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* gnu: Add r-sva.Raoul Jean Pierre Bonnal2017-01-14
| | | | * gnu/packages/bioinformatics.scm (r-sva): New variable.
* gnu: Add r-txdb-mmusculus-ucsc-mm10-knowngene.Roel Janssen2017-01-12
| | | | * gnu/packages/bioinformatics.scm (r-txdb-mmusculus-ucsc-mm10-knowngene): New variable.
* gnu: Add r-copywriter.Ricardo Wurmus2017-01-06
| | | | * gnu/packages/bioinformatics.scm (r-copywriter): New variable.
* gnu: Add r-copyhelper.Ricardo Wurmus2017-01-06
| | | | * gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
* gnu: Add r-chipseq.Ricardo Wurmus2017-01-06
| | | | * gnu/packages/bioinformatics.scm (r-chipseq): New variable.
* gnu: bioruby: Update to 1.5.1.Ben J Woodcroft2017-01-06
| | | | * gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
* gnu: cd-hit: Update to 4.6.6.Ben J Woodcroft2017-01-06
| | | | * gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
* gnu: Use HTTPS for all sourceforge.net home pages.Tobias Geerinckx-Rice2017-01-04
| | | | | | | | | | | | | | | | | | | | | | * gnu/packages/admin.scm (mingetty, clusterssh)[home-page]: Use HTTPS. * gnu/packages/audio.scm (libbs2b, soxr)[home-page]: Likewise. * gnu/packages/bioinformatics.scm (bless)[home-page]: Likewise. * gnu/packages/display-managers.scm (slim)[home-page]: Likewise. * gnu/packages/games.scm (extremetuxracer)[home-page]: Likewise. * gnu/packages/ghostscript.scm (gs-fonts)[home-page]: Likewise. * gnu/packages/haskell.scm (ghc-regex-base, ghc-regex-posix, ghc-regex-compat)[home-page]: Likewise. * gnu/packages/image.scm (imlib2)[home-page]: Likewise. * gnu/packages/libreoffice.scm (librevenge, libcmis, libodfgen, libmwaw) [home-page]: Likewise. * gnu/packages/linux.scm (hdparm, acpid, libavc1394, rng-tools) [home-page]: Likewise. * gnu/packages/mail.scm (esmtp)[home-page]: Likewise. * gnu/packages/mp3.scm (ripperx)[home-page]: Likewise. * gnu/packages/onc-rpc.scm (libtirpc)[home-page]: Likewise. * gnu/packages/perl.scm (perl-czplib)[home-page]: Likewise. * gnu/packages/python.scm (python-pyasn1-modules)[home-page]: Likewise. * gnu/packages/xdisorg.scm (xosd)[home-page]: Likewise.
* gnu: r-genomicranges: Update to 1.26.2.Roel Janssen2017-01-03
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
* gnu: r-genomeinfodb: Update to 1.10.2.Roel Janssen2017-01-03
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
* gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft2017-01-01
| | | | | | | | | * gnu/packages/bioinformatics.scm (python-dendropy): Update to 4.2.0. [source]: Remove patch. (python2-dendropy)[source]: Use the same source as python-dendropy. * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: diamond: Update to 0.8.31.Ben Woodcroft2017-01-01
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
* gnu: multiqc: Update to 0.9.Ben Woodcroft2016-12-30
| | | | | | | | | Suggested by Raoul Bonnal <ilpuccio.febo@gmail.com>. * gnu/packages/bioinformatics.scm (multiqc): Update to 0.9. [origin]: Add patch. * gnu/packages/patches/multiqc-fix-git-subprocess-error.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: r-genomicfeatures: Update to 1.26.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
* gnu: r-biostrings: Update to 2.42.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
* gnu: r-limma: Update to 3.30.7.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
* gnu: r-variantannotation: Update to 1.20.2.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
* gnu: r-edger: Update to 3.16.5.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
* gnu: r-genomeinfodb: Update to 1.10.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
* gnu: r-iranges: Update to 2.8.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
* gnu: r-s4vectors: Update to 0.12.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
* gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
* gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
* gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus2016-12-29
| | | | | * gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
* gnu: r-qtl: Update to 1.40-8.Ricardo Wurmus2016-12-29
| | | | * gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
* gnu: r-rcas: Update to 1.1.1.Ricardo Wurmus2016-12-27
| | | | | * gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1. [propagated-inputs]: Add plotrix.
* gnu: diamond: Update to 0.8.30.Ben Woodcroft2016-12-27
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
* gnu: cutadapt: Use ‘modify-phases’ syntax.Tobias Geerinckx-Rice2016-12-20
| | | | | * gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use ‘modify-phases’.
* gnu: cutadapt: Update to 1.12.Tobias Geerinckx-Rice2016-12-19
| | | | | * gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12. [inputs]: Add python-xopen.
* gnu: Add attribution line for Raoul Bonnal.Ben Woodcroft2016-12-18
| | | | | | This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24. * gnu/packages/bioinformatics.scm: Add attribution.
* gnu: star: Update to 2.5.2b.Raoul Bonnal2016-12-17
| | | | | | | * gnu/packages/bioinformatics (star): Update to 2.5.2b. [source]: Delete precompiled binary. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
* gnu: Update more dead Google Code home pages.Tobias Geerinckx-Rice2016-12-14
| | | | | * gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]: Update to their respective replacements.
* gnu: diamond: Update to 0.8.29.Ben Woodcroft2016-12-13
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
* gnu: orfm: Update to 0.6.1.Ben Woodcroft2016-12-13
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
* gnu: orfm: Update to 0.6.0.Ben Woodcroft2016-12-12
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
* gnu: vsearch: Update to 2.3.4.Ben Woodcroft2016-12-10
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
* gnu: pardre: Update to 1.1.5-1.Ben Woodcroft2016-12-10
| | | | | * gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1. [source]: Update source hash.
* gnu: vsearch: Update to 2.3.3.Ben Woodcroft2016-12-08
| | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
* gnu: aragorn: Update to 1.2.38.Ben Woodcroft2016-12-04
| | | | * gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
* Merge branch 'master' into python-build-systemHartmut Goebel2016-11-29
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| * gnu: Add r-gkmsvm.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
| * gnu: Add r-seqgl.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-seqgl): New variable.
| * gnu: Add r-chipkernels.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
| * gnu: Add r-wgcna.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-wgcna): New variable.
| * gnu: Add r-r4rna.Ricardo Wurmus2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (r-r4rna): New variable.
| * gnu: Add newick-utils.Ben Woodcroft2016-11-28
| | | | | | | | * gnu/packages/bioinformatics.scm (newick-utils): New variable.
| * gnu: roary: Update to 3.7.0.Ben Woodcroft2016-11-26
| | | | | | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
| * gnu: Add proteinortho.Ben Woodcroft2016-11-26
| | | | | | | | * gnu/packages/bioinformatics.scm (proteinortho): New variable.
* | Merge branch 'master' into python-build-systemLeo Famulari2016-11-25
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| * gnu: diamond: Update to 0.8.27.Ben Woodcroft2016-11-22
| | | | | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
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