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* gnu: discrover: Comment on attempt of minimal texlive-union.Pierre Neidhardt2018-12-20
| | | | | * gnu/packages/bioinformatics.scm (discrover): Comment on attempt of minimal texlive-union.
* gnu: gess: Don't hardcode python version.Efraim Flashner2018-12-17
| | | | | * gnu/packages/bioinformatics.scm (gess)[arguments]: Replace hardcoded python version with parameterized one.
* gnu: mash: Use C++ 14.Christopher Baines2018-12-05
| | | | | | | | | | | 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.
* gnu: pigx-rnaseq: Update to 0.0.5.Ricardo Wurmus2018-12-04
| | | | | * gnu/packages/bioinformatics.scm (pigx-rnaseq): Update to 0.0.5. [inputs]: Replace snakemake-4 with snakemake.
* gnu: bless: Adjust to zlib static output.Marius Bakke2018-11-24
| | | | | * gnu/packages/bioinformatics.scm (bless)[inputs]: Add ZLIB:STATIC. [arguments]: Adjust #:make-flags accordingly.
* gnu: mosaik: Fix FTBFS from b90289dadc8ee15848ce911a2bdcd3ae8302d58c.Marius Bakke2018-11-24
| | | | * gnu/packages/bioinformatics.scm (mosaik)[inputs]: Add ZLIB:STATIC.
* gnu: pigx-scrnaseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | * gnu/packages/bioinformatics.scm (pigx-scrnaseq)[inputs]: Replace snakemake-4 with snakemake.
* gnu: pigx-bsseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | * gnu/packages/bioinformatics.scm (pigx-bsseq)[inputs]: Replace snakemake-4 with snakemake.
* gnu: pigx-chipseq: Use latest snakemake.Ricardo Wurmus2018-11-23
| | | | | * gnu/packages/bioinformatics.scm (pigx-chipseq)[inputs]: Replace snakemake-4 with snakemake.
* gnu: python-loompy: Remove python-typing.Ricardo Wurmus2018-11-23
| | | | | * gnu/packages/bioinformatics.scm (python-loompy)[propagated-inputs]: Remove python-typing.
* Merge branch 'master' into core-updatesMarius Bakke2018-11-20
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| * gnu: r-ensembldb: Update to 2.6.2.Roel Janssen2018-11-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.2.
| * gnu: r-msnbase: Update to 2.8.1.Roel Janssen2018-11-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.8.1.
| * gnu: r-genomeinfodb: Update to 1.18.1.Roel Janssen2018-11-19
| | | | | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.18.1.
| * gnu: Add nanopolish.pimi2018-11-15
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (nanopolish): New variable. Signed-off-by: Ricardo Wurmus <rekado@elephly.net>
| * gnu: sambamba: Update to 0.6.8.Roel Janssen2018-11-15
| | | | | | | | * gnu/packages/bioinformatics.scm (sambamba): Update to 0.6.8.
* | gnu: bioinformatics: Return #t from all phases and snippets.Mark H Weaver2018-11-14
|/ | | | | | | * 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.
* gnu: Add jamm.Ricardo Wurmus2018-11-14
| | | | * gnu/packages/bioinformatics.scm (jamm): New variable.
* gnu: r-txdb-mmusculus-ucsc-mm10-knowngene: Update to 3.4.4.Ricardo Wurmus2018-11-13
| | | | | * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): Update to 3.4.4.
* gnu: r-org-mm-eg-db: Update to 3.7.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.7.0.
* gnu: r-org-dm-eg-db: Update to 3.7.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.7.0.
* gnu: r-org-ce-eg-db: Update to 3.7.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.7.0.
* gnu: r-org-hs-eg-db: Update to 3.7.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.7.0.
* gnu: r-genomationdata: Update to 1.14.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.14.0.
* gnu: r-go-db: Update to 3.7.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-go-db): Update to 3.7.0.
* gnu: r-genomeinfodbdata: Update to 1.2.0.Ricardo Wurmus2018-11-13
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata): Update to 1.2.0.
* gnu: r-s4vectors: Update to 0.20.1.Ricardo Wurmus2018-11-11
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.20.1.
* gnu: r-ensembldb: Update to 2.6.1.Ricardo Wurmus2018-11-09
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): Update to 2.6.1.
* gnu: r-biostrings: Update to 2.50.1.Ricardo Wurmus2018-11-09
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.50.1.
* gnu: r-biocviews: Update to 1.50.5.Ricardo Wurmus2018-11-09
| | | | * gnu/packages/bioinformatics.scm (r-biocviews): Update to 1.50.5.
* gnu: pplacer-scripts: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (pplacer-scripts)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: roary: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (roary)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: seek: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (seek)[arguments]: Use INVOKE and return #T unconditionally; patch "gen_tools_am" shebang in "bootstrap" phase.
* gnu: sailfish: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (sailfish)[arguments]: Use INVOKE instead of SYSTEM*.
* gnu: vsearch: Update to 2.9.1.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.9.1. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: Update.
* gnu: sra-tools: Update to 2.9.3.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.9.3. [arguments]: Remove build phase patch-away-glibc-conflict.
* gnu: plink-ng: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (plink-ng)[source]: Fetch from git.
* gnu: ncbi-vdb: Update to 2.9.3.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.9.3.
* gnu: ngs-sdk: Update to 2.9.3.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 2.9.3.
* gnu: ngs-sdk: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: emboss: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (emboss)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: taxtastic: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (taxtastic)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: sra-tools: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: muscle: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (muscle)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: newick-utils: Remove custom autoconf phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (newick-utils)[arguments]: Remove.
* gnu: mash: Remove custom autoconf phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (mash)[arguments]: Remove autoconf phase.
* gnu: vsearch: Remove custom autogen phase.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (vsearch)[arguments]: Remove.
* gnu: java-picard-1.113: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (java-picard-1.113)[arguments]: Use INVOKE and return #T unconditionally.
* gnu: fraggenescan: Use INVOKE.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (fraggenescan)[arguments]: Use INVOKE in build phases and return #T unconditionally.
* gnu: sailfish: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (sailfish)[source]: Fetch from git.
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