From 18a48ee46afcdfcc338e9eb5dcdc29f61c949d8c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sun, 1 Jan 2017 19:35:11 +0100 Subject: [PATCH 001/114] Add python-3.6 --- scripts/env_matrix.yml | 1 + 1 file changed, 1 insertion(+) diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml index 14a5fce5d1..076a2fbd68 100644 --- a/scripts/env_matrix.yml +++ b/scripts/env_matrix.yml @@ -2,6 +2,7 @@ CONDA_PY: - 27 - 34 - 35 + - 36 CONDA_BOOST: "1.60" CONDA_R: "3.3.1" CONDA_PERL: "5.22.0" From 9a97f096fc93a105a60777ac20af33641f882f95 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 08:10:28 +0200 Subject: [PATCH 002/114] Merged master. --- scripts/env_matrix.yml | 3 --- 1 file changed, 3 deletions(-) diff --git a/scripts/env_matrix.yml b/scripts/env_matrix.yml index c07c1cf1ba..160f266567 100644 --- a/scripts/env_matrix.yml +++ b/scripts/env_matrix.yml @@ -1,11 +1,8 @@ CONDA_PY: - 27 - 35 -<<<<<<< HEAD - 36 -======= CONDA_HTSLIB: "1.4" ->>>>>>> master CONDA_BOOST: "1.61" CONDA_R: "3.3.1" CONDA_PERL: "5.22.0" From b3256d5df77ac1216b645411880d6e20b8512e41 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 08:41:57 +0200 Subject: [PATCH 003/114] Do not skip build for bulk updates. --- scripts/travis-run.sh | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index 23287c1dcf..207a4bdaa8 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." From 3f0b9bacd6aabb819c4b4c8d5c76cb69c1e2c825 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 08:55:17 +0200 Subject: [PATCH 004/114] Fix skipping. --- scripts/travis-run.sh | 2 +- scripts/travis-setup.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index 207a4bdaa8..f5065612fa 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_BRANCH != "bulk") && $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." 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" && $TRAVIS_REPO_SLUG == "bioconda/bioconda-recipes" ]] then echo "" echo "Setup is skipped for pushes to the main bioconda-recipes repo." From 37a701758b3408d18e6f314ac36fcf34a7120cf6 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 09:12:46 +0200 Subject: [PATCH 005/114] Simplify filter logic. --- scripts/travis-run.sh | 29 ++++++++--------------------- 1 file changed, 8 insertions(+), 21 deletions(-) diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index f5065612fa..d60b1bfbba 100755 --- a/scripts/travis-run.sh +++ b/scripts/travis-run.sh @@ -32,36 +32,23 @@ then RANGE="${TRAVIS_COMMIT_RANGE/.../ }" 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 $RANGE" + else + # push on bulk: consider all recipes and do not lint (the bulk update)! + RANGE_ARG="" + SKIP_LINTING=true + echo "running bulk update" fi else # consider only recipes that (a) changed since the last build From 1692561abd03d87d55899d4a3eee36cd61bea583 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 11:24:37 +0200 Subject: [PATCH 006/114] Remove travis_wait, because bioconda-utils now prints a spinner for long-running tasks. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index c946bb6ff3..249bf901dc 100644 --- a/.travis.yml +++ b/.travis.yml @@ -11,7 +11,7 @@ services: install: scripts/travis-setup.sh -script: travis_wait 119 scripts/travis-run.sh +script: scripts/travis-run.sh env: global: From 0b52eb3708c5ed0a53e03bc04d1b45457e4c74e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 15:28:12 +0200 Subject: [PATCH 007/114] Remove phonenumbers (available in conda-forge). --- recipes/phonenumbers/build.sh | 4 ---- recipes/phonenumbers/meta.yaml | 35 ----------------------------------- 2 files changed, 39 deletions(-) delete mode 100644 recipes/phonenumbers/build.sh delete mode 100644 recipes/phonenumbers/meta.yaml diff --git a/recipes/phonenumbers/build.sh b/recipes/phonenumbers/build.sh deleted file mode 100644 index b161f631b7..0000000000 --- a/recipes/phonenumbers/build.sh +++ /dev/null @@ -1,4 +0,0 @@ -#!/bin/bash - -$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." - From 852369d7353745678d533f6f79ac5bccc5ca59e9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 17:44:15 +0200 Subject: [PATCH 008/114] Skip unnecessary tests in rpy2. --- recipes/pysam/0.9.1.4/build.sh | 15 -------------- recipes/pysam/0.9.1.4/meta.yaml | 44 ----------------------------------------- recipes/rpy2/meta.yaml | 19 ------------------ 3 files changed, 78 deletions(-) delete mode 100644 recipes/pysam/0.9.1.4/build.sh delete mode 100644 recipes/pysam/0.9.1.4/meta.yaml diff --git a/recipes/pysam/0.9.1.4/build.sh b/recipes/pysam/0.9.1.4/build.sh deleted file mode 100644 index 571d3c55db..0000000000 --- a/recipes/pysam/0.9.1.4/build.sh +++ /dev/null @@ -1,15 +0,0 @@ -#!/bin/bash -# Remove gcc statements that do not work on older compilers for CentOS5 -# support, from https://github.com/chapmanb/bcbio-conda/blob/master/pysam/build.sh -sed -i'' -e 's/"-Wno-error=declaration-after-statement",//g' setup.py -sed -i'' -e 's/"-Wno-error=declaration-after-statement"//g' setup.py -# linking htslib, see: -# http://pysam.readthedocs.org/en/latest/installation.html#external -# https://github.com/pysam-developers/pysam/blob/v0.9.0/setup.py#L79 -export CFLAGS="-I$PREFIX/include" -export CPPFLAGS="-I$PREFIX/include" -export LDFLAGS="-L$PREFIX/lib" - -export HTSLIB_LIBRARY_DIR=$PREFIX/lib -export HTSLIB_INCLUDE_DIR=$PREFIX/include -$PYTHON setup.py install diff --git a/recipes/pysam/0.9.1.4/meta.yaml b/recipes/pysam/0.9.1.4/meta.yaml deleted file mode 100644 index ca1167deaa..0000000000 --- a/recipes/pysam/0.9.1.4/meta.yaml +++ /dev/null @@ -1,44 +0,0 @@ -package: - name: pysam - version: 0.9.1.4 - -source: - fn: pysam-0.9.1.4.tar.gz - url: https://pypi.python.org/packages/de/03/02934438b204565bc5231f38a11da840a3c3e4b2beac8c8770d675770668/pysam-0.9.1.4.tar.gz - md5: a7e0e9cbc972618cde7aea54894067d6 - -build: - number: 1 - skip: False - -requirements: - build: - - gcc # [linux] - - llvm # [osx] - - htslib >=1.3 - - samtools >=1.3 - - bcftools >=1.3 - - cython - - python - - setuptools - - zlib - - curl - - run: - - libgcc # [linux] - - htslib >=1.3 - - samtools >=1.3 - - bcftools >=1.3 - - python - - zlib - - curl - -test: - - imports: - - pysam - -about: - home: https://github.com/pysam-developers/pysam - license: MIT - summary: "Pysam is a python module for reading and manipulating Samfiles. It is a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix." 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 From b8992f5686a3704d5af85e2993c78d7eb667da72 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 17:49:58 +0200 Subject: [PATCH 009/114] Add libgcc runtime dependency for scoop. --- recipes/scoop/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/scoop/meta.yaml b/recipes/scoop/meta.yaml index 727e24bc34..835864412b 100644 --- a/recipes/scoop/meta.yaml +++ b/recipes/scoop/meta.yaml @@ -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 From 59fd303fa541409466be53c5f42de11c15965c11 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 17:56:46 +0200 Subject: [PATCH 010/114] Add zlib to pytabix. Add gcc to python-igraph. --- recipes/pytabix/meta.yaml | 4 +++- recipes/python-igraph/meta.yaml | 4 +++- recipes/scoop/meta.yaml | 2 +- 3 files changed, 7 insertions(+), 3 deletions(-) diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index ac307d8d1f..23e00aeedc 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -2,7 +2,7 @@ package: name: pytabix version: 0.0.2 build: - number: 1 + number: 2 skip: True # [osx] source: fn: pytabix-e4a6f81.tar.gz @@ -12,10 +12,12 @@ requirements: build: - python - setuptools + - zlib run: - python - setuptools + - zlib test: imports: 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/scoop/meta.yaml b/recipes/scoop/meta.yaml index 835864412b..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: From 5d7da1d4b3ea3947637100a5a02b53d2d1e760a8 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 4 May 2017 18:00:37 +0200 Subject: [PATCH 011/114] Add bzip2 to libsbml. --- recipes/libsbml/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index fe1266a32b..73d1293ab1 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -11,7 +11,7 @@ source: - fix_path.patch build: - number: 0 + number: 1 skip: True # [osx] requirements: @@ -19,10 +19,12 @@ requirements: - python - libxml2 - gcc + - bzip2 run: - python - libgcc + - bzip2 test: imports: From 65347beca366d92e31bbce5a9bc4ae49d1eee72b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Thu, 4 May 2017 21:42:33 +0200 Subject: [PATCH 012/114] add libxml2 as dependency --- recipes/libsbml/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/libsbml/meta.yaml b/recipes/libsbml/meta.yaml index 73d1293ab1..bf2e0c4c3b 100644 --- a/recipes/libsbml/meta.yaml +++ b/recipes/libsbml/meta.yaml @@ -6,7 +6,6 @@ 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 @@ -20,11 +19,12 @@ requirements: - libxml2 - gcc - bzip2 - + - libxml2 run: - python - libgcc - bzip2 + - libxml2 test: imports: From bd4057b985a59379e94f4a8175eeab40277d4112 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 14:43:54 +0200 Subject: [PATCH 013/114] rebuild flowtools --- recipes/ig-flowtools/meta.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/recipes/ig-flowtools/meta.yaml b/recipes/ig-flowtools/meta.yaml index 6ab014deb7..1b6e798ea3 100644 --- a/recipes/ig-flowtools/meta.yaml +++ b/recipes/ig-flowtools/meta.yaml @@ -4,8 +4,11 @@ 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 requirements: build: @@ -15,7 +18,7 @@ requirements: - scipy - jinja2 - matplotlib - - r + - r-base - bioconductor-flowcore - bioconductor-flowcl - bioconductor-flowai @@ -28,7 +31,7 @@ requirements: - scipy - jinja2 - matplotlib - - r + - r-base - bioconductor-flowcore - bioconductor-flowcl - bioconductor-flowai From 6332d4beaba4ef933d1f81b93ca45928ec14c0ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 14:47:41 +0200 Subject: [PATCH 014/114] skip openbabel on py36 --- recipes/openbabel/2.4.1/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml index e3aca7b2b5..2c713ed3f0 100644 --- a/recipes/openbabel/2.4.1/meta.yaml +++ b/recipes/openbabel/2.4.1/meta.yaml @@ -14,6 +14,8 @@ source: - fix_babel_test_paths.diff build: + # https://bugs.archlinux.org/task/52409 + skip: true # [py36] number: 0 detect_binary_files_with_prefix: true From d1befbd7289be4477d0e8a4bf3cebfec7d8b314e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 16:03:38 +0200 Subject: [PATCH 015/114] try an other selector --- recipes/openbabel/2.4.1/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml index 2c713ed3f0..ae64220080 100644 --- a/recipes/openbabel/2.4.1/meta.yaml +++ b/recipes/openbabel/2.4.1/meta.yaml @@ -15,7 +15,7 @@ source: build: # https://bugs.archlinux.org/task/52409 - skip: true # [py36] + skip: true # [not py2k and not py35] number: 0 detect_binary_files_with_prefix: true From 329b3fba719a060a81bdb48c31f7afac0bd5dca3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 19:37:01 +0200 Subject: [PATCH 016/114] fix the builds a little bit, however this important package needs a some love --- recipes/hisat2/meta.yaml | 35 ++++++++++++++++++----------------- 1 file changed, 18 insertions(+), 17 deletions(-) diff --git a/recipes/hisat2/meta.yaml b/recipes/hisat2/meta.yaml index 73f72f11ae..ef681e1324 100644 --- a/recipes/hisat2/meta.yaml +++ b/recipes/hisat2/meta.yaml @@ -1,30 +1,31 @@ -build: - number: 1 - -about: - home: 'https://ccb.jhu.edu/software/hisat2/index.shtml' - license: GPLv3 - summary: graph-based alignment of next generation sequencing reads to a population of genomes - package: name: hisat2 version: 2.0.5 +source: + fn: hisat2-2.0.5-Linux_x86_64.zip #[linux] + url: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-Linux_x86_64.zip #[linux] + sha256: ca86d448475a7c9f9a2eb8915162ba83db3d1916eff03f431483d7558e4a4e75 #[linux] + + fn: hisat2-2.0.5-OSX_x86_64.zip #[osx] + url: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-OSX_x86_64.zip #[osx] + sha256: 35446d8f07c78ad3c755cb8994570469df1c27d9a88be6d1b9e2eefaf8b3d711 #[osx] + +build: + number: 2 + requirements: build: - python run: - python - - perl-threaded + - perl + - libgcc # [linux] test: commands: - hisat2 --version -source: - fn: hisat2-2.0.5-Linux_x86_64.zip #[linux] - url: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-Linux_x86_64.zip #[linux] - sha256: ca86d448475a7c9f9a2eb8915162ba83db3d1916eff03f431483d7558e4a4e75 #[linux] - - fn: hisat2-2.0.5-OSX_x86_64.zip #[osx] - url: ftp://ftp.ccb.jhu.edu/pub/infphilo/hisat2/downloads/hisat2-2.0.5-OSX_x86_64.zip #[osx] - sha256: 35446d8f07c78ad3c755cb8994570469df1c27d9a88be6d1b9e2eefaf8b3d711 #[osx] +about: + home: 'https://ccb.jhu.edu/software/hisat2/index.shtml' + license: GPLv3 + summary: graph-based alignment of next generation sequencing reads to a population of genomes From e3734e0ef39cc6c2a2f75f63e9228e4e3d4daa12 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Fri, 5 May 2017 23:54:33 +0200 Subject: [PATCH 017/114] fix URL ping @BioNinja, please don't remove tarballs :) --- recipes/gseapy/meta.yaml | 37 +++---------------------------------- 1 file changed, 3 insertions(+), 34 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 54110db1ad..07f1014071 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: 1 requirements: build: @@ -50,29 +35,13 @@ 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 From 4fd450c0ab9dee25b419f6d158e1c124702558f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 6 May 2017 05:59:53 +0200 Subject: [PATCH 018/114] Fix tests for mgf-formatter --- recipes/mgf-formatter/meta.yaml | 19 ++++++++----------- 1 file changed, 8 insertions(+), 11 deletions(-) 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 From 1f6b26633f3a2a6eb7a0f254a564b6dda4012b5c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 6 May 2017 14:31:18 +0200 Subject: [PATCH 019/114] That is scary, the checksum changed? --- recipes/nglview/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From ed477cd7be4a89a89010605405a7f93cd88edb0d Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Sat, 6 May 2017 18:59:48 +0200 Subject: [PATCH 020/114] removed in favor of https://github.com/conda-forge/python-magic-feedstock --- 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 ------------------- 4 files changed, 104 deletions(-) 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/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 From a2f0e9ca6272cd381e2b7d93e2bbf8d0d0fc1a0d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 6 May 2017 19:36:36 +0200 Subject: [PATCH 021/114] fix download path --- recipes/peakzilla/meta.yaml | 10 ++++------ 1 file changed, 4 insertions(+), 6 deletions(-) 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 From fd7071cce19ca0603419b3ae9ddcf7f949d73c99 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Sat, 6 May 2017 20:29:56 +0200 Subject: [PATCH 022/114] checksum incorrect :( --- recipes/ecmwfapi/meta.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) 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 From d0342b6fd547a524f128a219efdc333920b18b55 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 6 May 2017 21:02:11 +0200 Subject: [PATCH 023/114] Fix pybigwig test cases. --- recipes/pybigwig/0.1.11/meta.yaml | 9 ++------- recipes/pybigwig/meta.yaml | 12 ++++-------- 2 files changed, 6 insertions(+), 15 deletions(-) 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 From f89b45ad4e068e9407c81092e8201e00def40df2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 6 May 2017 21:38:59 +0200 Subject: [PATCH 024/114] Pin conda-build to a newer version. --- scripts/travis-setup.sh | 2 ++ 1 file changed, 2 insertions(+) diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh index ef16cb8f40..69f3156c73 100755 --- a/scripts/travis-setup.sh +++ b/scripts/travis-setup.sh @@ -38,5 +38,7 @@ export PATH=/anaconda/bin:$PATH $SCRIPT_DIR/../simulate-travis.py --set-channel-order $SCRIPT_DIR/../simulate-travis.py --install-requirements +conda install -y conda-build=2.1.10 + conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64 conda config --add channels file://anaconda/conda-bld From 4744ae8ee0967e8900ed4107310ac75e941b84ca Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sun, 7 May 2017 12:23:21 +0200 Subject: [PATCH 025/114] Revert conda pinning. --- scripts/travis-setup.sh | 2 -- 1 file changed, 2 deletions(-) diff --git a/scripts/travis-setup.sh b/scripts/travis-setup.sh index 69f3156c73..ef16cb8f40 100755 --- a/scripts/travis-setup.sh +++ b/scripts/travis-setup.sh @@ -38,7 +38,5 @@ export PATH=/anaconda/bin:$PATH $SCRIPT_DIR/../simulate-travis.py --set-channel-order $SCRIPT_DIR/../simulate-travis.py --install-requirements -conda install -y conda-build=2.1.10 - conda index /anaconda/conda-bld/linux-64 /anaconda/conda-bld/osx-64 conda config --add channels file://anaconda/conda-bld From 0b298fd0097d32156eb388658c4dc9314bfdcbfd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sun, 7 May 2017 17:10:03 +0200 Subject: [PATCH 026/114] Fix merge error. --- recipes/pytabix/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/pytabix/meta.yaml b/recipes/pytabix/meta.yaml index d7b51f2573..eb9b1b2a6d 100644 --- a/recipes/pytabix/meta.yaml +++ b/recipes/pytabix/meta.yaml @@ -16,7 +16,6 @@ requirements: - python - setuptools - zlib -<<<<<<< HEAD run: - python @@ -29,4 +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. From faff0c167889599ba7f2ee79387f81e322e615ae Mon Sep 17 00:00:00 2001 From: Ryan Dale Date: Sun, 7 May 2017 16:24:47 -0400 Subject: [PATCH 027/114] point to bioconda-utils:enable-build-ids branch --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 249bf901dc..10b3284b23 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_TAG=enable-build-ids - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info --mulled-test" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" From 4848ed62b94f72967ecc266abb40753e44ccac01 Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Mon, 8 May 2017 10:00:19 +0200 Subject: [PATCH 028/114] remove dev version from repository --- 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 ------- 6 files changed, 162 deletions(-) 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 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 From 2d936ad9a49dd26796ef2e0423384582a668e11f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Bj=C3=B6rn=20Gr=C3=BCning?= Date: Mon, 8 May 2017 12:06:36 +0200 Subject: [PATCH 029/114] add dependency on pyqt4 --- recipes/samsifter/meta.yaml | 32 +++----------------------------- 1 file changed, 3 insertions(+), 29 deletions(-) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 48b90437a8..6398fddac6 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: 1 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 @@ -47,13 +32,13 @@ requirements: - matplotlib >=1.3.1 - pandas >=0.14.1 - numpy >=1.6.1 - + - pyqt 4.11.