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2016-10-26gnu: r-genomicranges: Update to 1.26.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1. [propagated-inputs]: Add r-iranges, r-s4vectors.
2016-10-26gnu: r-xvector: Update to 0.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
2016-10-26gnu: r-limma: Update to 3.30.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
2016-10-26gnu: r-variantannotation: Update to 1.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.0. [propagated-inputs]: Add r-biobase, r-biostrings, r-iranges, r-rtracklayer, r-s4vectors, r-xvector.
2016-10-26gnu: r-edger: Update to 3.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0. [propagated-inputs]: Add r-locfit.
2016-10-26gnu: r-genomeinfodb: Update to 1.10.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
2016-10-26gnu: r-iranges: Update to 2.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
2016-10-26gnu: r-s4vectors: Update to 0.12.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
2016-10-26gnu: r-dnacopy: Update to 1.48.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
2016-10-26gnu: r-biocinstaller: Update to 1.24.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
2016-10-26gnu: r-biocgenerics: Update to 0.20.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
2016-10-26gnu: r-grohmm: Update to 1.8.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
2016-10-26gnu: r-systempiper: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
2016-10-26gnu: r-shortread: Update to 1.32.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
2016-10-26gnu: r-gostats: Update to 2.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
2016-10-26gnu: r-category: Update to 2.40.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
2016-10-26gnu: r-gseabase: Update to 1.36.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
2016-10-26gnu: r-rbgl: Update to 1.50.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
2016-10-26gnu: r-annotationforge: Update to 1.16.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0. [propagated-inputs]: Add r-rcurl.
2016-10-26gnu: r-deseq2: Update to 1.14.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
2016-10-26gnu: r-genefilter: Update to 1.56.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
2016-10-26gnu: r-geneplotter: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
2016-10-26gnu: r-annotate: Update to 1.52.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
2016-10-20gnu: Add r-bioccheck.Roel Janssen
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
2016-10-19gnu: Add r-biocstyle.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
2016-10-19gnu: Add r-biocviews.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
2016-10-19gnu: Add r-optparse.Roel Janssen
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
2016-10-19gnu: Add r-getopt.Roel Janssen
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
2016-10-17gnu: Add rcas-web.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
2016-10-17gnu: Add r-rcas.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
2016-10-11gnu: vsearch: Update to 2.3.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
2016-10-11gnu: diamond: Update to 0.8.23.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
2016-10-08gnu: python2-dendropy: Fix tests.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched source. [arguments]: Use nose to run tests. [native-inputs]: Add python2-nose.
2016-10-06gnu: Add r-bsgenome-celegans-ucsc-ce10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New variable.
2016-10-04gnu: metabat: Update to 0.32.4-1.cbdca756.Ben Woodcroft
* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756. * gnu/packages/patches/metabat-remove-compilation-date.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2016-10-02gnu: vsearch: Update to 2.1.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
2016-09-28gnu: sra-tools: Fix build on i686.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass "VDB_LIBDIR" in make-flags; dynamically link libmagic.
2016-09-27gnu: python-plastid: Update to 1.4.6.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to 1.4.6. [propagated-inputs]: Add python-termcolor.
2016-09-27gnu: python-pysam: Enable tests.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from PyPi to source archive due to missing test data. [arguments]: Add check phase after install. [native-inputs]: Add python-nose, samtools and bcftools.
2016-09-27gnu: python-pysam: Delete bundled htslib.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet to delete htslib. [arguments]: Add htslib flags in 'set-flags phase. [propagated-inputs]: New field. Add htslib.
2016-09-27gnu: python-pysam: Use 'modify-phases'.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use 'modify-phases'.
2016-09-27gnu: Add bcftools.Marius Bakke
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27gnu: python2-pbcore: Update to 1.2.10.Marius Bakke
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10. [propagated-inputs]: New field. Add python2-pyxb.
2016-09-27gnu: python-pysam: Update to 0.9.1.4.Marius Bakke
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update to 0.9.1.4.
2016-09-26gnu: ncbi-vdb: Only build on i686 and x86_64.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only build on i686 and x86_64. [arguments]: Add mandatory "-msse2" flag to CFLAGS.
2016-09-26gnu: vsearch: Update to 2.1.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
2016-09-26gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene): New variable.
2016-09-26gnu: Add r-grohmm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26gnu: Add r-systempiper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26gnu: Add r-shortread.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
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