.3.90dev7d621d9/meta.yaml delete mode 100644 recipes/openbabel/2.3.90dev7d621d9/run_test.py delete mode 100644 recipes/phonenumbers/build.sh delete mode 100644 recipes/phonenumbers/meta.yaml delete mode 100644 recipes/prosic/1.0/build.sh delete mode 100644 recipes/prosic/1.0/meta.yaml delete mode 100644 recipes/python-magic/0.4.6/build.sh delete mode 100644 recipes/python-magic/0.4.6/meta.yaml delete mode 100644 recipes/python-magic/build.sh delete mode 100644 recipes/python-magic/meta.yaml 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."