* run: - python - matplotlib >=1.3.1 - pandas >=0.14.1 - numpy >=1.6.1 - + - pyqt 4.11.* test: # Python imports imports: @@ -85,18 +70,7 @@ 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 From 1b2b52fdcf80df6beaea3eb24afa6eae141e9d24 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 16:57:43 +0200 Subject: [PATCH 030/114] Fix nanosimh source URL. --- recipes/nanosimh/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/nanosimh/meta.yaml b/recipes/nanosimh/meta.yaml index 4e509dacaa..a34c36cb37 100644 --- a/recipes/nanosimh/meta.yaml +++ b/recipes/nanosimh/meta.yaml @@ -1,5 +1,4 @@ {% set version = "v1.0.1.8" %} -{% set sha256 = "879310f6b8a07ab3412a674fda7b82b6f379bcf8d7853125bda1418dda239b19" %} package: name: nanosimh @@ -7,8 +6,8 @@ package: source: fn: nanosim-{{ version }}.tar.gz - url: https://github.com/karel-brinda/NanoSimH/archive/{{ version }}.tar.gz - sha256: {{ sha256 }} + url: https://pypi.io/packages/source/n/nanosimh/nanosimh-{{ version }}.tar.gz + sha256: 24bc013a06765f4a8b720f165ce9fd970a9a719e58e748a2e72d7167b153083c build: number: 1 From 61c8e77d4901636b422447c1868034fa33481ab5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 17:08:01 +0200 Subject: [PATCH 031/114] Add gcc/libgcc to illuminate. --- recipes/illuminate/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) 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 From 7664085f30287b9ad08d8cdfd56e3876ea692a81 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 17:14:14 +0200 Subject: [PATCH 032/114] Removed old busco recipe because the source code is not available anymore. --- recipes/busco/1.2/build.sh | 5 ----- recipes/busco/1.2/meta.yaml | 33 --------------------------------- recipes/chanjo/meta.yaml | 12 ------------ 3 files changed, 50 deletions(-) delete mode 100644 recipes/busco/1.2/build.sh delete mode 100644 recipes/busco/1.2/meta.yaml 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/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 6ca08f775e..3ee1582e50 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -33,7 +33,6 @@ requirements: - python - setuptools - click - - setuptools - toolz - path.py - pyyaml @@ -41,9 +40,7 @@ requirements: run: - python - - setuptools - click - - setuptools - toolz - path.py - pyyaml @@ -68,17 +65,8 @@ 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 - about: home: http://www.chanjo.co/ license: MIT License From 475fcd5ac0ae2441b116c9e5bd1609aad4e31f7f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 17:22:20 +0200 Subject: [PATCH 033/114] Add automake. Update numpy to 1.12, because 1.10 is not built with Python 3.6 support. --- recipes/amos/meta.yaml | 1 + scripts/env_matrix.yml | 2 +- 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index 950d0f517f..ce5df208af 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -27,6 +27,7 @@ requirements: - zlib - boost - autoconf + - automake - blat - mummer - perl-threaded 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" From a9511e91e53da45343cc2f822f8971d8615107ff Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 17:24:11 +0200 Subject: [PATCH 034/114] Remove superfluous test case. --- recipes/joblib/meta.yaml | 3 --- 1 file changed, 3 deletions(-) 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/ From 62197f307dcbab6ca4cf9560673935ef53e4bf93 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 8 May 2017 17:26:00 +0200 Subject: [PATCH 035/114] Minor. --- recipes/samsifter/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 6398fddac6..af4d4d267e 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -39,6 +39,7 @@ requirements: - pandas >=0.14.1 - numpy >=1.6.1 - pyqt 4.11.* + test: # Python imports imports: From 97bda3b955607990c020d7d026584648604f1374 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 09:55:54 +0200 Subject: [PATCH 036/114] Fix intarna build string. --- recipes/intarna/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 From 6e8927644c06c7b435e0e4ca388965f70ca66148 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 09:56:38 +0200 Subject: [PATCH 037/114] Remove old prosic version. --- recipes/prosic/1.0/build.sh | 6 ------ recipes/prosic/1.0/meta.yaml | 38 -------------------------------------- 2 files changed, 44 deletions(-) delete mode 100644 recipes/prosic/1.0/build.sh delete mode 100644 recipes/prosic/1.0/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. From 3150a62d46f0842a66300deb131eb3a4c79611c9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 10:43:40 +0200 Subject: [PATCH 038/114] Fix scipy dependency of igdiscover and cosmetic changes. --- recipes/igdiscover/meta.yaml | 17 ++++++++++++----- 1 file changed, 12 insertions(+), 5 deletions(-) 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 From fa48dbe3036e4a5ae0e49cb7785df8f7d308002a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 10:49:38 +0200 Subject: [PATCH 039/114] Add ncurses dependency. --- recipes/tabview/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) 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: From 047b4ce8b8b69fb55ca539f0695bf189d9840485 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 10:52:03 +0200 Subject: [PATCH 040/114] Add pyqt. --- recipes/yahmm/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index a7eff8dd59..4db1a0bfb7 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -18,6 +18,7 @@ requirements: - scipy >=0.13.3 - networkx >=1.8.1 - matplotlib >=1.3.1 + - pyqt run: - python @@ -26,6 +27,7 @@ requirements: - scipy >=0.13.3 - networkx >=1.8.1 - matplotlib >=1.3.1 + - pyqt test: imports: From 087f7b62add9ae156832f9fd2e84577f64ec0ba9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 11:16:46 +0200 Subject: [PATCH 041/114] Skip zeroc-ice because of segmentation fault. --- recipes/zeroc-ice/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/zeroc-ice/meta.yaml b/recipes/zeroc-ice/meta.yaml index 93a7c33019..fa6de32f6a 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 py27 and not py34 and not py35] requirements: build: From edae01b2666f3e7ea0ddf53ce7d5e4ed73168340 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 13:28:09 +0200 Subject: [PATCH 042/114] Try to fix selector. --- recipes/zeroc-ice/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/zeroc-ice/meta.yaml b/recipes/zeroc-ice/meta.yaml index fa6de32f6a..f08d0b6450 100644 --- a/recipes/zeroc-ice/meta.yaml +++ b/recipes/zeroc-ice/meta.yaml @@ -10,7 +10,7 @@ source: build: number: 0 # segmentation fault with Python 3.6 - skip: True # [not py27 and not py34 and not py35] + skip: True # [not py2k and not py35] requirements: build: From 7fd6b152865702391ddd7038fe7c1b37ccb6e61f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 13:36:10 +0200 Subject: [PATCH 043/114] Add pyqt4 dependency. --- recipes/gseapy/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 07f1014071..a6db9155a8 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -33,6 +33,7 @@ requirements: - requests - lxml - html5lib + - pyqt ==4.* test: imports: From 65bb37ba5daa5bdfd0afba1b5ac5d638146069e5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 13:45:11 +0200 Subject: [PATCH 044/114] Remove old version of bx-python. --- recipes/bx-python/0.7.2/build.sh | 3 -- recipes/bx-python/0.7.2/meta.yaml | 58 --------------------------------------- recipes/gseapy/meta.yaml | 2 +- recipes/validators/meta.yaml | 2 +- 4 files changed, 2 insertions(+), 63 deletions(-) delete mode 100644 recipes/bx-python/0.7.2/build.sh delete mode 100644 recipes/bx-python/0.7.2/meta.yaml 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/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index a6db9155a8..4d7aefd0e0 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -10,7 +10,7 @@ source: build: entry_points: - gseapy = gseapy.__main__:main - number: 1 + number: 2 requirements: build: 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.' From 92d9230e59bbfd9b78e70246efbfd09191b5c0a0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 13:50:58 +0200 Subject: [PATCH 045/114] Skip python 3.6 --- recipes/biopython/1.65/build.sh | 3 - recipes/biopython/1.65/meta.yaml | 113 ---------------------------------- recipes/sevenbridges-python/meta.yaml | 2 + recipes/spades/meta.yaml | 1 + 4 files changed, 3 insertions(+), 116 deletions(-) delete mode 100644 recipes/biopython/1.65/build.sh delete mode 100644 recipes/biopython/1.65/meta.yaml 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/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/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: From dcd17977a0c485a7a31f11db72e9bc4748bbd111 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 13:52:12 +0200 Subject: [PATCH 046/114] Skip Python 3.6 because it is unsupported. --- recipes/spades/3.9.0/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 11f8f256264c592c0a240387592c9663769e5caa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 16:37:06 +0200 Subject: [PATCH 047/114] Use bioconda-utils master again (after the merge). Suppress warnings in intarna build. --- .travis.yml | 2 +- recipes/intarna/build.sh | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index 10b3284b23..249bf901dc 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=enable-build-ids + - BIOCONDA_UTILS_TAG=master - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info --mulled-test" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index 8c34f67c6b..8a41b18991 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; From f2ad9937fc97785b2854b2072e46e486912604d3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Tue, 9 May 2017 17:33:09 +0200 Subject: [PATCH 048/114] Remove llvm dependency of whatshap. --- recipes/whatshap/meta.yaml | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index dd7ef75e2a..5daf20f660 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -15,8 +15,7 @@ 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 - pysam <0.9.0 @@ -24,7 +23,7 @@ requirements: - pyfaidx - xopen run: - - libgcc # [not osx] + - libgcc - python - setuptools ==23 - pysam <0.9.0 From dea26c52fcda8b0ecd987d917394f4a5b1cdc541 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 15:48:56 +0200 Subject: [PATCH 049/114] 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. --- recipes/bcbio-nextgen/meta.yaml | 5 +++++ recipes/bcl2fastq-nextseq/meta.yaml | 5 +++++ recipes/biom-format/2.1.5/meta.yaml | 14 +++++------- recipes/chanjo/meta.yaml | 20 +++++------------ recipes/cooler/meta.yaml | 5 ++++- recipes/crimson/meta.yaml | 5 +++++ recipes/dr-disco/meta.yaml | 8 +++++-- recipes/dr-disco/v0.3.4/meta.yaml | 7 +++++- recipes/extract_genome_region/meta.yaml | 31 ++++---------------------- recipes/fsnviz/0.1.0/meta.yaml | 5 +++++ recipes/fsnviz/meta.yaml | 5 +++++ recipes/genomebaser/meta.yaml | 38 +++++--------------------------- recipes/moca/meta.yaml | 5 +++++ recipes/multiqc/meta.yaml | 10 ++++----- recipes/onto2nx/meta.yaml | 5 +++++ recipes/ped_parser/meta.yaml | 39 ++++----------------------------- recipes/phizz/meta.yaml | 33 ++++------------------------ recipes/planemo/0.23.0/meta.yaml | 5 +++++ recipes/planemo/0.34.1/meta.yaml | 9 ++++---- recipes/planemo/meta.yaml | 6 ++++- recipes/platypus-conquistador/meta.yaml | 37 ++++--------------------------- recipes/pybel/meta.yaml | 8 +++++-- recipes/query_phenomizer/meta.yaml | 32 ++++----------------------- recipes/rapclust/meta.yaml | 4 ++++ recipes/segmentation-fold/meta.yaml | 11 ++++++---- recipes/swga/meta.yaml | 5 +++++ recipes/umis/meta.yaml | 5 +++++ 27 files changed, 133 insertions(+), 229 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index d3a929632c..0e2c6741c6 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -96,3 +96,8 @@ about: home: https://github.com/chapmanb/bcbio-nextgen license: MIT summary: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index 8ddba1e96f..926c4d6b7e 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -36,3 +36,8 @@ about: home: https://github.com/brwnj/bcl2fastq license: MIT summary: NextSeq .bcl Conversion + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 49551c505a..75407ff8f7 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -9,18 +9,9 @@ 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 requirements: @@ -59,3 +50,8 @@ about: home: http://www.biom-format.org license: BSD License summary: 'Biological Observation Matrix (BIOM) format' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 3ee1582e50..30fc1e4bce 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -11,21 +11,10 @@ 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 requirements: @@ -72,6 +61,7 @@ about: license: MIT License summary: 'Coverage analysis tool for clinical sequencing' -# See -# http://docs.continuum.io/conda/build.html for -# more information about meta.yaml +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index 780dd905eb..f46a683808 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -9,7 +9,6 @@ source: build: number: 0 - #noarch: python # not supported by bioconda yet entry_points: - cooler = cooler.cli:cli @@ -49,3 +48,7 @@ about: summary: 'Sparse binary format for genomic interaction matrices' license_family: BSD +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 50b6c90d91..52d17f8bb8 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -37,3 +37,8 @@ about: license: BSD License summary: 'Bioinformatics tool outputs converter to JSON or YAML.' license_family: BSD + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/dr-disco/meta.yaml b/recipes/dr-disco/meta.yaml index ca3cd80d42..c2a070519a 100644 --- a/recipes/dr-disco/meta.yaml +++ b/recipes/dr-disco/meta.yaml @@ -30,14 +30,13 @@ requirements: - fuma ==3.0.5 test: - # Python imports imports: - drdisco commands: - dr-disco --help - 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 @@ -46,3 +45,8 @@ about: home: https://github.com/yhoogstrate/dr-disco/ license: GNU General Public License v3 or later (GPLv3+) summary: 'Dr. Disco: fusion gene and genomic breakpoint detection in random hexamer RNA-seq data' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/dr-disco/v0.3.4/meta.yaml b/recipes/dr-disco/v0.3.4/meta.yaml index 03f054510b..1b8577a7bc 100644 --- a/recipes/dr-disco/v0.3.4/meta.yaml +++ b/recipes/dr-disco/v0.3.4/meta.yaml @@ -35,7 +35,7 @@ test: commands: - dr-disco --help - 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 @@ -44,3 +44,8 @@ about: home: https://github.com/yhoogstrate/dr-disco/ license: GNU General Public License v3 or later (GPLv3+) summary: 'Dr. Disco: fusion gene genomic breakpoint detection in random hexamer RNA-seq data' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index a25562060d..3efb7a31f0 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -6,23 +6,10 @@ 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 requirements: @@ -38,25 +25,15 @@ 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 - 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml index d158a2ec23..6af0d1334e 100644 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ b/recipes/fsnviz/0.1.0/meta.yaml @@ -34,3 +34,8 @@ about: license: BSD summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' license_family: BSD + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index 4d8eb673d2..2186a98648 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -36,3 +36,8 @@ about: license: BSD summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' license_family: BSD + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/genomebaser/meta.yaml b/recipes/genomebaser/meta.yaml index e230047283..6011ebb425 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 +24,15 @@ 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index 4b383bcc89..450a2e95b8 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -131,3 +131,8 @@ about: license: ISC License (ISCL) summary: 'Tool for motif conservation analysis' license_family: Public-Domain + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index f7e9b69c25..c1e4e6dbba 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -8,12 +8,8 @@ source: md5: 273c00ebd0f81025101c6b59b1cc1f77 build: - number: 3 + number: 4 preserve_egg_dir: True - # python 3 failing on - # FileNotFoundError: [Errno 2] No such file or directory: 'locale' - # https://travis-ci.org/bioconda/bioconda-recipes/jobs/191266605 - skip: true # [not py27] requirements: build: @@ -86,3 +82,7 @@ about: summary: 'Create aggregate bioinformatics analysis reports across many samples and tools' license_family: GPL3 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/onto2nx/meta.yaml b/recipes/onto2nx/meta.yaml index 76b730002d..f8e7daa93c 100644 --- a/recipes/onto2nx/meta.yaml +++ b/recipes/onto2nx/meta.yaml @@ -46,3 +46,8 @@ about: home: https://github.com/cthoyt/onto2nx license: GNU General Public License v3 or later (GPLv3+) summary: 'A package for parsing ontologies into NetworkX graphs' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index a2e26cfd79..8d53b65127 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -10,25 +10,6 @@ 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 +24,15 @@ 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 - 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/phizz/meta.yaml b/recipes/phizz/meta.yaml index 77abc47b40..d6af9d2f7e 100644 --- a/recipes/phizz/meta.yaml +++ b/recipes/phizz/meta.yaml @@ -6,27 +6,12 @@ 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 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 - requirements: build: - python @@ -41,30 +26,20 @@ 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 - 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/planemo/0.23.0/meta.yaml b/recipes/planemo/0.23.0/meta.yaml index f16f99cee3..6eec1b6ace 100644 --- a/recipes/planemo/0.23.0/meta.yaml +++ b/recipes/planemo/0.23.0/meta.yaml @@ -59,3 +59,8 @@ about: home: https://github.com/galaxyproject/planemo license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/planemo/0.34.1/meta.yaml b/recipes/planemo/0.34.1/meta.yaml index 0045e153b8..1ea69a0d94 100644 --- a/recipes/planemo/0.34.1/meta.yaml +++ b/recipes/planemo/0.34.1/meta.yaml @@ -12,7 +12,6 @@ build: 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 @@ -59,9 +57,7 @@ test: - planemo.shed2tap - planemo.test - planemo.xml - commands: - - planemo --help about: @@ -69,3 +65,8 @@ about: license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' license_family: Apache + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index f14bf133b3..f20c8f2ea9 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -42,7 +42,6 @@ requirements: - aenum test: - # Python imports imports: - planemo - planemo.commands @@ -69,3 +68,8 @@ about: license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' license_family: Apache + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index 7ad81a71ed..aa11e0fae7 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 requirements: