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2019-01-12gnu: r-deseq2: Update to 1.22.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.22.2.
2019-01-12gnu: r-scran: Update to 1.10.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-scran): Update to 1.10.2.
2019-01-12gnu: r-seqminer: Update to 7.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 7.1.
2019-01-12gnu: r-bookdown: Update to 0.9.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.9.
2019-01-12gnu: Move Java compression packages to new module.Ricardo Wurmus
* gnu/packages/compression.scm (bitshuffle-for-snappy): Export variable. (java-snappy, java-snappy-1, java-iq80-snappy, java-jbzip2, java-tukaani-xz): Move these variables from here... * gnu/packages/java-compression.scm: ...to this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/java.scm, gnu/packages/bioinformatics.scm: Adjust module references.
2019-01-11gnu: jamm: Remove broken "build" phase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm)[arguments]: Remove "build" phase.
2019-01-07gnu: mantis: Limit to x86_64-linux.Efraim Flashner
* gnu/packages/bioinformatics.scm (mantis)[supported-systems]: New field.
2019-01-07gnu: Add mantis.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (mantis): New variable.
2018-12-20gnu: discrover: Comment on attempt of minimal texlive-union.Pierre Neidhardt
* gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal texlive-union.
2018-12-17gnu: gess: Don't hardcode python version.Efraim Flashner
* gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded python version with parameterized one.
2018-12-05gnu: mash: Use C++ 14.Christopher Baines
I'm looking to upgrade capnproto, and mash fails to build with 0.7. Therefore, tweak the compilation to allow it to build with 0.7. The package also builds with the current version of capnproto. I got the idea of changing the c++ version from here [1]. 1: https://github.com/marbl/Mash/issues/98 * gnu/packages/bioinformatics.scm (mash)[arguments]: Add new use-c++14 phase.
2018-12-04gnu: pigx-rnaseq: Update to 0.0.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake.
2018-11-24gnu: bless: Adjust to zlib static output.Marius Bakke
* gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC. [arguments]: Adjust #:make-flags accordingly.
2018-11-24gnu: mosaik: Fix FTBFS from b90289dadc8ee15848ce911a2bdcd3ae8302d58c.Marius Bakke
* gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
2018-11-23gnu: pigx-scrnaseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: pigx-bsseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: pigx-chipseq: Use latest snakemake.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4 with snakemake.
2018-11-23gnu: python-loompy: Remove python-typing.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove python-typing.
2018-11-20Merge branch 'master' into core-updatesMarius Bakke
2018-11-19gnu: r-ensembldb: Update to 2.6.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
2018-11-19gnu: r-msnbase: Update to 2.8.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
2018-11-19gnu: r-genomeinfodb: Update to 1.18.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
2018-11-15gnu: Add nanopolish.pimi
* gnu/packages/bioinformatics.scm (nanopolish): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
2018-11-15gnu: sambamba: Update to 0.6.8.Roel Janssen
* gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
2018-11-14gnu: bioinformatics: Return #t from all phases and snippets.Mark H Weaver
* gnu/packages/bioinformatics.scm (bamtools, ribotaper, bioawk) (codingquarry, fraggenescan, minced, pplacer, star, subread, sailfish) (salmon): Return #t from all phases and snippets, use 'invoke' where appropriate, and remove vestigal plumbing.
2018-11-14gnu: Add jamm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (jamm): New variable.
2018-11-13gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4.
2018-11-13gnu: r-org-mm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-dm-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-ce-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
2018-11-13gnu: r-org-hs-eg-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
2018-11-13gnu: r-genomationdata: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
2018-11-13gnu: r-go-db: Update to 3.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
2018-11-13gnu: r-genomeinfodbdata: Update to 1.2.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
2018-11-11gnu: r-s4vectors: Update to 0.20.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
2018-11-09gnu: r-ensembldb: Update to 2.6.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
2018-11-09gnu: r-biostrings: Update to 2.50.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
2018-11-09gnu: r-biocviews: Update to 1.50.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
2018-11-08gnu: pplacer-scripts: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: roary: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: seek: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
2018-11-08gnu: sailfish: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of SYSTEM*.
2018-11-08gnu: vsearch: Update to 2.9.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
2018-11-08gnu: sra-tools: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict.
2018-11-08gnu: plink-ng: Fetch sources from git.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
2018-11-08gnu: ncbi-vdb: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
2018-11-08gnu: ngs-sdk: Update to 2.9.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
2018-11-08gnu: ngs-sdk: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: emboss: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally.
2018-11-08gnu: taxtastic: Use INVOKE.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally.
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