Push cb3 migration directly into master #9402
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* 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
* remove build string * remove conda vars (#9043)
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.
…ems to fail if host is not used for library dependencies.
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@bgruening @daler @mbargull @kyleabeauchamp @bioconda/core: CB3 migration is merged into master now. We will have to wait a couple of weeks until everything is build. |
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Nice work everyone, looking forward to the results!
…On Thu, Jun 14, 2018, 12:28 PM Johannes Köster ***@***.***> wrote:
@bgruening <https://github.com/bgruening> @daler
<https://github.com/daler> @mbargull <https://github.com/mbargull>
@kyleabeauchamp <https://github.com/kyleabeauchamp> @bioconda/core
<https://github.com/orgs/bioconda/teams/core>: CB3 migration is merged
into master now. We will have to wait a couple of weeks until everything is
build.
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3 tasks
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Oh gosh, thanks for pushing this over the line. I'm nervous! |
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One change I will do tomorrow: only build changed recipes on master, except [bulk] is specified in the commit message. This way we can trigger bulk builds in master without interfering with other merged PRs. |
5 tasks
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@johanneskoester this revamped a deleted recipe, such as https://github.com/bioconda/bioconda-recipes/blob/master/recipes/pbbam/meta.yaml which should have been long gone |
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xref: #9049