build: @@ -39,27 +22,15 @@ 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index 4f819cff5f..e3801bcbf4 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -46,10 +46,14 @@ 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] + - pybel --help about: home: https://github.com/pybel/pybel license: Apache Software License summary: 'Parsing, validation, and analysis of BEL graphs' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index 421b93a214..f4d3524031 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -6,26 +6,11 @@ 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 - # 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 +32,14 @@ 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 - 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 +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index c0dd2e3aeb..0547b3a17e 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -42,3 +42,7 @@ about: summary: 'Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes' license_family: BSD +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index 27f645232f..179f150a14 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 @@ -44,3 +42,8 @@ test: commands: - segmentation-fold --version - segmentation-fold-utils --help + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index eb22001fdb..ca5691dbd6 100644 --- a/recipes/swga/meta.yaml +++ b/recipes/swga/meta.yaml @@ -52,3 +52,8 @@ about: home: https://github.com/eclarke/swga license: GPLv3 summary: 'Select primer sets for selective whole genome amplification (SWGA)' + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index 0c99924f6c..b6901968c1 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -42,3 +42,8 @@ about: home: https://github.com/vals/umis license: MIT summary: Tools for processing UMI RNA-tag data + +extra: + container: + # click relies on unicode support, which is not present in the default busybox image + base: debian:latest From 7a84980a34a8518c12a3761fa053e7b8479dc318 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 17:19:09 +0200 Subject: [PATCH 050/114] Fixes and blacklisting. Temporarily use a fixed branch of bioconda-utils. --- .travis.yml | 2 +- recipes/fwdpy/meta.yaml | 2 ++ recipes/last/meta.yaml | 17 ++++++++++------- recipes/musicc/meta.yaml | 4 ++++ 4 files changed, 17 insertions(+), 8 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9566ca482f..e3b0618e8e 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_TAG=allow-multiple-recipes - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/recipes/fwdpy/meta.yaml b/recipes/fwdpy/meta.yaml index 60eb6d95e5..ff45f81a78 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 on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L416 + skip: true # [osx] requirements: build: diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index dc2aec9128..09cc4a3051 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 &> /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" diff --git a/recipes/musicc/meta.yaml b/recipes/musicc/meta.yaml index 3b3577f327..2e3d2cca40 100644 --- a/recipes/musicc/meta.yaml +++ b/recipes/musicc/meta.yaml @@ -7,6 +7,10 @@ source: url: https://pypi.python.org/packages/source/M/MUSiCC/MUSiCC-1.0.1.tar.gz md5: 270b23e925c6673643af8610d63070d4 +build: + # fails on osx with an encoding error: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L565 + skip: true # [osx and not py35 and not py27] + requirements: build: - python From b2b5b83f91b262e90e57415fa40026f9e4003091 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 17:35:15 +0200 Subject: [PATCH 051/114] Fix merge conflict in openbabel recipe. --- recipes/openbabel/2.4.1/meta.yaml | 4 ---- 1 file changed, 4 deletions(-) diff --git a/recipes/openbabel/2.4.1/meta.yaml b/recipes/openbabel/2.4.1/meta.yaml index 15d8571cdf..e20a0f6051 100644 --- a/recipes/openbabel/2.4.1/meta.yaml +++ b/recipes/openbabel/2.4.1/meta.yaml @@ -16,13 +16,9 @@ source: - 372.patch build: -<<<<<<< HEAD # https://bugs.archlinux.org/task/52409 skip: true # [not py2k and not py35] - number: 0 -======= number: 1 ->>>>>>> master detect_binary_files_with_prefix: true requirements: From 2a32a798aa929edf0d6ddc5c3c47efabf574d739 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 18:21:31 +0200 Subject: [PATCH 052/114] Skip py36 because pysamstats relies on old pysam which does not build on py36. --- recipes/pysamstats/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From 678c5a7ca163018671bc0bbbb2264568a3735d02 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 18:26:47 +0200 Subject: [PATCH 053/114] Use debian container for ggplot. --- recipes/ggplot/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/ggplot/meta.yaml b/recipes/ggplot/meta.yaml index 7d7f98b554..a8bde25788 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 + base: debian:latest From 6115564f529bb8bdf73937a64c1676a33f432a38 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 18:55:53 +0200 Subject: [PATCH 054/114] Revert skipping because of encoding errors. These should be fixed by bioconda/bioconda-utils#116. --- recipes/biomaj/meta.yaml | 1 - recipes/musicc/meta.yaml | 4 ---- 2 files changed, 5 deletions(-) diff --git a/recipes/biomaj/meta.yaml b/recipes/biomaj/meta.yaml index 4ccf6a07d5..4c3e08e8bc 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: Public-Domain summary: Automates the update cycle and the supervision of the locally mirrored databank repository diff --git a/recipes/musicc/meta.yaml b/recipes/musicc/meta.yaml index 2e3d2cca40..3b3577f327 100644 --- a/recipes/musicc/meta.yaml +++ b/recipes/musicc/meta.yaml @@ -7,10 +7,6 @@ source: url: https://pypi.python.org/packages/source/M/MUSiCC/MUSiCC-1.0.1.tar.gz md5: 270b23e925c6673643af8610d63070d4 -build: - # fails on osx with an encoding error: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L565 - skip: true # [osx and not py35 and not py27] - requirements: build: - python From 00c479f32e1abaac78af5605bf0290a61a2261a2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 18:56:55 +0200 Subject: [PATCH 055/114] Temporarily use fixed branch of bioconda-utils. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index e3b0618e8e..30ddae6ee4 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=allow-multiple-recipes + - BIOCONDA_UTILS_TAG=fix-mulled-error-handling - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" From 87e97383d0ab7a78f3f4df29936c1d8785e6a148 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:07:22 +0200 Subject: [PATCH 056/114] Bioconda-utils fix has been merged, use master again. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index 30ddae6ee4..9566ca482f 100644 --- a/.travis.yml +++ b/.travis.yml @@ -17,7 +17,7 @@ env: global: - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=fix-mulled-error-handling + - BIOCONDA_UTILS_TAG=master - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" From 8442015f7f1ffcd42bffdc2a4b3d84fd1555a5fd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:08:26 +0200 Subject: [PATCH 057/114] Add missing library. --- recipes/samsifter/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index af4d4d267e..a399477c0c 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -39,6 +39,8 @@ requirements: - pandas >=0.14.1 - numpy >=1.6.1 - pyqt 4.11.* + # workaround for missing dependency of pandas + - libgcc test: # Python imports From 236c1c54297c89f33a58bd3b8ede1f4ade6a493d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:10:44 +0200 Subject: [PATCH 058/114] Skip whole section outside of osx. --- recipes/python-bioext/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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: From a02369dccf1e9fe8801b8d16af7ba11c2e2dc9d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:13:13 +0200 Subject: [PATCH 059/114] Add missing dependency. --- recipes/biokit/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index d340701bec..c5bfea7ff4 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -12,7 +12,7 @@ source: build: skip: True # [py34] - number: 2 + number: 3 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda # Same with easydev @@ -25,6 +25,7 @@ requirements: - colormap - scipy - xmltodict + - numpydoc run: - python @@ -34,6 +35,7 @@ requirements: - colormap - scipy - xmltodict + - numpydoc #- matplotlib #- libgcc # [not osx] #- glib From c3df0d29e5eeb91a672e00c8d7f29624fa2eb3c3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:14:53 +0200 Subject: [PATCH 060/114] Show test results of last. --- recipes/last/490/meta.yaml | 12 ++++++------ recipes/last/638/meta.yaml | 17 +++++++++++------ 2 files changed, 17 insertions(+), 12 deletions(-) diff --git a/recipes/last/490/meta.yaml b/recipes/last/490/meta.yaml index 93f2c365d1..f752f1b8ed 100644 --- a/recipes/last/490/meta.yaml +++ b/recipes/last/490/meta.yaml @@ -21,9 +21,9 @@ requirements: - python 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..e54dc44df2 100644 --- a/recipes/last/638/meta.yaml +++ b/recipes/last/638/meta.yaml @@ -2,27 +2,32 @@ 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 run: - python + 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" From 7b1377b1f1ab438ffbc78c6db43d16ae0c61b203 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:17:20 +0200 Subject: [PATCH 061/114] Fix hmmlearn dependencies. --- recipes/hmmlearn/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) 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: From bb5ac0cec1993005fe9a3f8a9b2e43cffc9f4275 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:23:48 +0200 Subject: [PATCH 062/114] Relax setuptools dependency. --- recipes/whatshap/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 5daf20f660..1a7db62e6a 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -17,7 +17,7 @@ requirements: build: - gcc - python - - setuptools ==23 + - setuptools - pysam <0.9.0 - pyvcf - pyfaidx @@ -25,7 +25,7 @@ requirements: run: - libgcc - python - - setuptools ==23 + - setuptools - pysam <0.9.0 - pyvcf - pyfaidx From 55776fcfecc7551e463fe30a6c782746f21b69e3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:25:10 +0200 Subject: [PATCH 063/114] Update viral-ngs dependency in order to avoid conflict with py36. --- recipes/viral-ngs/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/viral-ngs/meta.yaml b/recipes/viral-ngs/meta.yaml index 52fee56147..21f811f94d 100644 --- a/recipes/viral-ngs/meta.yaml +++ b/recipes/viral-ngs/meta.yaml @@ -13,7 +13,7 @@ source: md5: 9c91ae07e5c818d9ab565ac82d473824 build: - number: 0 + number: 1 rpaths: - lib/ - lib// @@ -28,7 +28,7 @@ requirements: - pytest - pysam ==0.9.1 - pyyaml >=3.11 - - boto ==2.38.0 + - boto ==2.46.1 - snakemake >=3.9.0 # [py3k] - blast ==2.2.31 - bmtagger ==3.101 @@ -67,7 +67,7 @@ requirements: - pytest - pysam ==0.9.1 - pyyaml >=3.11 - - boto ==2.38.0 + - boto ==2.46.1 - snakemake >=3.9.0 # [py3k] - blast ==2.2.31 - bmtagger ==3.101 From 6d5964048d1a247773ec26fda5d568e8f82ef9a4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:29:30 +0200 Subject: [PATCH 064/114] Fix fsnviz dependency. --- recipes/fsnviz/0.1.0/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml index 6af0d1334e..7f991adcc2 100644 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ b/recipes/fsnviz/0.1.0/meta.yaml @@ -17,14 +17,14 @@ 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 From 7047c3b93c93b87d3a8e092c85e043cd4d538003 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:32:47 +0200 Subject: [PATCH 065/114] New garnet version. The old one was removed from pypi!! --- recipes/garnet/meta.yaml | 45 +++++++-------------------------------------- 1 file changed, 7 insertions(+), 38 deletions(-) diff --git a/recipes/garnet/meta.yaml b/recipes/garnet/meta.yaml index c2abda5032..62f17b5d57 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 From 6924ce6f5452700d412177f292b6fc103d1095dc Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:35:19 +0200 Subject: [PATCH 066/114] Disable make test for intarna. --- recipes/intarna/build.sh | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/intarna/build.sh b/recipes/intarna/build.sh index 8a41b18991..db9d6cca96 100644 --- a/recipes/intarna/build.sh +++ b/recipes/intarna/build.sh @@ -28,6 +28,5 @@ export LDFLAGS=${LDFLAGS} --disable-multithreading \ ${extra_config_options} \ -make -j ${CPU_COUNT} && \ -make tests && \ +make make install From b46da7560093fec5863cd41f3e87efd406b90add Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:38:56 +0200 Subject: [PATCH 067/114] Add pyqt as build requirement. --- recipes/gseapy/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 4d7aefd0e0..a9a9900635 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -23,6 +23,7 @@ requirements: - requests - lxml - html5lib + - pyqt ==4.* run: - python From 481421cba460284acb4bd7f5499b351a29e7d460 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:40:43 +0200 Subject: [PATCH 068/114] Relax bowtie dependency. --- recipes/transabyss/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 From fecb972d93c8eb5a21738ef0ac18155a0950959f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 24 May 2017 23:44:09 +0200 Subject: [PATCH 069/114] Skip osx. --- recipes/pybel/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index e3801bcbf4..bf211f2111 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -11,6 +11,8 @@ build: entry_points: - pybel = pybel.cli:main number: 0 + # tests fail on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235726973#L3656 + skip: true # [osx] requirements: build: From 9f5336d5f13c5040eb56d5a6f7359ed63b126515 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:23:16 +0200 Subject: [PATCH 070/114] Pyqt is not a dependency of gseapy. --- recipes/gseapy/meta.yaml | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index a9a9900635..1151feb922 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -10,7 +10,7 @@ source: build: entry_points: - gseapy = gseapy.__main__:main - number: 2 + number: 3 requirements: build: @@ -23,7 +23,6 @@ requirements: - requests - lxml - html5lib - - pyqt ==4.* run: - python @@ -34,7 +33,6 @@ requirements: - requests - lxml - html5lib - - pyqt ==4.* test: imports: From 4204350147fafde5cea9c64ce22189f0ed386aaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:26:57 +0200 Subject: [PATCH 071/114] Skip viral-ngs for py36. --- recipes/viral-ngs/meta.yaml | 1 + 1 file changed, 1 insertion(+) diff --git a/recipes/viral-ngs/meta.yaml b/recipes/viral-ngs/meta.yaml index 21f811f94d..14dc7bf8d0 100644 --- a/recipes/viral-ngs/meta.yaml +++ b/recipes/viral-ngs/meta.yaml @@ -17,6 +17,7 @@ build: rpaths: - lib/ - lib// + skip: true # [not py27 and not py35] requirements: build: From 1e6615553c02b95a30f79272483fbd429cdfabb2 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:28:51 +0200 Subject: [PATCH 072/114] Relax matplotlib pinning for qiime. --- recipes/qiime/1.9.1/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 72e4cb4ff3..96b37f0162 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -27,7 +27,7 @@ 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 <2.0.0 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 @@ -47,7 +47,7 @@ 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 <2.0.0 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 From dbc2f7a29be4a8f6264ad18144aecda3be01a82b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:33:20 +0200 Subject: [PATCH 073/114] Fix url. --- recipes/garnet/meta.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/recipes/garnet/meta.yaml b/recipes/garnet/meta.yaml index 62f17b5d57..0af66916ec 100644 --- a/recipes/garnet/meta.yaml +++ b/recipes/garnet/meta.yaml @@ -6,7 +6,7 @@ package: source: fn: GarNet-{{ version }}.tar.gz - url: https://pypi.io/packages/source/g/garnet/garnet-{{ version }}.tar.gz + url: https://pypi.io/packages/source/g/garnet/GarNet-{{ version }}.tar.gz md5: 53eaec2493856d8324ee1c630ce323dd build: From 3287601c64d4a81aaa38d04cad5eea4226f6c8bd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:35:44 +0200 Subject: [PATCH 074/114] Skip ig-flowtools until R dependencies have been updated. --- recipes/ig-flowtools/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/ig-flowtools/meta.yaml b/recipes/ig-flowtools/meta.yaml index 1b6e798ea3..e7b233c1b1 100644 --- a/recipes/ig-flowtools/meta.yaml +++ b/recipes/ig-flowtools/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 1 + # TODO reenable once R packages have been updated/rebuild with conda-build > 2.0 + skip: true requirements: build: From c26fa2aa369886f48f4fe5155d83abe183210f9f Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:47:56 +0200 Subject: [PATCH 075/114] Omit futures in python 3k. Add missing dependency. --- recipes/biokit/meta.yaml | 7 +++---- recipes/cnvkit/meta.yaml | 2 +- 2 files changed, 4 insertions(+), 5 deletions(-) diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index c5bfea7ff4..4c73ad9b0a 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: 3 + number: 4 # Set xmltodict >= 0.10.2 to use conda-forge version instead of bioconda # Same with easydev @@ -26,6 +23,7 @@ requirements: - scipy - xmltodict - numpydoc + - bioservices run: - python @@ -36,6 +34,7 @@ requirements: - scipy - xmltodict - numpydoc + - bioservices #- matplotlib #- libgcc # [not osx] #- glib diff --git a/recipes/cnvkit/meta.yaml b/recipes/cnvkit/meta.yaml index 7e0a7a04f2..d9a23d40e6 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -30,7 +30,7 @@ requirements: - r-cghflasso - pyfaidx >=0.4.7 - future >=0.15.2 - - futures >=3.0 + - futures >=3.0 # [py27] test: imports: From 50340a699bcb3c2a30f150fe89b753a04a79b7a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:51:40 +0200 Subject: [PATCH 076/114] Try simplifying osx setup for whatshap. The stdlib argument did not work anymore. --- recipes/whatshap/meta.yaml | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/recipes/whatshap/meta.yaml b/recipes/whatshap/meta.yaml index 1a7db62e6a..ef041d6356 100644 --- a/recipes/whatshap/meta.yaml +++ b/recipes/whatshap/meta.yaml @@ -33,8 +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: From 5c5a791d7efd3d2f3ea0f74f97ebb4ccb7d654d5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:53:38 +0200 Subject: [PATCH 077/114] Relax snakemake dependency. --- recipes/hlama/meta.yaml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/recipes/hlama/meta.yaml b/recipes/hlama/meta.yaml index 565f53109c..0a3b693a09 100644 --- a/recipes/hlama/meta.yaml +++ b/recipes/hlama/meta.yaml @@ -3,7 +3,7 @@ package: version: "0.3.1" build: - number: 0 + number: 1 skip: True # [py27 or osx] entry_points: - hlama = hlama.app:main @@ -17,10 +17,10 @@ requirements: build: - python - setuptools - - snakemake ==3.7.1 + - snakemake >=3.7.1 run: - python - - snakemake ==3.7.1 + - snakemake >=3.7.1 - optitype >=1.2 test: From d465239f2f3d40d999b7e208f073441cbd4d32c7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 11:54:58 +0200 Subject: [PATCH 078/114] Use debian container for samsifter because it depends on X11 libs. --- recipes/samsifter/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index a399477c0c..308a5d3028 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -77,3 +77,7 @@ about: home: http://pypi.python.org/pypi/SamSifter/ license: GNU General Public License v3 (GPLv3) summary: 'Workflow editor for metagenomic analysis' + +extra: + container: + base: "debian:latest" From b20c84985833792a63c850cbfbeb7e54096107c0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:19:13 +0200 Subject: [PATCH 079/114] Skip rapclust. --- recipes/rapclust/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index 0547b3a17e..ff39580d17 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -9,6 +9,8 @@ source: build: number: 0 + # coloredlogs is not py36 compatible yet + skip: true # [not py27 and not py35] requirements: build: From 27f103ead1a29f40a8e48a803df56aab8a384406 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:20:57 +0200 Subject: [PATCH 080/114] Fix matplotlib version. --- recipes/qiime/1.9.1/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 96b37f0162..307f885c8a 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -27,7 +27,7 @@ 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 <2.0.0 + - matplotlib <=1.9 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 @@ -47,7 +47,7 @@ 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 <2.0.0 + - matplotlib <=1.9 - burrito-fillings >=0.1.1,<0.2.0 - pandas >=0.13.1 - burrito >=0.9.1,<1.0.0 From d6b9b199804c3187e9160437762272361d2279ed Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:35:42 +0200 Subject: [PATCH 081/114] Skip chanjo --- recipes/chanjo/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 30fc1e4bce..3079b4534c 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -15,7 +15,10 @@ build: preserve_egg_dir: True entry_points: - chanjo = chanjo.