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* gnu: orfm: Update to 0.7.1.Ben Woodcroft2017-06-24
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
* gnu: orfm: Update to 0.7.0.Ben Woodcroft2017-06-23
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
* gnu: Add kentutils.Ricardo Wurmus2017-06-23
| | | | * gnu/packages/bioinformatics.scm (kentutils): New variable.
* gnu: python2-bx-python: Update to 0.7.3.Ricardo Wurmus2017-06-22
| | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
* gnu: Move contents of zip module into compression module.Arun Isaac2017-06-20
| | | | | | | | | | | | | | | * gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to... * gnu/packages/compression.scm: ...here. * gnu/packages/zip.scm: Delete file. * gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file. * po/packages/POTFILES.in: Unregister deleted file. * gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression, docbook, documentation, fonts, fpga, game-development, games, gl, gnome, gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice, markup, maths, mc, monitoring, music, php, pretty-print, python, scheme, smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml, zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm: Adapt module import.
* gnu: diamond: Update to 0.9.8.Ben Woodcroft2017-06-17
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
* gnu: tadbit: Fix typo in description.Tobias Geerinckx-Rice2017-06-16
| | | | * gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
* gnu: gemma: Fix indentation.Efraim Flashner2017-06-15
| | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
* gnu: gemma: Fix building on 32-bit architectures.Efraim Flashner2017-06-15
| | | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit architectures add 'FORCE_32BIT' flag.
* gnu: Add tadbit.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (tadbit): New variable.
* gnu: Add imp.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (imp): New variable.
* gnu: Add phylip.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (phylip): New variable.
* gnu: Add gess.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (gess): New variable.
* gnu: Add trim-galore.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (trim-galore): New variable.
* gnu: Add ritornello.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (ritornello): New variable.
* gnu: diamond: Update to 0.9.6.Ben Woodcroft2017-06-08
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
* gnu: Add kaiju.Roel Janssen2017-06-02
| | | | * gnu/packages/bioinformatics.scm (kaiju): New variable.
* gnu: diamond: Update to 0.9.3.Ben Woodcroft2017-05-28
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
* gnu: diamond: Update to 0.9.2.Ben Woodcroft2017-05-27
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
* gnu: diamond: Update to 0.9.1.Ben Woodcroft2017-05-22
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
* gnu: Add r-edaseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): New variable.
* gnu: Add r-deseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-deseq): New variable.
* gnu: Add r-aroma-light.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
* gnu: fraggenescan: Update to 1.30.Ben Woodcroft2017-05-22
| | | | | | * gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30. [arguments]: Update patching of paths, install procedure. Add new test case.
* gnu: roary: Update to 3.8.2.Ben Woodcroft2017-05-22
| | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
* gnu: taxtastic: Update to 0.6.4.Ben Woodcroft2017-05-22
| | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI.
* gnu: r-mutationalpatterns: Update to 1.2.1.Roel Janssen2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
* gnu: diamond: Update to 0.9.0.Ben Woodcroft2017-05-21
| | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0. [license]: Change to AGPL3+.
* gnu: fasttree: Update to 2.1.10.Ben Woodcroft2017-05-21
| | | | * gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
* gnu: python-biom-format: Update to 2.1.6.Ben Woodcroft2017-05-21
| | | | | * gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6. [propagated-inputs]: Add python-pandas.
* gnu: Add gemma.Pjotr Prins2017-05-18
| | | | | | * gnu/packages/bioinformatics.scm (gemma): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: guile-json: Rename "guile2.2-json" to "guile-json".Ludovic Courtès2017-05-13
| | | | | | | | | | * gnu/packages/guile.scm (guile-json)[native-inputs]: Change GUILE-2.0 to GUILE-2.2. (guile2.2-json): Define using 'deprecated-package'. (guile2.0-json): New variable. * gnu/packages/bioinformatics.scm (rcas-web)[inputs]: Update accordingly. * gnu/packages/ci.scm (cuirass)[inputs]: Likewise. * gnu/packages/package-management.scm (guix)[inputs]: Likewise.
* gnu: Add pplacer.Ben Woodcroft2017-05-10
| | | | | * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
* gnu: Add taxtastic.Ben Woodcroft2017-05-10
| | | | * gnu/packages/bioinformatics.scm (taxtastic): New variable.
* gnu: Avoid circular dependencies by Perl license.Petter2017-05-02
| | | | | | | | | | | | | | | | | | | | | | | | | * guix/licenses.scm (perl-license): New variable. * gnu/packages/bioinformatics.scm: Change (package-license perl) to perl-license. * gnu/packages/compression.scm: Same. * gnu/packages/databases.scm: Same. * gnu/packages/gd.scm: Same. * gnu/packages/language.scm: Same. * gnu/packages/libevent.scm: Same. * gnu/packages/mail.scm: Same. * gnu/packages/messaging.scm: Same. * gnu/packages/ncurses.scm: Same. * gnu/packages/networking.scm: Same. * gnu/packages/photo.scm: Same. * gnu/packages/tcl.scm: Same. * gnu/packages/tex.scm: Same. * gnu/packages/tls.scm: Same. * gnu/packages/web.scm: Same. * gnu/packages/wm.scm: Same. * gnu/packages/xml.scm: Same. * gnu/packages/xorg.scm: Same. * gnu/packages/zip.scm: Same. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: vcftools: Update to 0.1.15.Roel Janssen2017-05-01
| | | | * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
* gnu: r-genomeinfodbdata: Fix source url.Efraim Flashner2017-04-29
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use source uri and not bioconductor-uri shortener.
* gnu: r-msnid: Update to 1.10.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
* gnu: r-msnbase: Update to 2.2.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
* gnu: r-pcamethods: Update to 1.68.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
* gnu: r-mzid: Update to 1.14.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
* gnu: r-vsn: Update to 3.44.0.Roel Janssen2017-04-28
| | | | | | * gnu/packages/bioinformatics.scm (r-vsn): [source]: Update to 3.44.0, [propagated-inputs]: Add r-hexbin.
* gnu: r-affy: Update to 1.54.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
* gnu: r-affyio: Update to 1.46.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
* gnu: r-mzr: Update to 2.10.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
* gnu: r-protgenerics: Update to 1.8.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
* gnu: r-sva: Update to 3.24.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
* gnu: r-copywriter: Update to 2.8.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
* gnu: r-chipseq: Update to 1.26.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
* gnu: r-rhdf5: Update to 2.20.0.Roel Janssen2017-04-28
| | | | * gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
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