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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.
2016-09-26gnu: Add r-gostats.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26gnu: Add r-category.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26gnu: Add r-gseabase.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26gnu: Add r-rbgl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26gnu: Add r-annotationforge.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26gnu: Add r-deseq2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26gnu: Add r-genefilter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26gnu: Add r-geneplotter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
2016-09-26gnu: Add r-annotate.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
2016-09-23gnu: sra-tools: Update to 2.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0.
2016-09-23gnu: ncbi-vdb: Update to 2.7.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0.
2016-09-23gnu: ngs-sdk: Update to 1.2.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5.
2016-09-22gnu: plink: Set endian-ness on more architectures.Efraim Flashner
* gnu/packages/patches/plink-endian-detection.patch: New file. * gnu/packages/bioinformatics.scm (plink)[source]: Use it. * gnu/local.mk (dist_patch_DATA): Register it.
2016-09-22gnu: prank: Allow building on 32-bit machines.Efraim Flashner
* gnu/packages/bioinformatics.scm (prank)[arguments]: Add a phase removing the '-m64' compiler flag.
2016-09-22gnu: diamond: Update to 0.8.22.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.22.
2016-09-21gnu: jellyfish: Limit to x86_64.Efraim Flashner
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems}: New field, limit support to x86_64.
2016-09-21gnu: vsearch: Update to 2.1.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.0.
2016-09-19gnu: Add r-biocinstaller.Roel Janssen
* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable.
2016-09-19gnu: python-biom-format: Move inputs to propagated-inputs.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format) [inputs]: Move all from here ... [propagated-inputs]: ... to here.
2016-09-19gnu: seqmagick: Use BioPython 1.66.Ben Woodcroft
* gnu/packages/bioinformatics.scm (seqmagick)[inputs]: Use python2-biopython-1.66 instead of python2-biopython.
2016-09-19gnu: Add python2-biopython-1.66.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python2-biopython-1.66): New variable.
2016-09-19gnu: python-biopython: Use 'python2-variant'.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biopython)[properties]: New field. [native-inputs]: Remove field. (python-biopython): Use 'strip-python-variant'.
2016-09-19gnu: python-biopython: Update to 1.68.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.68. [arguments]: New field.
2016-09-13gnu: Add seqtk.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (seqtk): New variable.
2016-09-12gnu: bowtie: Update to 2.2.9.Leo Famulari
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.9.
2016-09-12gnu: r-org-mm-eg-db: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.3.0.
2016-09-12gnu: r-org-dm-eg-db: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.3.0.
2016-09-12gnu: r-org-ce-eg-db: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.3.0.
2016-09-12gnu: r-org-hs-eg-db: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.3.0.
2016-09-12gnu: r-go-db: Update to 3.3.0.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.3.0.
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