__main__:root_command - 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: From c0eb89757ef4b5873daa18f5681c94ab910103dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:37:31 +0200 Subject: [PATCH 082/114] Fix perl dependency. --- recipes/amos/meta.yaml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index ce5df208af..bc7d467184 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -30,7 +30,7 @@ requirements: - automake - blat - mummer - - perl-threaded + - perl - perl-statistics-descriptive - perl-xml-parser - perl-dbi @@ -39,7 +39,7 @@ requirements: run: - mummer - - perl-threaded + - perl - perl-statistics-descriptive - perl-xml-parser - perl-dbi From b393a5bdac36afb58c9527b1cc3a1c16513b0f6c Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:40:24 +0200 Subject: [PATCH 083/114] Fix last dependencies. --- recipes/last/490/meta.yaml | 9 ++++++++- recipes/last/638/meta.yaml | 2 ++ recipes/last/meta.yaml | 12 ++++++------ recipes/yahmm/meta.yaml | 4 ++++ 4 files changed, 20 insertions(+), 7 deletions(-) diff --git a/recipes/last/490/meta.yaml b/recipes/last/490/meta.yaml index f752f1b8ed..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 @@ -12,13 +14,18 @@ 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" diff --git a/recipes/last/638/meta.yaml b/recipes/last/638/meta.yaml index e54dc44df2..d732d4fac6 100644 --- a/recipes/last/638/meta.yaml +++ b/recipes/last/638/meta.yaml @@ -20,8 +20,10 @@ build: requirements: build: - python + - gcc run: - python + - libgcc test: commands: diff --git a/recipes/last/meta.yaml b/recipes/last/meta.yaml index 09cc4a3051..a50e1c5f67 100644 --- a/recipes/last/meta.yaml +++ b/recipes/last/meta.yaml @@ -29,9 +29,9 @@ requirements: 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/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index 4db1a0bfb7..bde980eae6 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -37,3 +37,7 @@ 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: + base: "debian:latest" From 6019f6bec5863355852a905df54558c92db134aa Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 13:42:23 +0200 Subject: [PATCH 084/114] Use extended container for fitter. --- recipes/fitter/meta.yaml | 23 +++-------------------- 1 file changed, 3 insertions(+), 20 deletions(-) diff --git a/recipes/fitter/meta.yaml b/recipes/fitter/meta.yaml index a680941af5..d67f27694e 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 +27,14 @@ 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: + base: "debian:latest" From b4e4e37324080c0d1be10e41b71dad277d8f91f5 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 14:21:24 +0200 Subject: [PATCH 085/114] Fix args. --- recipes/gseapy/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 1151feb922..869e060bab 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -45,3 +45,7 @@ about: license: MIT License summary: 'Gene Set Enrichment Analysis in Python' license_family: MIT + +extra: + container: + base: "debian:latest" From c728a5aad305e78a29198119793fb979558a3350 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 25 May 2017 14:21:24 +0200 Subject: [PATCH 086/114] Fix gseapy. --- recipes/gseapy/meta.yaml | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 1151feb922..869e060bab 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -45,3 +45,7 @@ about: license: MIT License summary: 'Gene Set Enrichment Analysis in Python' license_family: MIT + +extra: + container: + base: "debian:latest" From 97217e4fe235ed0630ec1ae495eabaa24c8d52b7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 11:28:35 +0200 Subject: [PATCH 087/114] Handle locale in test cases of click-related recipes. Fix swarm tests. --- recipes/bcbio-nextgen/meta.yaml | 7 ++++--- recipes/bcl2fastq-nextseq/meta.yaml | 3 ++- recipes/biom-format/2.1.5/meta.yaml | 5 ++--- recipes/chanjo/meta.yaml | 3 ++- recipes/cooler/meta.yaml | 3 ++- recipes/crimson/meta.yaml | 3 ++- recipes/dr-disco/meta.yaml | 4 ++-- recipes/dr-disco/v0.3.4/meta.yaml | 4 ++-- recipes/extract_genome_region/meta.yaml | 3 ++- recipes/fsnviz/0.1.0/meta.yaml | 5 +++++ recipes/fsnviz/meta.yaml | 6 ++++++ recipes/moca/meta.yaml | 3 ++- recipes/multiqc-bcbio/meta.yaml | 5 +++-- recipes/multiqc/meta.yaml | 3 ++- recipes/ped_parser/meta.yaml | 3 +++ recipes/phizz/meta.yaml | 3 ++- recipes/planemo/0.23.0/meta.yaml | 3 ++- recipes/planemo/0.34.1/meta.yaml | 3 ++- recipes/planemo/meta.yaml | 4 ++-- recipes/pybel/meta.yaml | 3 ++- recipes/query_phenomizer/meta.yaml | 3 ++- recipes/rapclust/meta.yaml | 3 +++ recipes/segmentation-fold/meta.yaml | 5 +++-- recipes/swarm/1.2.19/meta.yaml | 3 ++- recipes/swga/meta.yaml | 3 ++- recipes/umis/meta.yaml | 3 ++- 26 files changed, 65 insertions(+), 31 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 96377ec626..4c5d001d46 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 926c4d6b7e..5ac275bea9 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/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 75407ff8f7..ff25bc0993 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -42,9 +42,8 @@ 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/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 3079b4534c..c2d2bda731 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -57,7 +57,8 @@ test: - chanjo.store commands: - - chanjo --help + # click requires a unicode locale + - LANG=C.UTF-8 chanjo --help about: home: http://www.chanjo.co/ diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index 0f10a8fa0b..a925492879 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -43,7 +43,8 @@ test: - cooler.contrib commands: - - cooler --help + # click requires a unicode locale + - LANG=C.UTF-8 cooler --help about: home: https://github.com/mirnylab/cooler diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 52d17f8bb8..13d6e21da0 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -30,7 +30,8 @@ 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/dr-disco/meta.yaml b/recipes/dr-disco/meta.yaml index c2a070519a..d0981e1629 100644 --- a/recipes/dr-disco/meta.yaml +++ b/recipes/dr-disco/meta.yaml @@ -34,8 +34,8 @@ 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 diff --git a/recipes/dr-disco/v0.3.4/meta.yaml b/recipes/dr-disco/v0.3.4/meta.yaml index 1b8577a7bc..f26edf35e8 100644 --- a/recipes/dr-disco/v0.3.4/meta.yaml +++ b/recipes/dr-disco/v0.3.4/meta.yaml @@ -33,8 +33,8 @@ 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 diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index 3efb7a31f0..b0d3b3aee7 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -26,7 +26,8 @@ requirements: test: commands: - - "extract_genome_region --help > /dev/null" + # click requires a unicode locale + - LANG=C.UTF-8 extract_genome_region --help about: home: https://github.com/xguse/extract-genome-region diff --git a/recipes/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml index 7f991adcc2..3a97070233 100644 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ b/recipes/fsnviz/0.1.0/meta.yaml @@ -29,6 +29,11 @@ requirements: - 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 2186a98648..daa7c1858f 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -31,6 +31,12 @@ 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/moca/meta.yaml b/recipes/moca/meta.yaml index 450a2e95b8..a93ba81c9b 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -119,7 +119,8 @@ 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..4f34c8e4db 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -10,8 +10,6 @@ source: build: number: 4 preserve_egg_dir: True - # multiqc currently not compatible with py3 due to click locale issues - skip: true # [not py27] requirements: build: @@ -33,3 +31,6 @@ about: license: GNU General Public License v3 (GPLv3) summary: 'MultiQC plugin for bcbio report visualization.' +extra: + container: + base: debian:latest diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index b959f09a68..fe41c100bd 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -91,7 +91,8 @@ test: - multiqc.utils commands: - - multiqc --version + # click requires a unicode locale + - LANG=C.UTF-8 multiqc --version about: home: http://multiqc.info diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index 8d53b65127..9a9b5ae538 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -26,6 +26,9 @@ requirements: test: imports: - ped_parser + commands: + # click requires a unicode locale + - LANG=C.UTF-8 ped_parser --help about: home: https://github.com/moonso/ped_parser diff --git a/recipes/phizz/meta.yaml b/recipes/phizz/meta.yaml index d6af9d2f7e..b8c98f89af 100644 --- a/recipes/phizz/meta.yaml +++ b/recipes/phizz/meta.yaml @@ -32,7 +32,8 @@ test: - phizz.utils commands: - - phizz --help + # click requires a unicode locale + - LANG=C.UTF-8 phizz --help about: home: https://github.com/moonso/query_hpo diff --git a/recipes/planemo/0.23.0/meta.yaml b/recipes/planemo/0.23.0/meta.yaml index 6eec1b6ace..2b8ae56418 100644 --- a/recipes/planemo/0.23.0/meta.yaml +++ b/recipes/planemo/0.23.0/meta.yaml @@ -53,7 +53,8 @@ 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 1ea69a0d94..e6c1b0ddc5 100644 --- a/recipes/planemo/0.34.1/meta.yaml +++ b/recipes/planemo/0.34.1/meta.yaml @@ -58,7 +58,8 @@ test: - 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 c45cce4a11..895fe3a68d 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -64,8 +64,8 @@ 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/pybel/meta.yaml b/recipes/pybel/meta.yaml index bf211f2111..c4c8b4728b 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -48,7 +48,8 @@ test: - pybel.parser - pybel.parser.modifiers commands: - - pybel --help + # click requires a unicode locale + - LANG=C.UTF-8 pybel --help about: home: https://github.com/pybel/pybel diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index f4d3524031..278d35baf4 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -32,7 +32,8 @@ test: - query_phenomizer commands: - - query_phenomizer --help + # click requires a unicode locale + - LANG=C.UTF-8 query_phenomizer --help about: home: https://www.github.com/moonso/query_phenomizer diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index ff39580d17..b24ad9acc3 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -37,6 +37,9 @@ requirements: test: imports: - rapclust + commands: + # click requires a unicode locale + - LANG=C.UTF-8 RapClust --help about: home: https://github.com/COMBINE-lab/RapClust diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index 179f150a14..a6dc8221ec 100644 --- a/recipes/segmentation-fold/meta.yaml +++ b/recipes/segmentation-fold/meta.yaml @@ -40,8 +40,9 @@ 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 extra: container: diff --git a/recipes/swarm/1.2.19/meta.yaml b/recipes/swarm/1.2.19/meta.yaml index 7d78549ca1..b72feb481e 100644 --- a/recipes/swarm/1.2.19/meta.yaml +++ b/recipes/swarm/1.2.19/meta.yaml @@ -18,7 +18,8 @@ requirements: test: commands: - swarm_breaker.py --version - - swarm -v 2>&1 | grep Swarm > /dev/null + - swarm -v 2>&1 | grep Swarm + - swarm -v about: home: https://github.com/torognes/swarm diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index ca5691dbd6..afffabae39 100644 --- a/recipes/swga/meta.yaml +++ b/recipes/swga/meta.yaml @@ -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/umis/meta.yaml b/recipes/umis/meta.yaml index b6901968c1..e0710480a5 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 From 8dced153734ae576b39af330f9ed9de05dc1cda0 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 12:08:02 +0200 Subject: [PATCH 088/114] Fixes. --- .travis.yml | 3 +-- recipes/amos/meta.yaml | 2 +- recipes/biom-format/2.1.5/meta.yaml | 2 ++ 3 files changed, 4 insertions(+), 3 deletions(-) diff --git a/.travis.yml b/.travis.yml index 9566ca482f..d2984ab9e9 100644 --- a/.travis.yml +++ b/.travis.yml @@ -15,9 +15,8 @@ script: scripts/travis-run.sh env: global: - - secure: 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 - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_TAG=fix-custom-container - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index bc7d467184..9365cf24d2 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -25,7 +25,7 @@ requirements: build: - gcc - zlib - - boost + - boost - autoconf - automake - blat diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index ff25bc0993..7b8cfacf86 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -34,6 +34,8 @@ requirements: - numpy >=1.3.0 - future >=0.15.0 - scipy >=0.13.0 + # missing scipy dependency + - libgcc test: # Python imports From 8411440ec1cf991f759b649dafb32dd8013a6a79 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 13:01:19 +0200 Subject: [PATCH 089/114] Remove unnecessary dependencies. --- recipes/yahmm/meta.yaml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index bde980eae6..a7eff8dd59 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -18,7 +18,6 @@ requirements: - scipy >=0.13.3 - networkx >=1.8.1 - matplotlib >=1.3.1 - - pyqt run: - python @@ -27,7 +26,6 @@ requirements: - scipy >=0.13.3 - networkx >=1.8.1 - matplotlib >=1.3.1 - - pyqt test: imports: @@ -37,7 +35,3 @@ 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: - base: "debian:latest" From 1e0952d71186095116a54b8d4fb1287fb53167dd Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 13:26:28 +0200 Subject: [PATCH 090/114] Use our own extended base image. --- recipes/bcbio-nextgen/meta.yaml | 2 +- recipes/bcl2fastq-nextseq/meta.yaml | 2 +- recipes/biom-format/2.1.5/meta.yaml | 2 +- recipes/chanjo/meta.yaml | 2 +- recipes/cooler/meta.yaml | 2 +- recipes/crimson/meta.yaml | 2 +- recipes/dr-disco/meta.yaml | 2 +- recipes/dr-disco/v0.3.4/meta.yaml | 2 +- recipes/extract_genome_region/meta.yaml | 2 +- recipes/fitter/meta.yaml | 2 +- recipes/fsnviz/0.1.0/meta.yaml | 2 +- recipes/fsnviz/meta.yaml | 2 +- recipes/genomebaser/meta.yaml | 2 +- recipes/ggplot/meta.yaml | 2 +- recipes/gseapy/meta.yaml | 2 +- recipes/moca/meta.yaml | 2 +- recipes/multiqc-bcbio/meta.yaml | 2 +- recipes/multiqc/meta.yaml | 2 +- recipes/onto2nx/meta.yaml | 2 +- recipes/ped_parser/meta.yaml | 2 +- recipes/phizz/meta.yaml | 2 +- recipes/planemo/0.23.0/meta.yaml | 2 +- recipes/planemo/0.34.1/meta.yaml | 2 +- recipes/planemo/meta.yaml | 2 +- recipes/platypus-conquistador/meta.yaml | 2 +- recipes/pybel/meta.yaml | 2 +- recipes/query_phenomizer/meta.yaml | 2 +- recipes/rapclust/meta.yaml | 2 +- recipes/samsifter/meta.yaml | 2 +- recipes/segmentation-fold/meta.yaml | 2 +- recipes/swga/meta.yaml | 2 +- recipes/umis/meta.yaml | 2 +- 32 files changed, 32 insertions(+), 32 deletions(-) diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index 4c5d001d46..c5342e4542 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -97,4 +97,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index 5ac275bea9..ea5b81912d 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -41,4 +41,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 7b8cfacf86..79659019c2 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -55,4 +55,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index c2d2bda731..7590f5793b 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -68,4 +68,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index a925492879..b94696a555 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -54,4 +54,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 13d6e21da0..3d79fb356f 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -42,4 +42,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/dr-disco/meta.yaml b/recipes/dr-disco/meta.yaml index d0981e1629..bd8e3e8e20 100644 --- a/recipes/dr-disco/meta.yaml +++ b/recipes/dr-disco/meta.yaml @@ -49,4 +49,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/dr-disco/v0.3.4/meta.yaml b/recipes/dr-disco/v0.3.4/meta.yaml index f26edf35e8..3abc13b624 100644 --- a/recipes/dr-disco/v0.3.4/meta.yaml +++ b/recipes/dr-disco/v0.3.4/meta.yaml @@ -48,4 +48,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index b0d3b3aee7..06decd7ec9 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -37,4 +37,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/fitter/meta.yaml b/recipes/fitter/meta.yaml index d67f27694e..d398f2f9fd 100644 --- a/recipes/fitter/meta.yaml +++ b/recipes/fitter/meta.yaml @@ -37,4 +37,4 @@ about: extra: container: - base: "debian:latest" + base: "bioconda/extended-base-image" diff --git a/recipes/fsnviz/0.1.0/meta.yaml b/recipes/fsnviz/0.1.0/meta.yaml index 3a97070233..5da16fd948 100644 --- a/recipes/fsnviz/0.1.0/meta.yaml +++ b/recipes/fsnviz/0.1.0/meta.yaml @@ -43,4 +43,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index daa7c1858f..c73c171766 100644 --- a/recipes/fsnviz/meta.yaml +++ b/recipes/fsnviz/meta.yaml @@ -46,4 +46,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/genomebaser/meta.yaml b/recipes/genomebaser/meta.yaml index 6011ebb425..f9e794ecbc 100644 --- a/recipes/genomebaser/meta.yaml +++ b/recipes/genomebaser/meta.yaml @@ -35,4 +35,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/ggplot/meta.yaml b/recipes/ggplot/meta.yaml index a8bde25788..dc4d65a4ec 100644 --- a/recipes/ggplot/meta.yaml +++ b/recipes/ggplot/meta.yaml @@ -46,4 +46,4 @@ about: extra: container: # ggplot depends on libGL.so.1 from the system - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 869e060bab..11fcd8e9b7 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -48,4 +48,4 @@ about: extra: container: - base: "debian:latest" + base: bioconda/extended-base-image diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index a93ba81c9b..e13cead99b 100644 --- a/recipes/moca/meta.yaml +++ b/recipes/moca/meta.yaml @@ -136,4 +136,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index 4f34c8e4db..debc2ea73b 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -33,4 +33,4 @@ about: extra: container: - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index fe41c100bd..b85d43bda5 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -103,4 +103,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/onto2nx/meta.yaml b/recipes/onto2nx/meta.yaml index f8e7daa93c..8a5a1ed233 100644 --- a/recipes/onto2nx/meta.yaml +++ b/recipes/onto2nx/meta.yaml @@ -50,4 +50,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index 9a9b5ae538..c3e4c4597e 100644 --- a/recipes/ped_parser/meta.yaml +++ b/recipes/ped_parser/meta.yaml @@ -38,4 +38,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/phizz/meta.yaml b/recipes/phizz/meta.yaml index b8c98f89af..b1a6535ab7 100644 --- a/recipes/phizz/meta.yaml +++ b/recipes/phizz/meta.yaml @@ -43,4 +43,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/planemo/0.23.0/meta.yaml b/recipes/planemo/0.23.0/meta.yaml index 2b8ae56418..5e3af56c27 100644 --- a/recipes/planemo/0.23.0/meta.yaml +++ b/recipes/planemo/0.23.0/meta.yaml @@ -64,4 +64,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/planemo/0.34.1/meta.yaml b/recipes/planemo/0.34.1/meta.yaml index e6c1b0ddc5..facd09f6cf 100644 --- a/recipes/planemo/0.34.1/meta.yaml +++ b/recipes/planemo/0.34.1/meta.yaml @@ -70,4 +70,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 895fe3a68d..41bcc9fc09 100644 --- a/recipes/planemo/meta.yaml +++ b/recipes/planemo/meta.yaml @@ -76,4 +76,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index aa11e0fae7..f3eb6f5652 100644 --- a/recipes/platypus-conquistador/meta.yaml +++ b/recipes/platypus-conquistador/meta.yaml @@ -33,4 +33,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index c4c8b4728b..9de0dd5bb5 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -59,4 +59,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index 278d35baf4..6dde1a073e 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -43,4 +43,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index b24ad9acc3..6611d4c5c3 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -50,4 +50,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 308a5d3028..4788c7a6b1 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -80,4 +80,4 @@ about: extra: container: - base: "debian:latest" + base: "bioconda/extended-base-image" diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index a6dc8221ec..1db4ed7ac8 100644 --- a/recipes/segmentation-fold/meta.yaml +++ b/recipes/segmentation-fold/meta.yaml @@ -47,4 +47,4 @@ test: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index afffabae39..7cd7eb7385 100644 --- a/recipes/swga/meta.yaml +++ b/recipes/swga/meta.yaml @@ -57,4 +57,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index e0710480a5..a724ff9cf7 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -47,4 +47,4 @@ about: extra: container: # click relies on unicode support, which is not present in the default busybox image - base: debian:latest + base: bioconda/extended-base-image From b46344419bb8d305049b6d76b2087d3b1921a6b3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 13:27:21 +0200 Subject: [PATCH 091/114] Use master branch of bioconda-utils. --- .travis.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.travis.yml b/.travis.yml index d2984ab9e9..a9515727ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ script: scripts/travis-run.sh env: global: - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=fix-custom-container + - BIOCONDA_UTILS_TAG=master - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" From 31cb51a328fbc9183ce3298f0593c709be9c6bb3 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 13:30:32 +0200 Subject: [PATCH 092/114] Documentation and base image. --- recipes/gseapy/meta.yaml | 1 + recipes/yahmm/meta.yaml | 5 +++++ 2 files changed, 6 insertions(+) diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 11fcd8e9b7..3bcf214977 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -48,4 +48,5 @@ about: extra: container: + # matplotlib needs opengl support base: bioconda/extended-base-image diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index a7eff8dd59..1971a6e7c7 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 + base: bioconda/extended-base-image From c7d582f1b6b068496f2a0a30220b68d7353e5fa7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 14:12:25 +0200 Subject: [PATCH 093/114] Fix swarm dependencies. --- recipes/swarm/1.2.19/meta.yaml | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) diff --git a/recipes/swarm/1.2.19/meta.yaml b/recipes/swarm/1.2.19/meta.yaml index b72feb481e..88b1233792 100644 --- a/recipes/swarm/1.2.19/meta.yaml +++ b/recipes/swarm/1.2.19/meta.yaml @@ -8,18 +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 - - swarm -v about: home: https://github.com/torognes/swarm From 4cb1c5aa32399f9694cd22bd5cc415f74d1a867b Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 14:26:36 +0200 Subject: [PATCH 094/114] Skip until we have completely switched to conda-forge. --- recipes/amos/meta.yaml | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index 9365cf24d2..dc9436306f 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -14,7 +14,10 @@ source: build: number: 3 # OSX failing due to missing dependencies in OSX branch - skip: True # [osx] + # Linux failing due to broken automake in defaults. + # Conda-forge contains a fix. Once we have switched to conda-forge completely + # this will build again. + skip: True test: From cec3ccffcbc5aafcb0fc2c6881a7367b43a94b94 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 19:50:11 +0200 Subject: [PATCH 095/114] Use extended base image for dreamtools. --- recipes/dreamtools/meta.yaml | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) diff --git a/recipes/dreamtools/meta.yaml b/recipes/dreamtools/meta.yaml index bc1911e208..a2067bece4 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 +65,6 @@ 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: + base: bioconda/extended-base-image From da1425f6ad290ad18b998ea933f55069b896704d Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 27 May 2017 19:52:28 +0200 Subject: [PATCH 096/114] Skip fwdpy (missing headers in own source). --- recipes/fwdpy/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/recipes/fwdpy/meta.yaml b/recipes/fwdpy/meta.yaml index ff45f81a78..da7330db18 100644 --- a/recipes/fwdpy/meta.yaml +++ b/recipes/fwdpy/meta.yaml @@ -10,8 +10,8 @@ source: build: number: 0 string: "py{{CONDA_PY}}_gsl{{CONDA_GSL}}_{{PKG_BUILDNUM}}" - # does not build on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L416 - skip: true # [osx] + # does not build currently: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235650543#L416 + skip: true requirements: build: @@ -29,6 +29,7 @@ requirements: - pandas >=0.18 - libsequence - gsl {{CONDA_GSL}}* + - libgcc test: # Python imports From a1481fbeb68556f253bf2a149cfb191a8fed384a Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sun, 28 May 2017 21:37:04 +0200 Subject: [PATCH 097/114] Fixes and formatting. --- recipes/biokit/meta.yaml | 17 +++++++-------- recipes/cgat-pipelines-nosetests/meta.yaml | 1 - recipes/cgat-report/meta.yaml | 3 +-- recipes/cgat-scripts-devel/meta.yaml | 4 ++++ recipes/cgat-scripts-nosetests/meta.yaml | 1 - recipes/cgat-scripts/meta.yaml | 1 - recipes/checkm-genome/meta.yaml | 34 ------------------------------ recipes/cnvkit/meta.yaml | 1 - recipes/colormap/meta.yaml | 24 --------------------- recipes/crispresso/meta.yaml | 2 +- recipes/multiqc-bcbio/meta.yaml | 1 + recipes/scikit-bio/0.2.3/meta.yaml | 5 +++++ recipes/scikit-bio/meta.yaml | 5 +++++ 13 files changed, 25 insertions(+), 74 deletions(-) diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index 4c73ad9b0a..d1c80d7adf 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -35,18 +35,16 @@ requirements: - xmltodict - numpydoc - bioservices - #- matplotlib - #- libgcc # [not osx] - #- glib + - matplotlib + - libgcc #- 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'] @@ -55,5 +53,6 @@ about: extra: - recipe-maintainers: - - cokelaer + container: + # libGL.so.1 needed by matplotlib + base: bioconda/extended-base-image 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..adfab5e4c4 100644 --- a/recipes/cgat-scripts-devel/meta.yaml +++ b/recipes/cgat-scripts-devel/meta.yaml @@ -107,3 +107,7 @@ about: license: BSD summary: "Computational Genomics Analysis Toolkit" +extra: + container: + # libGL.so.1 needed by matplotlib + base: bioconda/extended-base-image 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/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 d9a23d40e6..06652dc6ea 100644 --- a/recipes/cnvkit/meta.yaml +++ b/recipes/cnvkit/meta.yaml @@ -9,7 +9,6 @@ source: build: number: 0 - skip: False requirements: build: 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/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/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index debc2ea73b..48ea825e6d 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -33,4 +33,5 @@ about: extra: container: + # multiqc needs this base: bioconda/extended-base-image diff --git a/recipes/scikit-bio/0.2.3/meta.yaml b/recipes/scikit-bio/0.2.3/meta.yaml index 26ad26e86c..f1835e53ed 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 + base: bioconda/extended-base-image diff --git a/recipes/scikit-bio/meta.yaml b/recipes/scikit-bio/meta.yaml index 446f4a765a..fd483a7995 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 + base: bioconda/extended-base-image From df4ca09bd23b8a9dc9a6d1ddaa80ec66fa1765a7 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sun, 28 May 2017 22:15:41 +0200 Subject: [PATCH 098/114] 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. --- recipes/hlama/meta.yaml | 8 +++++--- recipes/pomegranate/meta.yaml | 37 +++---------------------------------- 2 files changed, 8 insertions(+), 37 deletions(-) diff --git a/recipes/hlama/meta.yaml b/recipes/hlama/meta.yaml index 0a3b693a09..04de94a2f4 100644 --- a/recipes/hlama/meta.yaml +++ b/recipes/hlama/meta.yaml @@ -4,7 +4,9 @@ package: build: number: 1 - skip: True # [py27 or osx] + # 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 @@ -17,10 +19,10 @@ requirements: build: - python - setuptools - - snakemake >=3.7.1 + - snakemake ==3.7.1 run: - python - - snakemake >=3.7.1 + - snakemake ==3.7.1 - optitype >=1.2 test: 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 From 76146752eba24ef1419298723c8508ce14d366c1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Mon, 29 May 2017 14:37:44 +0200 Subject: [PATCH 099/114] Fixes --- recipes/amos/build.sh | 14 +++++++++++++- recipes/amos/meta.yaml | 5 +---- recipes/bcbio-nextgen/meta.yaml | 5 ----- recipes/bcl2fastq-nextseq/meta.yaml | 5 ----- recipes/biokit/meta.yaml | 8 ++------ recipes/biom-format/2.1.5/meta.yaml | 7 ++----- recipes/cgat-scripts-devel/meta.yaml | 6 +----- recipes/crimson/meta.yaml | 5 ----- 8 files changed, 19 insertions(+), 36 deletions(-) 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 dc9436306f..f42e1e952f 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -14,10 +14,7 @@ source: build: number: 3 # OSX failing due to missing dependencies in OSX branch - # Linux failing due to broken automake in defaults. - # Conda-forge contains a fix. Once we have switched to conda-forge completely - # this will build again. - skip: True + skip: true # [osx] test: diff --git a/recipes/bcbio-nextgen/meta.yaml b/recipes/bcbio-nextgen/meta.yaml index c5342e4542..79313fa772 100644 --- a/recipes/bcbio-nextgen/meta.yaml +++ b/recipes/bcbio-nextgen/meta.yaml @@ -93,8 +93,3 @@ about: home: https://github.com/chapmanb/bcbio-nextgen license: MIT summary: Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/bcl2fastq-nextseq/meta.yaml b/recipes/bcl2fastq-nextseq/meta.yaml index ea5b81912d..0011f8d828 100644 --- a/recipes/bcl2fastq-nextseq/meta.yaml +++ b/recipes/bcl2fastq-nextseq/meta.yaml @@ -37,8 +37,3 @@ about: home: https://github.com/brwnj/bcl2fastq license: MIT summary: NextSeq .bcl Conversion - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/biokit/meta.yaml b/recipes/biokit/meta.yaml index d1c80d7adf..cfbfd3d7f5 100644 --- a/recipes/biokit/meta.yaml +++ b/recipes/biokit/meta.yaml @@ -24,6 +24,7 @@ requirements: - xmltodict - numpydoc - bioservices + - mesalib run: - python @@ -37,6 +38,7 @@ requirements: - bioservices - matplotlib - libgcc + - mesalib #- xz #- libxcb @@ -50,9 +52,3 @@ about: home: ['http://pypi.python.org/pypi/biokit'] license: BSD summary: 'Set of visualisation and analysis tools for biological data sets' - - -extra: - container: - # libGL.so.1 needed by matplotlib - base: bioconda/extended-base-image diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 79659019c2..658464f3d2 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -13,6 +13,8 @@ build: entry_points: - biom=biom.cli:cli number: 3 + # click needs to be patched in order to work with busybox: + skip: true # [py3k] requirements: build: @@ -51,8 +53,3 @@ about: home: http://www.biom-format.org license: BSD License summary: 'Biological Observation Matrix (BIOM) format' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/cgat-scripts-devel/meta.yaml b/recipes/cgat-scripts-devel/meta.yaml index adfab5e4c4..38e4964b93 100644 --- a/recipes/cgat-scripts-devel/meta.yaml +++ b/recipes/cgat-scripts-devel/meta.yaml @@ -87,6 +87,7 @@ requirements: - bioconductor-qvalue - bioconductor-rtracklayer - bioconductor-siggenes + - libglu test: imports: @@ -106,8 +107,3 @@ about: home: https://www.cgat.org/downloads/public/cgat/documentation license: BSD summary: "Computational Genomics Analysis Toolkit" - -extra: - container: - # libGL.so.1 needed by matplotlib - base: bioconda/extended-base-image diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 3d79fb356f..5fa013721d 100644 --- a/recipes/crimson/meta.yaml +++ b/recipes/crimson/meta.yaml @@ -38,8 +38,3 @@ about: license: BSD License summary: 'Bioinformatics tool outputs converter to JSON or YAML.' license_family: BSD - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image From 98218311b4b50f6dd3e2af571e8f042f0ab67275 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Wed, 31 May 2017 15:07:49 +0200 Subject: [PATCH 100/114] Adapt container image definition to new syntax. Skip click-based recipes on py3k. --- recipes/amos/meta.yaml | 1 - recipes/biom-format/2.1.5/meta.yaml | 2 +- recipes/chanjo/meta.yaml | 5 ----- recipes/cooler/meta.yaml | 7 ++----- recipes/crimson/meta.yaml | 2 ++ recipes/dr-disco/meta.yaml | 9 ++------- recipes/dr-disco/v0.3.4/meta.yaml | 9 ++------- recipes/dreamtools/meta.yaml | 3 ++- recipes/extract_genome_region/meta.yaml | 7 ++----- recipes/fitter/meta.yaml | 3 ++- recipes/fsnviz/0.1.0/meta.yaml | 8 ++------ recipes/fsnviz/meta.yaml | 8 ++------ recipes/genomebaser/meta.yaml | 5 ----- recipes/genomepy/meta.yaml | 4 +++- recipes/ggplot/meta.yaml | 2 +- recipes/gseapy/meta.yaml | 2 +- recipes/moca/meta.yaml | 10 ++-------- recipes/multiqc-bcbio/meta.yaml | 7 ++----- recipes/multiqc/meta.yaml | 7 ++----- recipes/onto2nx/meta.yaml | 7 ++----- recipes/ped_parser/meta.yaml | 8 ++------ recipes/phizz/meta.yaml | 9 +++------ recipes/planemo/0.23.0/meta.yaml | 6 ------ recipes/planemo/0.34.1/meta.yaml | 9 ++------- recipes/planemo/meta.yaml | 10 ++-------- recipes/platypus-conquistador/meta.yaml | 7 +------ recipes/pybel/meta.yaml | 8 ++------ recipes/query_phenomizer/meta.yaml | 7 ++----- recipes/rapclust/meta.yaml | 9 ++------- recipes/samsifter/meta.yaml | 3 ++- recipes/scikit-bio/0.2.3/meta.yaml | 2 +- recipes/scikit-bio/meta.yaml | 2 +- recipes/segmentation-fold/meta.yaml | 5 ----- recipes/swga/meta.yaml | 7 +------ recipes/umis/meta.yaml | 5 ----- recipes/yahmm/meta.yaml | 2 +- 36 files changed, 54 insertions(+), 153 deletions(-) diff --git a/recipes/amos/meta.yaml b/recipes/amos/meta.yaml index f42e1e952f..5e75a5ecf9 100644 --- a/recipes/amos/meta.yaml +++ b/recipes/amos/meta.yaml @@ -16,7 +16,6 @@ build: # OSX failing due to missing dependencies in OSX branch skip: true # [osx] - test: commands: - Minimo -h > /dev/null diff --git a/recipes/biom-format/2.1.5/meta.yaml b/recipes/biom-format/2.1.5/meta.yaml index 658464f3d2..a270667518 100644 --- a/recipes/biom-format/2.1.5/meta.yaml +++ b/recipes/biom-format/2.1.5/meta.yaml @@ -13,7 +13,7 @@ build: entry_points: - biom=biom.cli:cli number: 3 - # click needs to be patched in order to work with busybox: + # click needs to be patched in order to properly detect unicode in py3k skip: true # [py3k] requirements: diff --git a/recipes/chanjo/meta.yaml b/recipes/chanjo/meta.yaml index 7590f5793b..25fe5bc9ab 100644 --- a/recipes/chanjo/meta.yaml +++ b/recipes/chanjo/meta.yaml @@ -64,8 +64,3 @@ about: home: http://www.chanjo.co/ license: MIT License summary: 'Coverage analysis tool for clinical sequencing' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/cooler/meta.yaml b/recipes/cooler/meta.yaml index b94696a555..facbe3524a 100644 --- a/recipes/cooler/meta.yaml +++ b/recipes/cooler/meta.yaml @@ -13,6 +13,8 @@ build: number: 0 entry_points: - cooler = cooler.cli:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -50,8 +52,3 @@ about: home: https://github.com/mirnylab/cooler license: BSD summary: 'Sparse binary format for genomic interaction matrices' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/crimson/meta.yaml b/recipes/crimson/meta.yaml index 5fa013721d..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: diff --git a/recipes/dr-disco/meta.yaml b/recipes/dr-disco/meta.yaml index bd8e3e8e20..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: @@ -45,8 +45,3 @@ about: home: https://github.com/yhoogstrate/dr-disco/ license: GNU General Public License v3 or later (GPLv3+) summary: 'Dr. Disco: fusion gene and genomic breakpoint detection in random hexamer RNA-seq data' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/dr-disco/v0.3.4/meta.yaml b/recipes/dr-disco/v0.3.4/meta.yaml index 3abc13b624..