Bulk remove conda_* pinnings #9043
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bgruening
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May 25, 2018
bgruening
commented
- I have read the guidelines for bioconda recipes.
- This PR adds a new recipe.
- AFAIK, this recipe is directly relevant to the biological sciences (otherwise, please submit to the more general purpose conda-forge channel).
- This PR updates an existing recipe.
- This PR does something else (explain below).
bgruening
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May 25, 2018
* remove build string * remove conda vars (#9043)
johanneskoester
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Jun 14, 2018
* bump CONDA_GSL to 2.4 (#8622) * update limma (#8616) * bumping groot to v0.7 (#8618) * New: GATK4 vqsr_cnn python module (#8617) Provides neural network based filtering for GATK4 variant calling https://gatkforums.broadinstitute.org/gatk/discussion/10996/deep-learning-in-gatk4 * Add EMA (#8612) * ema * Update ema * Update ema * Update ema * Add py{{ CONDA_PY }} to build string (#8611) * bump CONDA_GSL to 2.4 * use mktemp by default in bootstrap.py (#8625) * fix doi * use mktemp on osx * always use mktemp * Added new perl-extutils-cbuilder recipe (#8619) * Bump quasitools version to 0.3.1 (#8627) * Add recipe for fqtrim (#8629) * Add recipe for fqtrim 0.9.7 * Add variables * auto bump build numbers * attempt lint fix? * add missing hash for gfold * reverty fwdpy11 meta * add openblas to all packages that didn't already include it * bump packages except bioconductor-rmat and pymix. the latter fails lint tests, but CI doesn't give a reason * conda-forge seems to pin at 2.2, so I guess we should, too? * freaky magic courtesy of @johanneskoester * roll eqtlbma back to gsl 1.16 * pinning to 1.16 fails bioconda lint checks * add eigensoft and ea-utils to blacklist * attempt to build eqtlbma with GSL 1.16 * add linting exception * add lcfit * skip OSX for the moment * Use cb3-migration branch and latest miniconda release. * Check all recipes on bulk. * remove build string (#9042) * remove build string * remove conda vars (#9043) * Replace gcc with new compilers. I always replace with the c compiler. For c++, we manually have to manually modify the line. Anaconda upload is disabled for now, because we should check that pinning works before we start uploading. * Fixes. Enable upload. It should be no problem, because conda-build seems to fail if host is not used for library dependencies. * Fix version spec. * Trigger cache update. * Trigger cache update. * Trigger cache update. * Trigger cache update. * Trigger cache update. * add host section to python based packages with c/cxx compiler * replace build with host * small fixes * small fixes * fix spacing * replace numpy x.x * use pip install * some more python changes * minor * host and build section for perl-data-dumper and perl-extutils-makemaker. * small round of r recipes to check bulk building * r-* build -> host * temporarily disable cache * trailing whitespace * fix boost version specs * temporarily disable cache, try two * temporarily disable cache, try three * temporarily disable cache, try four * temporarly disable uploads for bulk branch * add noarch python * add build/number sections * split into host:/build: for bioconductor packages * c -> cxx compiler if using r-rcpp or r-cpparmadillo * build -> host for r/bioc recipes not otherwise using cb3 build: * trigger; try out logic for divergent build strings * Revert "temporarly disable uploads for bulk branch" This reverts commit 3cf5983. * Whitespace fixes [WIP] (#9085) * HiCExplorer version 2.1.4 (#9044) * Adding hic2cool version 0.4.1 * Update to version 2.1.4 of HiCExplorer * Update to asqcan v0.2 (#9047) * Update to asqcan v0.2 * Fixed md5 * [ci skip] add doi to deeptools (#8963) * hicexplorer fix * Update with new dependency (#9048) * vep: bumped subversion (#9051) * adding illumiprocessor v2.0.9 (#9045) * geneimpacts: bumped subversion (#9052) * r-geoaxe, r-oai, r-rbison, r-rebird, r-ridigbio, r-rvertnet, r-wicket (#8994) * r cran packages dependencies for rspocc and rgbif, recipes generated with skeleton. Ecology tools, for integration in Galaxy * Rpackages for ecology * rm win tags * Bumped star-fusion version (#9034) * Bumped star-fusion version * conda considers 2.6.0b<2.6 * snpsplit : new version added (#9054) * Mmseqs2 (#9055) * Update MMseqs2 recipe to new release 3-be8f6 * Update r-biodb to 1.1.0. (#9057) * OrthoFinder: update to 2.2.6 (#9060) * Orthofinder: update to 2.2.6 * fix link * snakemake 5.1.4 * Update BioConda pypeFLOW package to v1.0.0 (#9024) * pypyFLOW v1.0.0 In the absense of an official tag on the upstream repository, this is the commit which bumped the version number to 1.0.0 See PacificBiosciences/pypeFLOW#51 Note that the dependencies declared in the setup.py changed, which is reflected in the meta.yaml dependencies. It now requires networkx. Also, the updated setup.py declares additional python libraries which we now test can be imported. * Use the merge commit for the v1.0.0 version bump. Hat tip Renan Valieris, the version 1.0.0 bump commit 79c77235eb10e7b36a98ada891e1e6ef454aed58 was part of a pull request which make other changes, thus merge commit e331fad50be98d83e95a4a354bed2c81a8351392 is a better representative of v1.0.0. See PacificBiosciences/pypeFLOW#39 This pull request also expanded the supported range of networkx versions. * Remove space in networkx dependency version definition * Bump dimspy version to 1.2.0 (#9063) * Update to pypeFLOW v1.1.0 (#9064) In the absense of an official tag on the upstream repository, this is the commit which merged pull request 20 into the master branch, and that included the version bump. See PacificBiosciences/pypeFLOW#51 There is a new futures dependency declared in their setup.py, which is a backport for Python 2 only. Given pypeFLOW does not yet support Python 3 this is perhaps not worth noting, but I marked this dependency as conditional. * pypeFLOW 2 0 0 (#9065) * Update for pypeFLOW v2.0.0 In the absense of an official tag on the upstream repository, this is the commit which merged pull request 23 into the master branch, and that included the version bump. See PacificBiosciences/pypeFLOW#51 * Add basic about section to pypeFLOW recipe * Fix URL for abundancebin (#9066) * Remove duplicated pypeFLOW about metadata (#9068) Keeps the license clarification, not just normal BSD. * trigger; try out logic for divergent build strings * Update: peddy, simple_sv_annotation, bcbio (#9069) - peddy: latest development version with support for hg38. Drops bioconda patch which they incorporated upstream. - simple_sv_annotation: Fix for REJECT filter not in VCF header. - bcbio: support for moving output and better debugging with Cromwell. * Revert "temporarly disable uploads for bulk branch" This reverts commit 3cf5983. * Update for pypeFLOW v2.0.1 (#9070) In the absence of an official tag on the upstream repository, this is the commit which merged pull request 26 into the master branch, and that included the version bump. See PacificBiosciences/pypeFLOW#51 * salmon v0.10.0 This bumps salmon to v0.10.0. This release uses the `CONDA_BUILD=TRUE` flag during CMake configuration to force C++11 (instead of C++14) compilation. Once conda-build 3 migration is complete, we should move this to build with C++14. * AMPtk update to v1.2.3 (#9071) * update to v1.2.3 * fix tab error * Bissnp update (#9074) * Updated to VERSION 1.0.1 * Fixed test. * PacBio: Initial addition of `lima` (#9075) * cyvcf2: remove plotting dependencies (see brentp/cyvcf2#83) (#9078) * Update for pypeFLOW v2.0.2 (#9080) In the absence of an official tag on the upstream repository, this is the commit which merged pull request 33 into the master branch, and that included the version bump. See PacificBiosciences/pypeFLOW#51 * PacBio: Initial addition of `isoseq3` (#9076) * rtg-tools: Update to 3.9.1 (#9077) * PacBio: pull in lima as runtime dep for isoseq3 (#9081) * This facilitates a simpler workflow, where all workflow dependencies are pulled in by just one recipe. * Add rgbif and spocc recipes (#9067) * rgbif recipe created with conda skeleton cran * fix recipes * spocc recipe, build with conda skeleton cran * enforce 2-space indentation * enforce 2-space indentation * first round of indentation fixes * refactor * recipes c-f whitespace * recipes f-l whitespace * recipes m-o whitespace * recipes p-z whitespace * migrate java recipes to noarch: generic (#9086) * cleanup perl recipe * fix all build/number sections and set it to 0 * fix all build/number sections and set it to 0 * change perl-threaded to perl * fix recipes * lint fixes again * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * lint fixes * remove fn: from all recipes * fix linting * lint fixes * fix linting * fix linting * linting fix * fix lint * fix lint * fix linting * fix linting * fix lint * fix linting * add more debug output to the lint step * lint fixes * lint fixes * remove JE rc * fix linting * blacklist recipes found on conda-forge and defaults * use --prelint for bioconda-utils build * add script to bump builds * fix merge * fix merge * bump build numbers for all recipes * --prelint on bulk workflows * add missing build numbers and set to 1 * adjustments for old viennnarna recipes * bump build numbers.
bgruening
added a commit
that referenced
this pull request
Jun 17, 2018
* bump CONDA_GSL to 2.4 (#8622) * update limma (#8616) * bumping groot to v0.7 (#8618) * New: GATK4 vqsr_cnn python module (#8617) Provides neural network based filtering for GATK4 variant calling https://gatkforums.broadinstitute.org/gatk/discussion/10996/deep-learning-in-gatk4 * Add EMA (#8612) * ema * Update ema * Update ema * Update ema * Add py{{ CONDA_PY }} to build string (#8611) * bump CONDA_GSL to 2.4 * use mktemp by default in bootstrap.py (#8625) * fix doi * use mktemp on osx * always use mktemp * Added new perl-extutils-cbuilder recipe (#8619) * Bump quasitools version to 0.3.1 (#8627) * Add recipe for fqtrim (#8629) * Add recipe for fqtrim 0.9.7 * Add variables * auto bump build numbers * attempt lint fix? * add missing hash for gfold * reverty fwdpy11 meta * add openblas to all packages that didn't already include it * bump packages except bioconductor-rmat and pymix. the latter fails lint tests, but CI doesn't give a reason * conda-forge seems to pin at 2.2, so I guess we should, too? * freaky magic courtesy of @johanneskoester * roll eqtlbma back to gsl 1.16 * pinning to 1.16 fails bioconda lint checks * add eigensoft and ea-utils to blacklist * attempt to build eqtlbma with GSL 1.16 * add linting exception * add lcfit * skip OSX for the moment * Use cb3-migration branch and latest miniconda release. * Check all recipes on bulk. * remove build string (#9042) * remove build string * remove conda vars (#9043) * Replace gcc with new compilers. I always replace with the c compiler. For c++, we manually have to manually modify the line. Anaconda upload is disabled for now, because we should check that pinning works before we start uploading. * Fixes. Enable upload. It should be no problem, because conda-build seems to fail if host is not used for library dependencies. * Fix version spec. * Trigger cache update. * Trigger cache update. * Trigger cache update. * Trigger cache update. * Trigger cache update. * add host section to python based packages with c/cxx compiler * replace build with host * small fixes * small fixes * fix spacing * replace numpy x.x * use pip install * minor * host and build section for perl-data-dumper and perl-extutils-makemaker. * small round of r recipes to check bulk building * r-* build -> host * temporarily disable cache * trailing whitespace * fix boost version specs * temporarily disable cache, try two * temporarily disable cache, try three * temporarily disable cache, try four * temporarly disable uploads for bulk branch * trigger; try out logic for divergent build strings * Revert "temporarly disable uploads for bulk branch" This reverts commit 3cf5983. * fix linting and recipe errors * add cxx compiler * add cxx compiler * fixes * remove intervaltree
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