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* 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.
* gnu: ngs-sdk: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[source]: Fetch from git.
* gnu: ncbi-vdb: Use INVOKE and end phases on #T.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Use INVOKE and unconditionally end phases with #T.
* gnu: ncbi-vdb: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (ncbi-vdb)[source]: Fetch from git. [arguments]: Add phase to make checkout writable.
* gnu: tadbit: Fetch sources from git.Ricardo Wurmus2018-11-08
| | | | | * gnu/packages/bioinformatics.scm (tadbit)[source]: Fetch from git. [version]: Use "2.0.0" instead of "2.0".
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