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: @@ -44,8 +44,3 @@ about: home: https://github.com/yhoogstrate/dr-disco/ license: GNU General Public License v3 or later (GPLv3+) summary: 'Dr. Disco: fusion gene genomic breakpoint detection in random hexamer RNA-seq data' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/dreamtools/meta.yaml b/recipes/dreamtools/meta.yaml index a2067bece4..132b5f8e03 100644 --- a/recipes/dreamtools/meta.yaml +++ b/recipes/dreamtools/meta.yaml @@ -67,4 +67,5 @@ about: extra: container: - base: bioconda/extended-base-image + # fitter depends on libGl.so.1 + extended-base: true diff --git a/recipes/extract_genome_region/meta.yaml b/recipes/extract_genome_region/meta.yaml index 06decd7ec9..45c82d03ea 100644 --- a/recipes/extract_genome_region/meta.yaml +++ b/recipes/extract_genome_region/meta.yaml @@ -11,6 +11,8 @@ build: entry_points: - extract_genome_region = extract_genome_region.__main__:main number: 0 + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -33,8 +35,3 @@ 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.' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/fitter/meta.yaml b/recipes/fitter/meta.yaml index d398f2f9fd..3bd3dbad69 100644 --- a/recipes/fitter/meta.yaml +++ b/recipes/fitter/meta.yaml @@ -37,4 +37,5 @@ about: extra: container: - base: "bioconda/extended-base-image" + # 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 5da16fd948..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 @@ -39,8 +40,3 @@ about: license: BSD summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' license_family: BSD - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/fsnviz/meta.yaml b/recipes/fsnviz/meta.yaml index c73c171766..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 @@ -42,8 +43,3 @@ about: license: BSD summary: 'Tool for plotting gene fusion events detected by various tools using Circos.' license_family: BSD - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/genomebaser/meta.yaml b/recipes/genomebaser/meta.yaml index f9e794ecbc..ff26d99847 100644 --- a/recipes/genomebaser/meta.yaml +++ b/recipes/genomebaser/meta.yaml @@ -31,8 +31,3 @@ about: home: http://github.com/mscook/GenomeBaser license: ECL 2.0 summary: 'GenomeBaser manages complete (bacterial) genomes from NCBI' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image 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 dc4d65a4ec..8f9076cb45 100644 --- a/recipes/ggplot/meta.yaml +++ b/recipes/ggplot/meta.yaml @@ -46,4 +46,4 @@ about: extra: container: # ggplot depends on libGL.so.1 from the system - base: bioconda/extended-base-image + extended-base: true diff --git a/recipes/gseapy/meta.yaml b/recipes/gseapy/meta.yaml index 3bcf214977..832f63f7e9 100644 --- a/recipes/gseapy/meta.yaml +++ b/recipes/gseapy/meta.yaml @@ -49,4 +49,4 @@ about: extra: container: # matplotlib needs opengl support - base: bioconda/extended-base-image + extended-base: true diff --git a/recipes/moca/meta.yaml b/recipes/moca/meta.yaml index e13cead99b..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 @@ -132,8 +131,3 @@ about: license: ISC License (ISCL) summary: 'Tool for motif conservation analysis' license_family: Public-Domain - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/multiqc-bcbio/meta.yaml b/recipes/multiqc-bcbio/meta.yaml index 48ea825e6d..535d8425ea 100644 --- a/recipes/multiqc-bcbio/meta.yaml +++ b/recipes/multiqc-bcbio/meta.yaml @@ -10,6 +10,8 @@ source: build: number: 4 preserve_egg_dir: True + # multiqc does not support py3k because of click + skip: true # [py3k] requirements: build: @@ -30,8 +32,3 @@ about: home: http://multiqc.info license: GNU General Public License v3 (GPLv3) summary: 'MultiQC plugin for bcbio report visualization.' - -extra: - container: - # multiqc needs this - base: bioconda/extended-base-image diff --git a/recipes/multiqc/meta.yaml b/recipes/multiqc/meta.yaml index b85d43bda5..28d318d0ad 100644 --- a/recipes/multiqc/meta.yaml +++ b/recipes/multiqc/meta.yaml @@ -10,6 +10,8 @@ source: build: number: 4 preserve_egg_dir: True + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -99,8 +101,3 @@ about: license: GNU General Public License v3 (GPLv3) summary: 'Create aggregate bioinformatics analysis reports across many samples and tools' license_family: GPL3 - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/onto2nx/meta.yaml b/recipes/onto2nx/meta.yaml index 8a5a1ed233..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: @@ -46,8 +48,3 @@ about: home: https://github.com/cthoyt/onto2nx license: GNU General Public License v3 or later (GPLv3+) summary: 'A package for parsing ontologies into NetworkX graphs' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/ped_parser/meta.yaml b/recipes/ped_parser/meta.yaml index c3e4c4597e..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 @@ -34,8 +35,3 @@ about: home: https://github.com/moonso/ped_parser license: BSD License summary: 'A ped file parser.' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/phizz/meta.yaml b/recipes/phizz/meta.yaml index b1a6535ab7..1484e99ee6 100644 --- a/recipes/phizz/meta.yaml +++ b/recipes/phizz/meta.yaml @@ -8,9 +8,11 @@ source: md5: 29387dba01cd9148e47d2998fa932961 build: - preserve_egg_dir: True + preserve_egg_dir: true entry_points: - phizz = phizz.__main__:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -39,8 +41,3 @@ about: home: https://github.com/moonso/query_hpo license: MIT License summary: 'Tool to query hpo database and some other sources' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/planemo/0.23.0/meta.yaml b/recipes/planemo/0.23.0/meta.yaml index 5e3af56c27..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] @@ -60,8 +59,3 @@ about: home: https://github.com/galaxyproject/planemo license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/planemo/0.34.1/meta.yaml b/recipes/planemo/0.34.1/meta.yaml index facd09f6cf..a7b2454916 100644 --- a/recipes/planemo/0.34.1/meta.yaml +++ b/recipes/planemo/0.34.1/meta.yaml @@ -8,8 +8,8 @@ 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 @@ -66,8 +66,3 @@ about: license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' license_family: Apache - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/planemo/meta.yaml b/recipes/planemo/meta.yaml index 41bcc9fc09..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: @@ -72,8 +71,3 @@ about: license: Academic Free License (AFL) summary: 'Command-line utilities to assist in building tools for the Galaxy project (http://galaxyproject.org/).' license_family: Apache - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/platypus-conquistador/meta.yaml b/recipes/platypus-conquistador/meta.yaml index f3eb6f5652..4b4c518dde 100644 --- a/recipes/platypus-conquistador/meta.yaml +++ b/recipes/platypus-conquistador/meta.yaml @@ -8,7 +8,7 @@ source: md5: 609e38711a1ebc7cb2b54a14c3a258f3 build: - skip: True # [not py27 or osx] + skip: true # [not py27 or osx] requirements: build: @@ -29,8 +29,3 @@ about: home: http://github.com/biocore/platypus license: BSD License summary: 'Platypus Conquistador: Confirming specific taxonomic groups within your metagenomic samples.' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/pybel/meta.yaml b/recipes/pybel/meta.yaml index 9de0dd5bb5..425043c900 100644 --- a/recipes/pybel/meta.yaml +++ b/recipes/pybel/meta.yaml @@ -12,7 +12,8 @@ build: - pybel = pybel.cli:main number: 0 # tests fail on osx: https://travis-ci.org/bioconda/bioconda-recipes/jobs/235726973#L3656 - skip: true # [osx] + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [osx or py3k] requirements: build: @@ -55,8 +56,3 @@ about: home: https://github.com/pybel/pybel license: Apache Software License summary: 'Parsing, validation, and analysis of BEL graphs' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/query_phenomizer/meta.yaml b/recipes/query_phenomizer/meta.yaml index 6dde1a073e..36cc942914 100644 --- a/recipes/query_phenomizer/meta.yaml +++ b/recipes/query_phenomizer/meta.yaml @@ -10,6 +10,8 @@ source: build: entry_points: - query_phenomizer = query_phenomizer.__main__:cli + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: @@ -39,8 +41,3 @@ about: home: https://www.github.com/moonso/query_phenomizer license: MIT License summary: 'Tool for query and parsing the phenomizer tool' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/rapclust/meta.yaml b/recipes/rapclust/meta.yaml index 6611d4c5c3..b1360702c3 100644 --- a/recipes/rapclust/meta.yaml +++ b/recipes/rapclust/meta.yaml @@ -9,8 +9,8 @@ source: build: number: 0 - # coloredlogs is not py36 compatible yet - skip: true # [not py27 and not py35] + # click needs to be patched in order to properly detect unicode in py3k + skip: true # [py3k] requirements: build: @@ -46,8 +46,3 @@ about: license: BSD with attribution summary: 'Accurate, Fast and Lightweight Clustering of de novo Transcriptomes using Fragment Equivalence Classes' license_family: BSD - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 4788c7a6b1..02a171f795 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -80,4 +80,5 @@ about: extra: container: - base: "bioconda/extended-base-image" + # 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 f1835e53ed..48d60f5eb4 100644 --- a/recipes/scikit-bio/0.2.3/meta.yaml +++ b/recipes/scikit-bio/0.2.3/meta.yaml @@ -81,4 +81,4 @@ about: extra: container: # needs libGL.so.1 - base: bioconda/extended-base-image + extended-base: true diff --git a/recipes/scikit-bio/meta.yaml b/recipes/scikit-bio/meta.yaml index fd483a7995..aad129f0aa 100644 --- a/recipes/scikit-bio/meta.yaml +++ b/recipes/scikit-bio/meta.yaml @@ -90,4 +90,4 @@ about: extra: container: # needs libGL.so.1 - base: bioconda/extended-base-image + extended-base: true diff --git a/recipes/segmentation-fold/meta.yaml b/recipes/segmentation-fold/meta.yaml index 1db4ed7ac8..7c55e6a026 100644 --- a/recipes/segmentation-fold/meta.yaml +++ b/recipes/segmentation-fold/meta.yaml @@ -43,8 +43,3 @@ test: # click requires a unicode locale - LANG=C.UTF-8 segmentation-fold --version - LANG=C.UTF-8 segmentation-fold-utils --help - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/swga/meta.yaml b/recipes/swga/meta.yaml index 7cd7eb7385..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 @@ -53,8 +53,3 @@ about: home: https://github.com/eclarke/swga license: GPLv3 summary: 'Select primer sets for selective whole genome amplification (SWGA)' - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/umis/meta.yaml b/recipes/umis/meta.yaml index a724ff9cf7..0bf5f5698f 100644 --- a/recipes/umis/meta.yaml +++ b/recipes/umis/meta.yaml @@ -43,8 +43,3 @@ about: home: https://github.com/vals/umis license: MIT summary: Tools for processing UMI RNA-tag data - -extra: - container: - # click relies on unicode support, which is not present in the default busybox image - base: bioconda/extended-base-image diff --git a/recipes/yahmm/meta.yaml b/recipes/yahmm/meta.yaml index 1971a6e7c7..9b6e61948a 100644 --- a/recipes/yahmm/meta.yaml +++ b/recipes/yahmm/meta.yaml @@ -39,4 +39,4 @@ about: extra: container: # matplotlib needs opengl support - base: bioconda/extended-base-image + extended-base: true From 21ef87b6312a8d48c27629c630fb579b193e5808 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 09:32:07 +0200 Subject: [PATCH 101/114] Add zlib to bx-python. --- recipes/bx-python/0.7.1/meta.yaml | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/recipes/bx-python/0.7.1/meta.yaml b/recipes/bx-python/0.7.1/meta.yaml index 296e96b548..df0b49a778 100644 --- a/recipes/bx-python/0.7.1/meta.yaml +++ b/recipes/bx-python/0.7.1/meta.yaml @@ -18,11 +18,14 @@ requirements: - cython - nose - numpy x.x + - zlib run: - python - setuptools - numpy x.x + - zlib + source: fn: bx-python-0.7.1.tar.gz sha256: 9ff7b5354de03c463da6d245d3256a41966e718a16f4021b7f8d4861305c9ea1 @@ -54,4 +57,3 @@ test: requires: # Put any additional test requirements here. For example - nose - From 364f7c20a7a2a705c7d1d9d0dc6b3057a032f02e Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 10:10:47 +0200 Subject: [PATCH 102/114] Fixes. --- recipes/bx-python/0.7.1/meta.yaml | 4 ---- recipes/bx-python/meta.yaml | 4 ---- 2 files changed, 8 deletions(-) diff --git a/recipes/bx-python/0.7.1/meta.yaml b/recipes/bx-python/0.7.1/meta.yaml index df0b49a778..96b396096d 100644 --- a/recipes/bx-python/0.7.1/meta.yaml +++ b/recipes/bx-python/0.7.1/meta.yaml @@ -53,7 +53,3 @@ test: - bx.align.tools - bx - bx.intseq - - requires: - # Put any additional test requirements here. For example - - nose diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index d051e5317b..3ab40b236f 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -48,10 +48,6 @@ 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 From 57f6a1dc27cdc22ce7a83b353fd33eb364205933 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 14:43:25 +0200 Subject: [PATCH 103/114] Add missing dependency. --- recipes/samsifter/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 02a171f795..f858bb12ad 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -33,6 +33,7 @@ requirements: - pandas >=0.14.1 - numpy >=1.6.1 - pyqt 4.11.* + - glib run: - python - matplotlib >=1.3.1 @@ -41,6 +42,7 @@ requirements: - pyqt 4.11.* # workaround for missing dependency of pandas - libgcc + - glib test: # Python imports From 94f0bd7f4c0896ead5ad01457ecf0d1f24084f36 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 14:47:36 +0200 Subject: [PATCH 104/114] Add gcc. --- recipes/bx-python/0.7.1/meta.yaml | 2 ++ recipes/bx-python/meta.yaml | 2 ++ recipes/samsifter/meta.yaml | 4 +++- 3 files changed, 7 insertions(+), 1 deletion(-) diff --git a/recipes/bx-python/0.7.1/meta.yaml b/recipes/bx-python/0.7.1/meta.yaml index 96b396096d..2b3c6b90b3 100644 --- a/recipes/bx-python/0.7.1/meta.yaml +++ b/recipes/bx-python/0.7.1/meta.yaml @@ -19,12 +19,14 @@ requirements: - nose - numpy x.x - zlib + - gcc run: - python - setuptools - numpy x.x - zlib + - libgcc source: fn: bx-python-0.7.1.tar.gz diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index 3ab40b236f..9794b094da 100644 --- a/recipes/bx-python/meta.yaml +++ b/recipes/bx-python/meta.yaml @@ -19,11 +19,13 @@ requirements: - cython - nose - numpy x.x + - gcc run: - python - setuptools - numpy x.x + - libgcc test: imports: diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index f858bb12ad..902d1e093d 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -9,7 +9,7 @@ source: build: skip: True # [py27] - number: 1 + number: 2 entry_points: - compile_stats=samsifter.stats.compile_stats:main - count_taxon_reads=samsifter.tools.count_taxon_reads:main @@ -34,6 +34,7 @@ requirements: - numpy >=1.6.1 - pyqt 4.11.* - glib + - xorg-libsm run: - python - matplotlib >=1.3.1 @@ -43,6 +44,7 @@ requirements: # workaround for missing dependency of pandas - libgcc - glib + - xorg-libsm test: # Python imports From 5aaf23b516936000065871037b2b2faede254dbe Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 15:31:56 +0200 Subject: [PATCH 105/114] Add missing dependency xz. --- recipes/qiime/1.9.1/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 307f885c8a..577281ee4f 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -34,6 +34,7 @@ requirements: - qiime-default-reference >=0.1.2,<0.2.0 - mock - nose + - xz run: - python @@ -61,6 +62,7 @@ requirements: - xorg-libsm - xorg-libxrender - xorg-libxau + - xz test: # Python imports From 06bc5709bc5dbe4c1c7626c7f6d8786d08af0ef9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 17:39:07 +0200 Subject: [PATCH 106/114] Remove bx-python 0.7.1 because it does not build even on python 2.7 --- recipes/bx-python/0.7.1/build.sh | 2 -- recipes/bx-python/0.7.1/meta.yaml | 57 --------------------------------------- 2 files changed, 59 deletions(-) delete mode 100644 recipes/bx-python/0.7.1/build.sh delete mode 100644 recipes/bx-python/0.7.1/meta.yaml 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 2b3c6b90b3..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 - - zlib - - gcc - - run: - - python - - setuptools - - numpy x.x - - zlib - - libgcc - -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 From 305cfcd9e2fbd5036a7025406f093c53806c6fb1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 17:41:05 +0200 Subject: [PATCH 107/114] Use extended base image. --- recipes/mercat/meta.yaml | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) 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 From 789408fe6ef77309c1c84b59591d636c71961968 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Thu, 1 Jun 2017 17:44:16 +0200 Subject: [PATCH 108/114] Add missing lib. --- recipes/samsifter/meta.yaml | 2 ++ 1 file changed, 2 insertions(+) diff --git a/recipes/samsifter/meta.yaml b/recipes/samsifter/meta.yaml index 902d1e093d..fae476f90f 100644 --- a/recipes/samsifter/meta.yaml +++ b/recipes/samsifter/meta.yaml @@ -35,6 +35,7 @@ requirements: - pyqt 4.11.