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* gnu: diamond: Update to 0.9.13.Ben Woodcroft2017-11-14
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.13.
* gnu: Move test packages from perl to perl-check.Ricardo Wurmus2017-11-13
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * gnu/packages/perl.scm (perl-test2-bundle-extended, perl-test2-plugin-nowarnings, perl-test-base, perl-test-class, perl-test-class-most, perl-test-cleannamespaces, perl-test-command, perl-test-cpan-meta, perl-test-cpan-meta-json, perl-test-deep, perl-test-differences, perl-test-directory, perl-test-eol, perl-test-exception, perl-test-fatal, perl-test-file-sharedir-dist, perl-test-files, perl-test-harness, perl-test-leaktrace, perl-test-longstring, perl-test-manifest, perl-test-memory-cycle, perl-test-mockobject, perl-test-mocktime, perl-test-most, perl-test-needs, perl-test-notabs, perl-test-nowarnings, perl-test-number-delta, perl-test-output, perl-test-pod, perl-test-pod-coverage, perl-test-requires, perl-test-script, perl-test-sharedfork, perl-test-simple, perl-test-taint, perl-test-tester, perl-test-trap, perl-test-utf8, perl-test-warn, perl-test-warnings, perl-test-without-module, perl-test-writevariants, perl-test-yaml, perl-test-trailingspace): Move variables to ... * gnu/packages/perl-check.scm: ... this new file. * gnu/local.mk (GNU_SYSTEM_MODULES): Add it. * gnu/packages/admin.scm, gnu/packages/bioinformatics.scm, gnu/packages/crypto.scm, gnu/packages/databases.scm, gnu/packages/glib.scm, gnu/packages/gnupg.scm, gnu/packages/image-viewers.scm, gnu/packages/language.scm, gnu/packages/networking.scm, gnu/packages/package-management.scm, gnu/packages/perl.scm, gnu/packages/terminals.scm, gnu/packages/tex.scm, gnu/packages/version-control.scm, gnu/packages/web.scm, gnu/packages/xml.scm, gnu/packages/xorg.scm: Use perl-check module.
* gnu: cd-hit: Update source tarball hash.Ricardo Wurmus2017-11-13
| | | | * gnu/packages/bioinformatics.scm (cd-hit)[source]: Update hash.
* gnu: methylkit: Use new home page.Tobias Geerinckx-Rice2017-11-11
| | | | * gnu/packages/bioinformatics.scm (methylkit)[home-page]: Update.
* gnu: vsearch: Update to 2.6.0.Ben Woodcroft2017-11-11
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.6.0.
* gnu: cutadapt: Update to 1.14.Ricardo Wurmus2017-11-10
| | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.14.
* gnu: roary: Update to 3.11.0.Ben Woodcroft2017-11-09
| | | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.11.0. [inputs]: Add perl-digest-md5-file.
* gnu: miso: Use pypi-uri.Ricardo Wurmus2017-11-08
| | | | * gnu/packages/bioinformatics.scm (miso)[source]: Use pypi-uri.
* gnu: Add r-hitc.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-hitc): New variable.
* gnu: Add r-fithic.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-fithic): New variable.
* gnu: Add r-sushi.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-sushi): New variable.
* gnu: Add r-gwascat.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gwascat): New variable.
* gnu: Add r-gviz.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gviz): New variable.
* gnu: Add r-gqtlstats.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gqtlstats): New variable.
* gnu: Add r-ldblock.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-ldblock): New variable.
* gnu: Add r-erma.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-erma): New variable.
* gnu: Add r-homo-sapiens.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-homo-sapiens): New variable.
* gnu: Add r-org-hs-eg-db.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-org-hs-eg-db): New variable.
* gnu: Add r-snpstats.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-snpstats): New variable.
* gnu: Add r-gqtlbase.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gqtlbase): New variable.
* gnu: Add r-gprofiler.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gprofiler): New variable.
* gnu: Add r-ggbio.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-ggbio): New variable.
* gnu: Add r-biovizbase.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-biovizbase): New variable.
* gnu: Add r-organismdbi.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-organismdbi): New variable.
* gnu: Add r-ensembldb.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-ensembldb): New variable.
* gnu: Add r-annotationfilter.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-annotationfilter): New variable.
* gnu: Add r-dirichletmultinomial.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-dirichletmultinomial): New variable.
* gnu: Add r-complexheatmap.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-complexheatmap): New variable.
* gnu: Add r-genomicfiles.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-genomicfiles): New variable.
* gnu: Add r-gage.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-gage): New variable.
* gnu: Add r-keggrest.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-keggrest): New variable.
* gnu: r-msnbase: Update to 2.4.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.4.0. [propagated-inputs]: Add r-lattice; remove r-reshape2.
* gnu: r-mutationalpatterns: Update to 1.4.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.4.0. [propagated-inputs]: Add r-cowplot, r-ggdendro, and r-s4vectors.
* gnu: r-annotationhub: Update to 2.10.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-annotationhub): Update to 2.10.0. [propagated-inputs]: Add r-curl.
* gnu: r-mzr: Remove bundled copy of boost.Ricardo Wurmus2017-11-07
| | | | | | * gnu/packages/bioinformatics.scm (r-mzr)[source]: Remove boost source. [arguments]: Add build phase "use-system-boost" to link with our boost package and avoid building the bundled sources.
* gnu: r-mzr: Update to 2.12.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.12.0.
* gnu: r-mzid: Update to 1.16.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.16.0.
* gnu: r-chipseq: Update to 1.28.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.28.0. [propagated-inputs]: Add r-lattice.
* gnu: r-genomicfeatures: Update to 1.30.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.30.0. [propagated-inputs]: Add r-rmysql.
* gnu: r-rtracklayer: Update to 1.38.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.38.0. [arguments]: Adjust patch to use system zlib.
* gnu: r-biocparallel: Update to 1.12.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.12.0. [propagated-inputs]: Add r-bh.
* gnu: r-biomart: Update to 2.34.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-biomart): Update to 2.34.0. [propagated-inputs]: Add r-progress and r-stringr.
* gnu: r-edger: Update to 3.20.1.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.20.1. [propagated-inputs]: Add r-rcpp.
* gnu: r-gostats: Update to 2.44.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-gostats): Update to 2.44.0. [propagated-inputs]: Add r-rgraphviz.
* gnu: r-category: Update to 2.44.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-category): Update to 2.44.0. [propagated-inputs]: Remove r-rsqlite; add r-dbi.
* gnu: r-vsn: Update to 3.46.0.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-vsn): Update to 3.46.0. [propagated-inputs]: Remove r-hexbin.
* gnu: r-motifrg: Rename input label.Ricardo Wurmus2017-11-07
| | | | | * gnu/packages/bioinformatics.scm (r-motifrg)[propagated-inputs]: Rename label of r-bsgenome-hsapiens-ucsc-hg19.
* gnu: r-motifrg: Update to 1.22.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.22.0.
* gnu: r-qvalue: Update to 2.10.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-qvalue): Update to 2.10.0.
* gnu: r-fastseq: Update to 1.24.0.Ricardo Wurmus2017-11-07
| | | | * gnu/packages/bioinformatics.scm (r-fastseq): Update to 1.24.0.
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