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2017-01-06gnu: Add r-copywriter.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copywriter): New variable.
2017-01-06gnu: Add r-copyhelper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-copyhelper): New variable.
2017-01-06gnu: Add r-chipseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipseq): New variable.
2017-01-06gnu: bioruby: Update to 1.5.1.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (bioruby): Update to 1.5.1.
2017-01-06gnu: cd-hit: Update to 4.6.6.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.6.
2017-01-04gnu: Use HTTPS for all sourceforge.net home pages.Tobias Geerinckx-Rice
* 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.
2017-01-03gnu: r-genomicranges: Update to 1.26.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.2.
2017-01-03gnu: r-genomeinfodb: Update to 1.10.2.Roel Janssen
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.2.
2017-01-01gnu: python-dendropy: Update to 4.2.0.Ben Woodcroft
* 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.
2017-01-01gnu: diamond: Update to 0.8.31.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.31.
2016-12-30gnu: multiqc: Update to 0.9.Ben Woodcroft
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.
2016-12-29gnu: r-genomicfeatures: Update to 1.26.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.2.
2016-12-29gnu: r-biostrings: Update to 2.42.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.1.
2016-12-29gnu: r-limma: Update to 3.30.7.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.7.
2016-12-29gnu: r-variantannotation: Update to 1.20.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.2.
2016-12-29gnu: r-edger: Update to 3.16.5.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.5.
2016-12-29gnu: r-genomeinfodb: Update to 1.10.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.1.
2016-12-29gnu: r-iranges: Update to 2.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.1.
2016-12-29gnu: r-s4vectors: Update to 0.12.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.1.
2016-12-29gnu: r-biocstyle: Update to 2.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.2.1.
2016-12-29gnu: r-deseq2: Update to 1.14.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.1.
2016-12-29gnu: r-annotate: Update to 1.52.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.1. [propagated-inputs]: Add r-rcurl.
2016-12-29gnu: r-qtl: Update to 1.40-8.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.40-8.
2016-12-27gnu: r-rcas: Update to 1.1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.1.1. [propagated-inputs]: Add plotrix.
2016-12-27gnu: diamond: Update to 0.8.30.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.30.
2016-12-20gnu: cutadapt: Use ‘modify-phases’ syntax.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (cutadapt)[arguments]: Use ‘modify-phases’.
2016-12-19gnu: cutadapt: Update to 1.12.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (cutadapt): Update to 1.12. [inputs]: Add python-xopen.
2016-12-18gnu: Add attribution line for Raoul Bonnal.Ben Woodcroft
This is a follow-up commit to c9e9154e993f055a438e2e43518bbd0740aaaf24. * gnu/packages/bioinformatics.scm: Add attribution.
2016-12-17gnu: star: Update to 2.5.2b.Raoul Bonnal
* gnu/packages/bioinformatics (star): Update to 2.5.2b. [source]: Delete precompiled binary. Co-authored-by: Ben Woodcroft <donttrustben@gmail.com>
2016-12-14gnu: Update more dead Google Code home pages.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (cutadapt, mosaik, pepr)[home-page]: Update to their respective replacements.
2016-12-13gnu: diamond: Update to 0.8.29.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.29.
2016-12-13gnu: orfm: Update to 0.6.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.1.
2016-12-12gnu: orfm: Update to 0.6.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.6.0.
2016-12-10gnu: vsearch: Update to 2.3.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.4.
2016-12-10gnu: pardre: Update to 1.1.5-1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (pardre): update to 1.1.5-1. [source]: Update source hash.
2016-12-08gnu: vsearch: Update to 2.3.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.3.
2016-12-04gnu: aragorn: Update to 1.2.38.Ben Woodcroft
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.38.
2016-11-29Merge branch 'master' into python-build-systemHartmut Goebel
2016-11-28gnu: Add r-gkmsvm.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-gkmsvm): New variable.
2016-11-28gnu: Add r-seqgl.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqgl): New variable.
2016-11-28gnu: Add r-chipkernels.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-chipkernels): New variable.
2016-11-28gnu: Add r-wgcna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-wgcna): New variable.
2016-11-28gnu: Add r-r4rna.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-r4rna): New variable.
2016-11-28gnu: Add newick-utils.Ben Woodcroft
* gnu/packages/bioinformatics.scm (newick-utils): New variable.
2016-11-26gnu: roary: Update to 3.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (roary): Update to 3.7.0.
2016-11-26gnu: Add proteinortho.Ben Woodcroft
* gnu/packages/bioinformatics.scm (proteinortho): New variable.
2016-11-25Merge branch 'master' into python-build-systemLeo Famulari
2016-11-22gnu: diamond: Update to 0.8.27.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.27.
2016-11-21gnu: Remove redundancy where mkdir-p <dir> is followed by install-file ↵Petter
<file> <dir>. * gnu/packages/bioinformatics.scm (bwa)[arguments]: Remove redundant mkdir-p. (eigensoft)[arguments]: Likewise. (snap-aligner)[arguments]: Likewise. (pardre)[arguments]: Likewise. (piranha)[arguments]: Likewise. * gnu/packages/maths.scm (hypre)[arguments]: Likewise. * gnu/packages/mp3.scm (mpc123)[arguments]: Likewise. * gnu/packages/music.scm (tuxguitar)[arguments]: Likewise. * gnu/packages/pdf.scm (impressive)[arguments]: Likewise. * gnu/packages/qemu.scm (qemu)[arguments]: Likewise. Signed-off-by: Leo Famulari <leo@famulari.name>
2016-11-15gnu: python2-pbcore: Fix inputs:Hartmut Goebel
* gnu/packages/bioinformatics.scm (python2-pbcore) [inputs] change to [propagated-inputs]. [native-inputs]: Remove python-docutils, which comes with sphinx. [former propagated-inputs]: move all (which is only pyxb) to [inputs].
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