* - glib - xorg-libsm + - xorg-libxrender run: - python - matplotlib >=1.3.1 @@ -45,6 +46,7 @@ requirements: - libgcc - glib - xorg-libsm + - xorg-libxrender test: # Python imports From 23956d16f22bbf9934be69df7b81b00284e7f0ab Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 2 Jun 2017 11:31:58 +0200 Subject: [PATCH 109/114] Use UTF-8 in test cases. --- recipes/qiime/1.9.1/meta.yaml | 314 +++++++++++++++++++++--------------------- 1 file changed, 157 insertions(+), 157 deletions(-) diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 577281ee4f..55747c4fd8 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -73,163 +73,163 @@ test: - qiime.sort commands: - - add_alpha_to_mapping_file.py -h - - add_qiime_labels.py -h - - adjust_seq_orientation.py -h - - align_seqs.py -h - - alpha_diversity.py -h - - alpha_rarefaction.py -h - - amplicon_contingency_table.py # no option - - ampliconnoise.py -h - - assign_taxonomy.py -h - - beta_diversity.py -h - - beta_diversity_through_plots.py -h - - beta_significance.py -h - - blast_wrapper.py -h - - categorized_dist_scatterplot.py -h - - check_id_map.py -h - - clean_raxml_parsimony_tree.py -h - - cluster_quality.py -h - - collapse_samples.py -h - - collate_alpha.py -h - - compare_alpha_diversity.py -h - - compare_categories.py -h - - compare_distance_matrices.py -h - - compare_taxa_summaries.py -h - - compare_trajectories.py -h - - compute_core_microbiome.py -h - - compute_taxonomy_ratios.py -h - - conditional_uncovered_probability.py -h - - consensus_tree.py -h - - convert_fastaqual_fastq.py -h - - convert_unifrac_sample_mapping_to_otu_table.py -h - - core_diversity_analyses.py -h - - count_seqs.py -h - - demultiplex_fasta.py -h - - denoise_wrapper.py -h - - denoiser.py -h - - denoiser_preprocess.py -h - - denoiser_worker.py -h - - detrend.py -h - - differential_abundance.py -h - - dissimilarity_mtx_stats.py -h - - distance_matrix_from_mapping.py -h - - estimate_observation_richness.py -h - - exclude_seqs_by_blast.py -h - - extract_barcodes.py -h - - extract_reads_from_interleaved_file.py -h - - extract_seqs_by_sample_id.py -h - - filter_alignment.py -h - - filter_distance_matrix.py -h - - filter_fasta.py -h - - filter_otus_by_sample.py -h - - filter_otus_from_otu_table.py -h - - filter_samples_from_otu_table.py -h - - filter_taxa_from_otu_table.py -h - - filter_tree.py -h - - fix_arb_fasta.py -h - - group_significance.py -h - - identify_chimeric_seqs.py -h - - identify_missing_files.py -h - - identify_paired_differences.py -h - - inflate_denoiser_output.py -h - - jackknifed_beta_diversity.py -h - - join_paired_ends.py -h - - load_remote_mapping_file.py -h - - make_2d_plots.py -h - - make_bipartite_network.py -h - - make_bootstrapped_tree.py -h - - make_distance_boxplots.py -h - - make_distance_comparison_plots.py -h - - make_fastq.py -h - - make_library_id_lists.py -h - - make_otu_heatmap.py -h - - make_otu_heatmap_html.py -h - - make_otu_network.py -h - - make_otu_table.py -h - - make_per_library_sff.py -h - - make_phylogeny.py -h - - make_prefs_file.py -h - - make_qiime_py_file.py -h - - make_rarefaction_plots.py -h - - make_tep.py -h - - map_reads_to_reference.py -h - - merge_mapping_files.py -h - - merge_otu_maps.py -h - - merge_otu_tables.py -h - - multiple_extract_barcodes.py -h - - multiple_join_paired_ends.py -h - - multiple_rarefactions.py -h - - multiple_rarefactions_even_depth.py -h - - multiple_split_libraries_fastq.py -h - - neighbor_joining.py -h - - nmds.py -h - - normalize_table.py -h - - observation_metadata_correlation.py -h - - otu_category_significance.py -h - - parallel_align_seqs_pynast.py -h - - parallel_alpha_diversity.py -h - - parallel_assign_taxonomy_blast.py -h - - parallel_assign_taxonomy_rdp.py -h - - parallel_assign_taxonomy_uclust.py -h - - parallel_beta_diversity.py -h - - parallel_blast.py -h - - parallel_identify_chimeric_seqs.py -h - - parallel_map_reads_to_reference.py -h - - parallel_merge_otu_tables.py -h - - parallel_multiple_rarefactions.py -h - - parallel_pick_otus_blast.py -h - - parallel_pick_otus_sortmerna.py -h - - parallel_pick_otus_trie.py -h - - parallel_pick_otus_uclust_ref.py -h - - parallel_pick_otus_usearch61_ref.py -h - - pick_closed_reference_otus.py -h - - pick_de_novo_otus.py -h - - pick_open_reference_otus.py -h - - pick_otus.py -h - - pick_rep_set.py -h - - plot_rank_abundance_graph.py -h - - plot_semivariogram.py -h - - plot_taxa_summary.py -h - - poller.py -h - - principal_coordinates.py -h - - print_metadata_stats.py -h - - print_qiime_config.py -h - - process_iseq.py -h - - process_qseq.py -h - - process_sff.py -h - - quality_scores_plot.py -h - - relatedness.py -h - - shared_phylotypes.py -h - - simsam.py -h - - single_rarefaction.py -h - - sort_otu_table.py -h - - split_libraries.py -h - - split_libraries_fastq.py -h - - split_libraries_lea_seq.py -h - - split_otu_table.py -h - - split_otu_table_by_taxonomy.py -h - - split_sequence_file_on_sample_ids.py -h - - start_parallel_jobs.py -h - - start_parallel_jobs_sc.py -h - - start_parallel_jobs_slurm.py -h - - start_parallel_jobs_torque.py -h - - subsample_fasta.py -h - - summarize_otu_by_cat.py -h - - summarize_taxa.py -h - - summarize_taxa_through_plots.py -h - - supervised_learning.py -h - - swarm_breaker.py -h - - transform_coordinate_matrices.py -h - - tree_compare.py -h - - trflp_file_to_otu_table.py -h - - trim_sff_primers.py -h - - truncate_fasta_qual_files.py -h - - truncate_reverse_primer.py -h - - unweight_fasta.py -h - - upgma_cluster.py -h - - validate_demultiplexed_fasta.py -h - - validate_mapping_file.py -h + - LANG=C.UTF-8 add_alpha_to_mapping_file.py -h + - LANG=C.UTF-8 add_qiime_labels.py -h + - LANG=C.UTF-8 adjust_seq_orientation.py -h + - LANG=C.UTF-8 align_seqs.py -h + - LANG=C.UTF-8 alpha_diversity.py -h + - LANG=C.UTF-8 alpha_rarefaction.py -h + - LANG=C.UTF-8 amplicon_contingency_table.py # no option + - LANG=C.UTF-8 ampliconnoise.py -h + - LANG=C.UTF-8 assign_taxonomy.py -h + - LANG=C.UTF-8 beta_diversity.py -h + - LANG=C.UTF-8 beta_diversity_through_plots.py -h + - LANG=C.UTF-8 beta_significance.py -h + - LANG=C.UTF-8 blast_wrapper.py -h + - LANG=C.UTF-8 categorized_dist_scatterplot.py -h + - LANG=C.UTF-8 check_id_map.py -h + - LANG=C.UTF-8 clean_raxml_parsimony_tree.py -h + - LANG=C.UTF-8 cluster_quality.py -h + - LANG=C.UTF-8 collapse_samples.py -h + - LANG=C.UTF-8 collate_alpha.py -h + - LANG=C.UTF-8 compare_alpha_diversity.py -h + - LANG=C.UTF-8 compare_categories.py -h + - LANG=C.UTF-8 compare_distance_matrices.py -h + - LANG=C.UTF-8 compare_taxa_summaries.py -h + - LANG=C.UTF-8 compare_trajectories.py -h + - LANG=C.UTF-8 compute_core_microbiome.py -h + - LANG=C.UTF-8 compute_taxonomy_ratios.py -h + - LANG=C.UTF-8 conditional_uncovered_probability.py -h + - LANG=C.UTF-8 consensus_tree.py -h + - LANG=C.UTF-8 convert_fastaqual_fastq.py -h + - LANG=C.UTF-8 convert_unifrac_sample_mapping_to_otu_table.py -h + - LANG=C.UTF-8 core_diversity_analyses.py -h + - LANG=C.UTF-8 count_seqs.py -h + - LANG=C.UTF-8 demultiplex_fasta.py -h + - LANG=C.UTF-8 denoise_wrapper.py -h + - LANG=C.UTF-8 denoiser.py -h + - LANG=C.UTF-8 denoiser_preprocess.py -h + - LANG=C.UTF-8 denoiser_worker.py -h + - LANG=C.UTF-8 detrend.py -h + - LANG=C.UTF-8 differential_abundance.py -h + - LANG=C.UTF-8 dissimilarity_mtx_stats.py -h + - LANG=C.UTF-8 distance_matrix_from_mapping.py -h + - LANG=C.UTF-8 estimate_observation_richness.py -h + - LANG=C.UTF-8 exclude_seqs_by_blast.py -h + - LANG=C.UTF-8 extract_barcodes.py -h + - LANG=C.UTF-8 extract_reads_from_interleaved_file.py -h + - LANG=C.UTF-8 extract_seqs_by_sample_id.py -h + - LANG=C.UTF-8 filter_alignment.py -h + - LANG=C.UTF-8 filter_distance_matrix.py -h + - LANG=C.UTF-8 filter_fasta.py -h + - LANG=C.UTF-8 filter_otus_by_sample.py -h + - LANG=C.UTF-8 filter_otus_from_otu_table.py -h + - LANG=C.UTF-8 filter_samples_from_otu_table.py -h + - LANG=C.UTF-8 filter_taxa_from_otu_table.py -h + - LANG=C.UTF-8 filter_tree.py -h + - LANG=C.UTF-8 fix_arb_fasta.py -h + - LANG=C.UTF-8 group_significance.py -h + - LANG=C.UTF-8 identify_chimeric_seqs.py -h + - LANG=C.UTF-8 identify_missing_files.py -h + - LANG=C.UTF-8 identify_paired_differences.py -h + - LANG=C.UTF-8 inflate_denoiser_output.py -h + - LANG=C.UTF-8 jackknifed_beta_diversity.py -h + - LANG=C.UTF-8 join_paired_ends.py -h + - LANG=C.UTF-8 load_remote_mapping_file.py -h + - LANG=C.UTF-8 make_2d_plots.py -h + - LANG=C.UTF-8 make_bipartite_network.py -h + - LANG=C.UTF-8 make_bootstrapped_tree.py -h + - LANG=C.UTF-8 make_distance_boxplots.py -h + - LANG=C.UTF-8 make_distance_comparison_plots.py -h + - LANG=C.UTF-8 make_fastq.py -h + - LANG=C.UTF-8 make_library_id_lists.py -h + - LANG=C.UTF-8 make_otu_heatmap.py -h + - LANG=C.UTF-8 make_otu_heatmap_html.py -h + - LANG=C.UTF-8 make_otu_network.py -h + - LANG=C.UTF-8 make_otu_table.py -h + - LANG=C.UTF-8 make_per_library_sff.py -h + - LANG=C.UTF-8 make_phylogeny.py -h + - LANG=C.UTF-8 make_prefs_file.py -h + - LANG=C.UTF-8 make_qiime_py_file.py -h + - LANG=C.UTF-8 make_rarefaction_plots.py -h + - LANG=C.UTF-8 make_tep.py -h + - LANG=C.UTF-8 map_reads_to_reference.py -h + - LANG=C.UTF-8 merge_mapping_files.py -h + - LANG=C.UTF-8 merge_otu_maps.py -h + - LANG=C.UTF-8 merge_otu_tables.py -h + - LANG=C.UTF-8 multiple_extract_barcodes.py -h + - LANG=C.UTF-8 multiple_join_paired_ends.py -h + - LANG=C.UTF-8 multiple_rarefactions.py -h + - LANG=C.UTF-8 multiple_rarefactions_even_depth.py -h + - LANG=C.UTF-8 multiple_split_libraries_fastq.py -h + - LANG=C.UTF-8 neighbor_joining.py -h + - LANG=C.UTF-8 nmds.py -h + - LANG=C.UTF-8 normalize_table.py -h + - LANG=C.UTF-8 observation_metadata_correlation.py -h + - LANG=C.UTF-8 otu_category_significance.py -h + - LANG=C.UTF-8 parallel_align_seqs_pynast.py -h + - LANG=C.UTF-8 parallel_alpha_diversity.py -h + - LANG=C.UTF-8 parallel_assign_taxonomy_blast.py -h + - LANG=C.UTF-8 parallel_assign_taxonomy_rdp.py -h + - LANG=C.UTF-8 parallel_assign_taxonomy_uclust.py -h + - LANG=C.UTF-8 parallel_beta_diversity.py -h + - LANG=C.UTF-8 parallel_blast.py -h + - LANG=C.UTF-8 parallel_identify_chimeric_seqs.py -h + - LANG=C.UTF-8 parallel_map_reads_to_reference.py -h + - LANG=C.UTF-8 parallel_merge_otu_tables.py -h + - LANG=C.UTF-8 parallel_multiple_rarefactions.py -h + - LANG=C.UTF-8 parallel_pick_otus_blast.py -h + - LANG=C.UTF-8 parallel_pick_otus_sortmerna.py -h + - LANG=C.UTF-8 parallel_pick_otus_trie.py -h + - LANG=C.UTF-8 parallel_pick_otus_uclust_ref.py -h + - LANG=C.UTF-8 parallel_pick_otus_usearch61_ref.py -h + - LANG=C.UTF-8 pick_closed_reference_otus.py -h + - LANG=C.UTF-8 pick_de_novo_otus.py -h + - LANG=C.UTF-8 pick_open_reference_otus.py -h + - LANG=C.UTF-8 pick_otus.py -h + - LANG=C.UTF-8 pick_rep_set.py -h + - LANG=C.UTF-8 plot_rank_abundance_graph.py -h + - LANG=C.UTF-8 plot_semivariogram.py -h + - LANG=C.UTF-8 plot_taxa_summary.py -h + - LANG=C.UTF-8 poller.py -h + - LANG=C.UTF-8 principal_coordinates.py -h + - LANG=C.UTF-8 print_metadata_stats.py -h + - LANG=C.UTF-8 print_qiime_config.py -h + - LANG=C.UTF-8 process_iseq.py -h + - LANG=C.UTF-8 process_qseq.py -h + - LANG=C.UTF-8 process_sff.py -h + - LANG=C.UTF-8 quality_scores_plot.py -h + - LANG=C.UTF-8 relatedness.py -h + - LANG=C.UTF-8 shared_phylotypes.py -h + - LANG=C.UTF-8 simsam.py -h + - LANG=C.UTF-8 single_rarefaction.py -h + - LANG=C.UTF-8 sort_otu_table.py -h + - LANG=C.UTF-8 split_libraries.py -h + - LANG=C.UTF-8 split_libraries_fastq.py -h + - LANG=C.UTF-8 split_libraries_lea_seq.py -h + - LANG=C.UTF-8 split_otu_table.py -h + - LANG=C.UTF-8 split_otu_table_by_taxonomy.py -h + - LANG=C.UTF-8 split_sequence_file_on_sample_ids.py -h + - LANG=C.UTF-8 start_parallel_jobs.py -h + - LANG=C.UTF-8 start_parallel_jobs_sc.py -h + - LANG=C.UTF-8 start_parallel_jobs_slurm.py -h + - LANG=C.UTF-8 start_parallel_jobs_torque.py -h + - LANG=C.UTF-8 subsample_fasta.py -h + - LANG=C.UTF-8 summarize_otu_by_cat.py -h + - LANG=C.UTF-8 summarize_taxa.py -h + - LANG=C.UTF-8 summarize_taxa_through_plots.py -h + - LANG=C.UTF-8 supervised_learning.py -h + - LANG=C.UTF-8 swarm_breaker.py -h + - LANG=C.UTF-8 transform_coordinate_matrices.py -h + - LANG=C.UTF-8 tree_compare.py -h + - LANG=C.UTF-8 trflp_file_to_otu_table.py -h + - LANG=C.UTF-8 trim_sff_primers.py -h + - LANG=C.UTF-8 truncate_fasta_qual_files.py -h + - LANG=C.UTF-8 truncate_reverse_primer.py -h + - LANG=C.UTF-8 unweight_fasta.py -h + - LANG=C.UTF-8 upgma_cluster.py -h + - LANG=C.UTF-8 validate_demultiplexed_fasta.py -h + - LANG=C.UTF-8 validate_mapping_file.py -h about: home: http://www.qiime.org From 7532b1221cfe7e919fc01b66db384175fa19bdaf Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 2 Jun 2017 11:33:27 +0200 Subject: [PATCH 110/114] Debug bx-python. --- recipes/bx-python/build.sh | 7 ++----- 1 file changed, 2 insertions(+), 5 deletions(-) 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. From cb195980c48f1bfba3030a95bcb3d06d23379b15 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 2 Jun 2017 13:48:28 +0200 Subject: [PATCH 111/114] Fix qiime. Use test branch of bioconda-utils. --- .travis.yml | 2 +- recipes/qiime/1.9.1/meta.yaml | 320 +++++++++++++++++++++--------------------- 2 files changed, 164 insertions(+), 158 deletions(-) diff --git a/.travis.yml b/.travis.yml index a9515727ff..d3c3a5f2e6 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ script: scripts/travis-run.sh env: global: - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=master + - BIOCONDA_UTILS_TAG=quiet-docker-build-output - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 55747c4fd8..9a9e109370 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -73,165 +73,171 @@ test: - qiime.sort commands: - - LANG=C.UTF-8 add_alpha_to_mapping_file.py -h - - LANG=C.UTF-8 add_qiime_labels.py -h - - LANG=C.UTF-8 adjust_seq_orientation.py -h - - LANG=C.UTF-8 align_seqs.py -h - - LANG=C.UTF-8 alpha_diversity.py -h - - LANG=C.UTF-8 alpha_rarefaction.py -h - - LANG=C.UTF-8 amplicon_contingency_table.py # no option - - LANG=C.UTF-8 ampliconnoise.py -h - - LANG=C.UTF-8 assign_taxonomy.py -h - - LANG=C.UTF-8 beta_diversity.py -h - - LANG=C.UTF-8 beta_diversity_through_plots.py -h - - LANG=C.UTF-8 beta_significance.py -h - - LANG=C.UTF-8 blast_wrapper.py -h - - LANG=C.UTF-8 categorized_dist_scatterplot.py -h - - LANG=C.UTF-8 check_id_map.py -h - - LANG=C.UTF-8 clean_raxml_parsimony_tree.py -h - - LANG=C.UTF-8 cluster_quality.py -h - - LANG=C.UTF-8 collapse_samples.py -h - - LANG=C.UTF-8 collate_alpha.py -h - - LANG=C.UTF-8 compare_alpha_diversity.py -h - - LANG=C.UTF-8 compare_categories.py -h - - LANG=C.UTF-8 compare_distance_matrices.py -h - - LANG=C.UTF-8 compare_taxa_summaries.py -h - - LANG=C.UTF-8 compare_trajectories.py -h - - LANG=C.UTF-8 compute_core_microbiome.py -h - - LANG=C.UTF-8 compute_taxonomy_ratios.py -h - - LANG=C.UTF-8 conditional_uncovered_probability.py -h - - LANG=C.UTF-8 consensus_tree.py -h - - LANG=C.UTF-8 convert_fastaqual_fastq.py -h - - LANG=C.UTF-8 convert_unifrac_sample_mapping_to_otu_table.py -h - - LANG=C.UTF-8 core_diversity_analyses.py -h - - LANG=C.UTF-8 count_seqs.py -h - - LANG=C.UTF-8 demultiplex_fasta.py -h - - LANG=C.UTF-8 denoise_wrapper.py -h - - LANG=C.UTF-8 denoiser.py -h - - LANG=C.UTF-8 denoiser_preprocess.py -h - - LANG=C.UTF-8 denoiser_worker.py -h - - LANG=C.UTF-8 detrend.py -h - - LANG=C.UTF-8 differential_abundance.py -h - - LANG=C.UTF-8 dissimilarity_mtx_stats.py -h - - LANG=C.UTF-8 distance_matrix_from_mapping.py -h - - LANG=C.UTF-8 estimate_observation_richness.py -h - - LANG=C.UTF-8 exclude_seqs_by_blast.py -h - - LANG=C.UTF-8 extract_barcodes.py -h - - LANG=C.UTF-8 extract_reads_from_interleaved_file.py -h - - LANG=C.UTF-8 extract_seqs_by_sample_id.py -h - - LANG=C.UTF-8 filter_alignment.py -h - - LANG=C.UTF-8 filter_distance_matrix.py -h - - LANG=C.UTF-8 filter_fasta.py -h - - LANG=C.UTF-8 filter_otus_by_sample.py -h - - LANG=C.UTF-8 filter_otus_from_otu_table.py -h - - LANG=C.UTF-8 filter_samples_from_otu_table.py -h - - LANG=C.UTF-8 filter_taxa_from_otu_table.py -h - - LANG=C.UTF-8 filter_tree.py -h - - LANG=C.UTF-8 fix_arb_fasta.py -h - - LANG=C.UTF-8 group_significance.py -h - - LANG=C.UTF-8 identify_chimeric_seqs.py -h - - LANG=C.UTF-8 identify_missing_files.py -h - - LANG=C.UTF-8 identify_paired_differences.py -h - - LANG=C.UTF-8 inflate_denoiser_output.py -h - - LANG=C.UTF-8 jackknifed_beta_diversity.py -h - - LANG=C.UTF-8 join_paired_ends.py -h - - LANG=C.UTF-8 load_remote_mapping_file.py -h - - LANG=C.UTF-8 make_2d_plots.py -h - - LANG=C.UTF-8 make_bipartite_network.py -h - - LANG=C.UTF-8 make_bootstrapped_tree.py -h - - LANG=C.UTF-8 make_distance_boxplots.py -h - - LANG=C.UTF-8 make_distance_comparison_plots.py -h - - LANG=C.UTF-8 make_fastq.py -h - - LANG=C.UTF-8 make_library_id_lists.py -h - - LANG=C.UTF-8 make_otu_heatmap.py -h - - LANG=C.UTF-8 make_otu_heatmap_html.py -h - - LANG=C.UTF-8 make_otu_network.py -h - - LANG=C.UTF-8 make_otu_table.py -h - - LANG=C.UTF-8 make_per_library_sff.py -h - - LANG=C.UTF-8 make_phylogeny.py -h - - LANG=C.UTF-8 make_prefs_file.py -h - - LANG=C.UTF-8 make_qiime_py_file.py -h - - LANG=C.UTF-8 make_rarefaction_plots.py -h - - LANG=C.UTF-8 make_tep.py -h - - LANG=C.UTF-8 map_reads_to_reference.py -h - - LANG=C.UTF-8 merge_mapping_files.py -h - - LANG=C.UTF-8 merge_otu_maps.py -h - - LANG=C.UTF-8 merge_otu_tables.py -h - - LANG=C.UTF-8 multiple_extract_barcodes.py -h - - LANG=C.UTF-8 multiple_join_paired_ends.py -h - - LANG=C.UTF-8 multiple_rarefactions.py -h - - LANG=C.UTF-8 multiple_rarefactions_even_depth.py -h - - LANG=C.UTF-8 multiple_split_libraries_fastq.py -h - - LANG=C.UTF-8 neighbor_joining.py -h - - LANG=C.UTF-8 nmds.py -h - - LANG=C.UTF-8 normalize_table.py -h - - LANG=C.UTF-8 observation_metadata_correlation.py -h - - LANG=C.UTF-8 otu_category_significance.py -h - - LANG=C.UTF-8 parallel_align_seqs_pynast.py -h - - LANG=C.UTF-8 parallel_alpha_diversity.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_blast.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_rdp.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_uclust.py -h - - LANG=C.UTF-8 parallel_beta_diversity.py -h - - LANG=C.UTF-8 parallel_blast.py -h - - LANG=C.UTF-8 parallel_identify_chimeric_seqs.py -h - - LANG=C.UTF-8 parallel_map_reads_to_reference.py -h - - LANG=C.UTF-8 parallel_merge_otu_tables.py -h - - LANG=C.UTF-8 parallel_multiple_rarefactions.py -h - - LANG=C.UTF-8 parallel_pick_otus_blast.py -h - - LANG=C.UTF-8 parallel_pick_otus_sortmerna.py -h - - LANG=C.UTF-8 parallel_pick_otus_trie.py -h - - LANG=C.UTF-8 parallel_pick_otus_uclust_ref.py -h - - LANG=C.UTF-8 parallel_pick_otus_usearch61_ref.py -h - - LANG=C.UTF-8 pick_closed_reference_otus.py -h - - LANG=C.UTF-8 pick_de_novo_otus.py -h - - LANG=C.UTF-8 pick_open_reference_otus.py -h - - LANG=C.UTF-8 pick_otus.py -h - - LANG=C.UTF-8 pick_rep_set.py -h - - LANG=C.UTF-8 plot_rank_abundance_graph.py -h - - LANG=C.UTF-8 plot_semivariogram.py -h - - LANG=C.UTF-8 plot_taxa_summary.py -h - - LANG=C.UTF-8 poller.py -h - - LANG=C.UTF-8 principal_coordinates.py -h - - LANG=C.UTF-8 print_metadata_stats.py -h - - LANG=C.UTF-8 print_qiime_config.py -h - - LANG=C.UTF-8 process_iseq.py -h - - LANG=C.UTF-8 process_qseq.py -h - - LANG=C.UTF-8 process_sff.py -h - - LANG=C.UTF-8 quality_scores_plot.py -h - - LANG=C.UTF-8 relatedness.py -h - - LANG=C.UTF-8 shared_phylotypes.py -h - - LANG=C.UTF-8 simsam.py -h - - LANG=C.UTF-8 single_rarefaction.py -h - - LANG=C.UTF-8 sort_otu_table.py -h - - LANG=C.UTF-8 split_libraries.py -h - - LANG=C.UTF-8 split_libraries_fastq.py -h - - LANG=C.UTF-8 split_libraries_lea_seq.py -h - - LANG=C.UTF-8 split_otu_table.py -h - - LANG=C.UTF-8 split_otu_table_by_taxonomy.py -h - - LANG=C.UTF-8 split_sequence_file_on_sample_ids.py -h - - LANG=C.UTF-8 start_parallel_jobs.py -h - - LANG=C.UTF-8 start_parallel_jobs_sc.py -h - - LANG=C.UTF-8 start_parallel_jobs_slurm.py -h - - LANG=C.UTF-8 start_parallel_jobs_torque.py -h - - LANG=C.UTF-8 subsample_fasta.py -h - - LANG=C.UTF-8 summarize_otu_by_cat.py -h - - LANG=C.UTF-8 summarize_taxa.py -h - - LANG=C.UTF-8 summarize_taxa_through_plots.py -h - - LANG=C.UTF-8 supervised_learning.py -h - - LANG=C.UTF-8 swarm_breaker.py -h - - LANG=C.UTF-8 transform_coordinate_matrices.py -h - - LANG=C.UTF-8 tree_compare.py -h - - LANG=C.UTF-8 trflp_file_to_otu_table.py -h - - LANG=C.UTF-8 trim_sff_primers.py -h - - LANG=C.UTF-8 truncate_fasta_qual_files.py -h - - LANG=C.UTF-8 truncate_reverse_primer.py -h - - LANG=C.UTF-8 unweight_fasta.py -h - - LANG=C.UTF-8 upgma_cluster.py -h - - LANG=C.UTF-8 validate_demultiplexed_fasta.py -h - - LANG=C.UTF-8 validate_mapping_file.py -h + - add_alpha_to_mapping_file.py -h + - add_qiime_labels.py -h + - adjust_seq_orientation.py -h + - align_seqs.py -h + - alpha_diversity.py -h + - alpha_rarefaction.py -h + - amplicon_contingency_table.py # no option + - ampliconnoise.py -h + - assign_taxonomy.py -h + - beta_diversity.py -h + - beta_diversity_through_plots.py -h + - beta_significance.py -h + - blast_wrapper.py -h + - categorized_dist_scatterplot.py -h + - check_id_map.py -h + - clean_raxml_parsimony_tree.py -h + - cluster_quality.py -h + - collapse_samples.py -h + - collate_alpha.py -h + - compare_alpha_diversity.py -h + - compare_categories.py -h + - compare_distance_matrices.py -h + - compare_taxa_summaries.py -h + - compare_trajectories.py -h + - compute_core_microbiome.py -h + - compute_taxonomy_ratios.py -h + - conditional_uncovered_probability.py -h + - consensus_tree.py -h + - convert_fastaqual_fastq.py -h + - convert_unifrac_sample_mapping_to_otu_table.py -h + - core_diversity_analyses.py -h + - count_seqs.py -h + - demultiplex_fasta.py -h + - denoise_wrapper.py -h + - denoiser.py -h + - denoiser_preprocess.py -h + - denoiser_worker.py -h + - detrend.py -h + - differential_abundance.py -h + - dissimilarity_mtx_stats.py -h + - distance_matrix_from_mapping.py -h + - estimate_observation_richness.py -h + - exclude_seqs_by_blast.py -h + - extract_barcodes.py -h + - extract_reads_from_interleaved_file.py -h + - extract_seqs_by_sample_id.py -h + - filter_alignment.py -h + - filter_distance_matrix.py -h + - filter_fasta.py -h + - filter_otus_by_sample.py -h + - filter_otus_from_otu_table.py -h + - filter_samples_from_otu_table.py -h + - filter_taxa_from_otu_table.py -h + - filter_tree.py -h + - fix_arb_fasta.py -h + - group_significance.py -h + - identify_chimeric_seqs.py -h + - identify_missing_files.py -h + - identify_paired_differences.py -h + - inflate_denoiser_output.py -h + - jackknifed_beta_diversity.py -h + - join_paired_ends.py -h + - load_remote_mapping_file.py -h + - make_2d_plots.py -h + - make_bipartite_network.py -h + - make_bootstrapped_tree.py -h + - make_distance_boxplots.py -h + - make_distance_comparison_plots.py -h + - make_fastq.py -h + - make_library_id_lists.py -h + - make_otu_heatmap.py -h + - make_otu_heatmap_html.py -h + - make_otu_network.py -h + - make_otu_table.py -h + - make_per_library_sff.py -h + - make_phylogeny.py -h + - make_prefs_file.py -h + - make_qiime_py_file.py -h + - make_rarefaction_plots.py -h + - make_tep.py -h + - map_reads_to_reference.py -h + - merge_mapping_files.py -h + - merge_otu_maps.py -h + - merge_otu_tables.py -h + - multiple_extract_barcodes.py -h + - multiple_join_paired_ends.py -h + - multiple_rarefactions.py -h + - multiple_rarefactions_even_depth.py -h + - multiple_split_libraries_fastq.py -h + - neighbor_joining.py -h + - nmds.py -h + - normalize_table.py -h + - observation_metadata_correlation.py -h + - otu_category_significance.py -h + - parallel_align_seqs_pynast.py -h + - parallel_alpha_diversity.py -h + - parallel_assign_taxonomy_blast.py -h + - parallel_assign_taxonomy_rdp.py -h + - parallel_assign_taxonomy_uclust.py -h + - parallel_beta_diversity.py -h + - parallel_blast.py -h + - parallel_identify_chimeric_seqs.py -h + - parallel_map_reads_to_reference.py -h + - parallel_merge_otu_tables.py -h + - parallel_multiple_rarefactions.py -h + - parallel_pick_otus_blast.py -h + - parallel_pick_otus_sortmerna.py -h + - parallel_pick_otus_trie.py -h + - parallel_pick_otus_uclust_ref.py -h + - parallel_pick_otus_usearch61_ref.py -h + - pick_closed_reference_otus.py -h + - pick_de_novo_otus.py -h + - pick_open_reference_otus.py -h + - pick_otus.py -h + - pick_rep_set.py -h + - plot_rank_abundance_graph.py -h + - plot_semivariogram.py -h + - plot_taxa_summary.py -h + - poller.py -h + - principal_coordinates.py -h + - print_metadata_stats.py -h + - print_qiime_config.py -h + - process_iseq.py -h + - process_qseq.py -h + - process_sff.py -h + - quality_scores_plot.py -h + - relatedness.py -h + - shared_phylotypes.py -h + - simsam.py -h + - single_rarefaction.py -h + - sort_otu_table.py -h + - split_libraries.py -h + - split_libraries_fastq.py -h + - split_libraries_lea_seq.py -h + - split_otu_table.py -h + - split_otu_table_by_taxonomy.py -h + - split_sequence_file_on_sample_ids.py -h + - start_parallel_jobs.py -h + - start_parallel_jobs_sc.py -h + - start_parallel_jobs_slurm.py -h + - start_parallel_jobs_torque.py -h + - subsample_fasta.py -h + - summarize_otu_by_cat.py -h + - summarize_taxa.py -h + - summarize_taxa_through_plots.py -h + - supervised_learning.py -h + - swarm_breaker.py -h + - transform_coordinate_matrices.py -h + - tree_compare.py -h + - trflp_file_to_otu_table.py -h + - trim_sff_primers.py -h + - truncate_fasta_qual_files.py -h + - truncate_reverse_primer.py -h + - unweight_fasta.py -h + - upgma_cluster.py -h + - validate_demultiplexed_fasta.py -h + - validate_mapping_file.py -h 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 From 9cb7c8006295fbd244d0910cd09b123565b3a6d1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Fri, 2 Jun 2017 13:48:28 +0200 Subject: [PATCH 112/114] Fix qiime. Use test branch of bioconda-utils. --- recipes/bx-python/meta.yaml | 7 +- recipes/qiime/1.9.1/meta.yaml | 320 +++++++++++++++++++++--------------------- 2 files changed, 168 insertions(+), 159 deletions(-) diff --git a/recipes/bx-python/meta.yaml b/recipes/bx-python/meta.yaml index 9794b094da..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: diff --git a/recipes/qiime/1.9.1/meta.yaml b/recipes/qiime/1.9.1/meta.yaml index 55747c4fd8..9a9e109370 100644 --- a/recipes/qiime/1.9.1/meta.yaml +++ b/recipes/qiime/1.9.1/meta.yaml @@ -73,165 +73,171 @@ test: - qiime.sort commands: - - LANG=C.UTF-8 add_alpha_to_mapping_file.py -h - - LANG=C.UTF-8 add_qiime_labels.py -h - - LANG=C.UTF-8 adjust_seq_orientation.py -h - - LANG=C.UTF-8 align_seqs.py -h - - LANG=C.UTF-8 alpha_diversity.py -h - - LANG=C.UTF-8 alpha_rarefaction.py -h - - LANG=C.UTF-8 amplicon_contingency_table.py # no option - - LANG=C.UTF-8 ampliconnoise.py -h - - LANG=C.UTF-8 assign_taxonomy.py -h - - LANG=C.UTF-8 beta_diversity.py -h - - LANG=C.UTF-8 beta_diversity_through_plots.py -h - - LANG=C.UTF-8 beta_significance.py -h - - LANG=C.UTF-8 blast_wrapper.py -h - - LANG=C.UTF-8 categorized_dist_scatterplot.py -h - - LANG=C.UTF-8 check_id_map.py -h - - LANG=C.UTF-8 clean_raxml_parsimony_tree.py -h - - LANG=C.UTF-8 cluster_quality.py -h - - LANG=C.UTF-8 collapse_samples.py -h - - LANG=C.UTF-8 collate_alpha.py -h - - LANG=C.UTF-8 compare_alpha_diversity.py -h - - LANG=C.UTF-8 compare_categories.py -h - - LANG=C.UTF-8 compare_distance_matrices.py -h - - LANG=C.UTF-8 compare_taxa_summaries.py -h - - LANG=C.UTF-8 compare_trajectories.py -h - - LANG=C.UTF-8 compute_core_microbiome.py -h - - LANG=C.UTF-8 compute_taxonomy_ratios.py -h - - LANG=C.UTF-8 conditional_uncovered_probability.py -h - - LANG=C.UTF-8 consensus_tree.py -h - - LANG=C.UTF-8 convert_fastaqual_fastq.py -h - - LANG=C.UTF-8 convert_unifrac_sample_mapping_to_otu_table.py -h - - LANG=C.UTF-8 core_diversity_analyses.py -h - - LANG=C.UTF-8 count_seqs.py -h - - LANG=C.UTF-8 demultiplex_fasta.py -h - - LANG=C.UTF-8 denoise_wrapper.py -h - - LANG=C.UTF-8 denoiser.py -h - - LANG=C.UTF-8 denoiser_preprocess.py -h - - LANG=C.UTF-8 denoiser_worker.py -h - - LANG=C.UTF-8 detrend.py -h - - LANG=C.UTF-8 differential_abundance.py -h - - LANG=C.UTF-8 dissimilarity_mtx_stats.py -h - - LANG=C.UTF-8 distance_matrix_from_mapping.py -h - - LANG=C.UTF-8 estimate_observation_richness.py -h - - LANG=C.UTF-8 exclude_seqs_by_blast.py -h - - LANG=C.UTF-8 extract_barcodes.py -h - - LANG=C.UTF-8 extract_reads_from_interleaved_file.py -h - - LANG=C.UTF-8 extract_seqs_by_sample_id.py -h - - LANG=C.UTF-8 filter_alignment.py -h - - LANG=C.UTF-8 filter_distance_matrix.py -h - - LANG=C.UTF-8 filter_fasta.py -h - - LANG=C.UTF-8 filter_otus_by_sample.py -h - - LANG=C.UTF-8 filter_otus_from_otu_table.py -h - - LANG=C.UTF-8 filter_samples_from_otu_table.py -h - - LANG=C.UTF-8 filter_taxa_from_otu_table.py -h - - LANG=C.UTF-8 filter_tree.py -h - - LANG=C.UTF-8 fix_arb_fasta.py -h - - LANG=C.UTF-8 group_significance.py -h - - LANG=C.UTF-8 identify_chimeric_seqs.py -h - - LANG=C.UTF-8 identify_missing_files.py -h - - LANG=C.UTF-8 identify_paired_differences.py -h - - LANG=C.UTF-8 inflate_denoiser_output.py -h - - LANG=C.UTF-8 jackknifed_beta_diversity.py -h - - LANG=C.UTF-8 join_paired_ends.py -h - - LANG=C.UTF-8 load_remote_mapping_file.py -h - - LANG=C.UTF-8 make_2d_plots.py -h - - LANG=C.UTF-8 make_bipartite_network.py -h - - LANG=C.UTF-8 make_bootstrapped_tree.py -h - - LANG=C.UTF-8 make_distance_boxplots.py -h - - LANG=C.UTF-8 make_distance_comparison_plots.py -h - - LANG=C.UTF-8 make_fastq.py -h - - LANG=C.UTF-8 make_library_id_lists.py -h - - LANG=C.UTF-8 make_otu_heatmap.py -h - - LANG=C.UTF-8 make_otu_heatmap_html.py -h - - LANG=C.UTF-8 make_otu_network.py -h - - LANG=C.UTF-8 make_otu_table.py -h - - LANG=C.UTF-8 make_per_library_sff.py -h - - LANG=C.UTF-8 make_phylogeny.py -h - - LANG=C.UTF-8 make_prefs_file.py -h - - LANG=C.UTF-8 make_qiime_py_file.py -h - - LANG=C.UTF-8 make_rarefaction_plots.py -h - - LANG=C.UTF-8 make_tep.py -h - - LANG=C.UTF-8 map_reads_to_reference.py -h - - LANG=C.UTF-8 merge_mapping_files.py -h - - LANG=C.UTF-8 merge_otu_maps.py -h - - LANG=C.UTF-8 merge_otu_tables.py -h - - LANG=C.UTF-8 multiple_extract_barcodes.py -h - - LANG=C.UTF-8 multiple_join_paired_ends.py -h - - LANG=C.UTF-8 multiple_rarefactions.py -h - - LANG=C.UTF-8 multiple_rarefactions_even_depth.py -h - - LANG=C.UTF-8 multiple_split_libraries_fastq.py -h - - LANG=C.UTF-8 neighbor_joining.py -h - - LANG=C.UTF-8 nmds.py -h - - LANG=C.UTF-8 normalize_table.py -h - - LANG=C.UTF-8 observation_metadata_correlation.py -h - - LANG=C.UTF-8 otu_category_significance.py -h - - LANG=C.UTF-8 parallel_align_seqs_pynast.py -h - - LANG=C.UTF-8 parallel_alpha_diversity.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_blast.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_rdp.py -h - - LANG=C.UTF-8 parallel_assign_taxonomy_uclust.py -h - - LANG=C.UTF-8 parallel_beta_diversity.py -h - - LANG=C.UTF-8 parallel_blast.py -h - - LANG=C.UTF-8 parallel_identify_chimeric_seqs.py -h - - LANG=C.UTF-8 parallel_map_reads_to_reference.py -h - - LANG=C.UTF-8 parallel_merge_otu_tables.py -h - - LANG=C.UTF-8 parallel_multiple_rarefactions.py -h - - LANG=C.UTF-8 parallel_pick_otus_blast.py -h - - LANG=C.UTF-8 parallel_pick_otus_sortmerna.py -h - - LANG=C.UTF-8 parallel_pick_otus_trie.py -h - - LANG=C.UTF-8 parallel_pick_otus_uclust_ref.py -h - - LANG=C.UTF-8 parallel_pick_otus_usearch61_ref.py -h - - LANG=C.UTF-8 pick_closed_reference_otus.py -h - - LANG=C.UTF-8 pick_de_novo_otus.py -h - - LANG=C.UTF-8 pick_open_reference_otus.py -h - - LANG=C.UTF-8 pick_otus.py -h - - LANG=C.UTF-8 pick_rep_set.py -h - - LANG=C.UTF-8 plot_rank_abundance_graph.py -h - - LANG=C.UTF-8 plot_semivariogram.py -h - - LANG=C.UTF-8 plot_taxa_summary.py -h - - LANG=C.UTF-8 poller.py -h - - LANG=C.UTF-8 principal_coordinates.py -h - - LANG=C.UTF-8 print_metadata_stats.py -h - - LANG=C.UTF-8 print_qiime_config.py -h - - LANG=C.UTF-8 process_iseq.py -h - - LANG=C.UTF-8 process_qseq.py -h - - LANG=C.UTF-8 process_sff.py -h - - LANG=C.UTF-8 quality_scores_plot.py -h - - LANG=C.UTF-8 relatedness.py -h - - LANG=C.UTF-8 shared_phylotypes.py -h - - LANG=C.UTF-8 simsam.py -h - - LANG=C.UTF-8 single_rarefaction.py -h - - LANG=C.UTF-8 sort_otu_table.py -h - - LANG=C.UTF-8 split_libraries.py -h - - LANG=C.UTF-8 split_libraries_fastq.py -h - - LANG=C.UTF-8 split_libraries_lea_seq.py -h - - LANG=C.UTF-8 split_otu_table.py -h - - LANG=C.UTF-8 split_otu_table_by_taxonomy.py -h - - LANG=C.UTF-8 split_sequence_file_on_sample_ids.py -h - - LANG=C.UTF-8 start_parallel_jobs.py -h - - LANG=C.UTF-8 start_parallel_jobs_sc.py -h - - LANG=C.UTF-8 start_parallel_jobs_slurm.py -h - - LANG=C.UTF-8 start_parallel_jobs_torque.py -h - - LANG=C.UTF-8 subsample_fasta.py -h - - LANG=C.UTF-8 summarize_otu_by_cat.py -h - - LANG=C.UTF-8 summarize_taxa.py -h - - LANG=C.UTF-8 summarize_taxa_through_plots.py -h - - LANG=C.UTF-8 supervised_learning.py -h - - LANG=C.UTF-8 swarm_breaker.py -h - - LANG=C.UTF-8 transform_coordinate_matrices.py -h - - LANG=C.UTF-8 tree_compare.py -h - - LANG=C.UTF-8 trflp_file_to_otu_table.py -h - - LANG=C.UTF-8 trim_sff_primers.py -h - - LANG=C.UTF-8 truncate_fasta_qual_files.py -h - - LANG=C.UTF-8 truncate_reverse_primer.py -h - - LANG=C.UTF-8 unweight_fasta.py -h - - LANG=C.UTF-8 upgma_cluster.py -h - - LANG=C.UTF-8 validate_demultiplexed_fasta.py -h - - LANG=C.UTF-8 validate_mapping_file.py -h + - add_alpha_to_mapping_file.py -h + - add_qiime_labels.py -h + - adjust_seq_orientation.py -h + - align_seqs.py -h + - alpha_diversity.py -h + - alpha_rarefaction.py -h + - amplicon_contingency_table.py # no option + - ampliconnoise.py -h + - assign_taxonomy.py -h + - beta_diversity.py -h + - beta_diversity_through_plots.py -h + - beta_significance.py -h + - blast_wrapper.py -h + - categorized_dist_scatterplot.py -h + - check_id_map.py -h + - clean_raxml_parsimony_tree.py -h + - cluster_quality.py -h + - collapse_samples.py -h + - collate_alpha.py -h + - compare_alpha_diversity.py -h + - compare_categories.py -h + - compare_distance_matrices.py -h + - compare_taxa_summaries.py -h + - compare_trajectories.py -h + - compute_core_microbiome.py -h + - compute_taxonomy_ratios.py -h + - conditional_uncovered_probability.py -h + - consensus_tree.py -h + - convert_fastaqual_fastq.py -h + - convert_unifrac_sample_mapping_to_otu_table.py -h + - core_diversity_analyses.py -h + - count_seqs.py -h + - demultiplex_fasta.py -h + - denoise_wrapper.py -h + - denoiser.py -h + - denoiser_preprocess.py -h + - denoiser_worker.py -h + - detrend.py -h + - differential_abundance.py -h + - dissimilarity_mtx_stats.py -h + - distance_matrix_from_mapping.py -h + - estimate_observation_richness.py -h + - exclude_seqs_by_blast.py -h + - extract_barcodes.py -h + - extract_reads_from_interleaved_file.py -h + - extract_seqs_by_sample_id.py -h + - filter_alignment.py -h + - filter_distance_matrix.py -h + - filter_fasta.py -h + - filter_otus_by_sample.py -h + - filter_otus_from_otu_table.py -h + - filter_samples_from_otu_table.py -h + - filter_taxa_from_otu_table.py -h + - filter_tree.py -h + - fix_arb_fasta.py -h + - group_significance.py -h + - identify_chimeric_seqs.py -h + - identify_missing_files.py -h + - identify_paired_differences.py -h + - inflate_denoiser_output.py -h + - jackknifed_beta_diversity.py -h + - join_paired_ends.py -h + - load_remote_mapping_file.py -h + - make_2d_plots.py -h + - make_bipartite_network.py -h + - make_bootstrapped_tree.py -h + - make_distance_boxplots.py -h + - make_distance_comparison_plots.py -h + - make_fastq.py -h + - make_library_id_lists.py -h + - make_otu_heatmap.py -h + - make_otu_heatmap_html.py -h + - make_otu_network.py -h + - make_otu_table.py -h + - make_per_library_sff.py -h + - make_phylogeny.py -h + - make_prefs_file.py -h + - make_qiime_py_file.py -h + - make_rarefaction_plots.py -h + - make_tep.py -h + - map_reads_to_reference.py -h + - merge_mapping_files.py -h + - merge_otu_maps.py -h + - merge_otu_tables.py -h + - multiple_extract_barcodes.py -h + - multiple_join_paired_ends.py -h + - multiple_rarefactions.py -h + - multiple_rarefactions_even_depth.py -h + - multiple_split_libraries_fastq.py -h + - neighbor_joining.py -h + - nmds.py -h + - normalize_table.py -h + - observation_metadata_correlation.py -h + - otu_category_significance.py -h + - parallel_align_seqs_pynast.py -h + - parallel_alpha_diversity.py -h + - parallel_assign_taxonomy_blast.py -h + - parallel_assign_taxonomy_rdp.py -h + - parallel_assign_taxonomy_uclust.py -h + - parallel_beta_diversity.py -h + - parallel_blast.py -h + - parallel_identify_chimeric_seqs.py -h + - parallel_map_reads_to_reference.py -h + - parallel_merge_otu_tables.py -h + - parallel_multiple_rarefactions.py -h + - parallel_pick_otus_blast.py -h + - parallel_pick_otus_sortmerna.py -h + - parallel_pick_otus_trie.py -h + - parallel_pick_otus_uclust_ref.py -h + - parallel_pick_otus_usearch61_ref.py -h + - pick_closed_reference_otus.py -h + - pick_de_novo_otus.py -h + - pick_open_reference_otus.py -h + - pick_otus.py -h + - pick_rep_set.py -h + - plot_rank_abundance_graph.py -h + - plot_semivariogram.py -h + - plot_taxa_summary.py -h + - poller.py -h + - principal_coordinates.py -h + - print_metadata_stats.py -h + - print_qiime_config.py -h + - process_iseq.py -h + - process_qseq.py -h + - process_sff.py -h + - quality_scores_plot.py -h + - relatedness.py -h + - shared_phylotypes.py -h + - simsam.py -h + - single_rarefaction.py -h + - sort_otu_table.py -h + - split_libraries.py -h + - split_libraries_fastq.py -h + - split_libraries_lea_seq.py -h + - split_otu_table.py -h + - split_otu_table_by_taxonomy.py -h + - split_sequence_file_on_sample_ids.py -h + - start_parallel_jobs.py -h + - start_parallel_jobs_sc.py -h + - start_parallel_jobs_slurm.py -h + - start_parallel_jobs_torque.py -h + - subsample_fasta.py -h + - summarize_otu_by_cat.py -h + - summarize_taxa.py -h + - summarize_taxa_through_plots.py -h + - supervised_learning.py -h + - swarm_breaker.py -h + - transform_coordinate_matrices.py -h + - tree_compare.py -h + - trflp_file_to_otu_table.py -h + - trim_sff_primers.py -h + - truncate_fasta_qual_files.py -h + - truncate_reverse_primer.py -h + - unweight_fasta.py -h + - upgma_cluster.py -h + - validate_demultiplexed_fasta.py -h + - validate_mapping_file.py -h 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 From f715be64df4df827e4ed21bd3580ded16cec39a1 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 3 Jun 2017 12:23:04 +0200 Subject: [PATCH 113/114] Skip cgat-scripts-devel on py36. Use master branch of bioconda-utils again after PR has been merged. --- .travis.yml | 2 +- recipes/cgat-scripts-devel/meta.yaml | 3 ++- 2 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.travis.yml b/.travis.yml index d3c3a5f2e6..a9515727ff 100644 --- a/.travis.yml +++ b/.travis.yml @@ -16,7 +16,7 @@ script: scripts/travis-run.sh env: global: - SUBDAGS=1 - - BIOCONDA_UTILS_TAG=quiet-docker-build-output + - BIOCONDA_UTILS_TAG=master - BIOCONDA_UTILS_BUILD_ARGS="--loglevel=info" - BIOCONDA_UTILS_LINT_ARGS= - MINICONDA_VER="4.2.12" diff --git a/recipes/cgat-scripts-devel/meta.yaml b/recipes/cgat-scripts-devel/meta.yaml index 38e4964b93..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: From 36078eedeba87137c8e3831347b73dcd19dd7987 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Johannes=20K=C3=B6ster?= Date: Sat, 3 Jun 2017 13:06:01 +0200 Subject: [PATCH 114/114] Skip linting when PR comes from the special bulk branch. --- scripts/travis-run.sh | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/scripts/travis-run.sh b/scripts/travis-run.sh index bf78f32642..2a3f652294 100755 --- a/scripts/travis-run.sh +++ b/scripts/travis-run.sh @@ -54,7 +54,11 @@ then # 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