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* gnu: vsearch: Update to 2.4.0.Ben Woodcroft2017-02-09
| | | | | | | | * gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.0. [source]: Convert most operations in the snippet to patch form and adjust for 2.4.0. * gnu/packages/patches/vsearch-unbundle-cityhash.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: r-edger: Add r-statmod to inputs.Ricardo Wurmus2017-02-01
| | | | * gnu/packages/bioinformatics.scm (r-edger)[propagated-inputs]: Add r-statmod.
* download: url-fetch/tarball: Make ‘name’ truly optional.Tobias Geerinckx-Rice2017-02-01
| | | | | | | | * guix/download.scm (url-fetch/tarbomb): Fall back to ‘file-name’ if ‘name’ is #f, like the regular ‘url-fetch’ does. * gnu/packages/bioinformatics.scm (muscle)[source]: Remove ‘file-name’. * gnu/packages/engineering.scm (fastcap)[source]: Likewise. * gnu/packages/scheme.scm (scmutils)[source]: Likewise.
* gnu: Add r-rhdf5.Raoul Jean Pierre Bonnal2017-01-31
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* gnu: Add r-tximport.Raoul Jean Pierre Bonnal2017-01-31
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* gnu: Add r-bsgenome-hsapiens-1000genomes-hs37d5.Roel Janssen2017-01-30
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-1000genomes-hs37d5): New variable.
* gnu: r-vegan: Update to 2.4-2.Ben Woodcroft2017-01-21
| | | | * gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-2.
* gnu: diamond: Update to 0.8.34.Ben Woodcroft2017-01-21
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.8.34.
* gnu: r-msnid: Expand abbreviation in description.Ricardo Wurmus2017-01-20
| | | | | * gnu/packages/bioinformatics.scm (r-msnid)[description]: Expand "MS/MS" to "tandem mass spectrometry".
* gnu: r-msnbase: Expand abbreviation in description.Ricardo Wurmus2017-01-20
| | | | | * gnu/packages/bioinformatics.scm (r-msnbase)[description]: Expand "MS" to "mass spectrometry".
* gnu: multiqc: Add python-nose to inputs.Ricardo Wurmus2017-01-18
| | | | | * gnu/packages/bioinformatics.scm (multiqc)[propagated-inputs]: Add python-nose.
* gnu: Add r-msnid.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-msnid): New variable.
* gnu: Add r-msnbase.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): New variable.
* gnu: Add r-pcamethods.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-pcamethods): New variable.
* gnu: Add r-mzid.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-mzid): New variable.
* gnu: Add r-vsn.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-vsn): New variable.
* gnu: Add r-affy.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-affy): New variable.
* gnu: Add r-affyio.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-affyio): New variable.
* gnu: Add r-mzr.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-mzr): New variable.
* gnu: Add r-protgenerics.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-protgenerics): New variable.
* gnu: Add r-maldiquant.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-maldiquant): New variable.
* gnu: Add r-raremetals2.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-raremetals2): New variable.
* gnu: Add r-seqminer.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (r-seqminer): New variable.
* gnu: Add ribodiff.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (ribodiff): New variable.
* gnu: Add hisat2.Ricardo Wurmus2017-01-17
| | | | * gnu/packages/bioinformatics.scm (hisat2): New variable.
* gnu: Add r-centipede.Ricardo Wurmus2017-01-16
| | | | * gnu/packages/bioinformatics.scm (r-centipede): New variable.
* 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.
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