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2017-07-09gnu: deeptools: Update to 2.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1. [arguments]: Remove. [native-inputs]: Use "python-" instead of "python2-" variants. [inputs]: Likewise; add python-py2bit.
2017-07-09gnu: Add python-py2bit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-08gnu: blast+: Update to 2.6.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. Add patch. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. * gnu/packages/patches/blast+-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2017-07-06Revert "gnu: blast+: Update to 2.6.0."Leo Famulari
This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
2017-07-04gnu: gemma: Fix building on non-Intel architectures.Efraim Flashner
* gnu/packages/patches/gemma-intel-compat.patch: New file. * gnu/packages/bioinformatics.scm (gemma)[source]: Add patch. [arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures. * gnu/local.mk (dist_patch_DATA): Register patch.
2017-07-04gnu: diamond: Update to 0.9.9.Ben J Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
2017-07-04gnu: blast+: Update to 2.6.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python.
2017-07-01gnu: cd-hit: Update to 4.6.8.Ben Woodcroft
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
2017-07-01gnu: bwa: Update to 0.7.15.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
2017-06-25gnu: Add f-seq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-24gnu: orfm: Update to 0.7.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
2017-06-23gnu: orfm: Update to 0.7.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
2017-06-23gnu: Add kentutils.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (kentutils): New variable.
2017-06-22gnu: python2-bx-python: Update to 0.7.3.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
2017-06-20gnu: Move contents of zip module into compression module.Arun Isaac
* 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.
2017-06-17gnu: diamond: Update to 0.9.8.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
2017-06-16gnu: tadbit: Fix typo in description.Tobias Geerinckx-Rice
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
2017-06-15gnu: gemma: Fix indentation.Efraim Flashner
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
2017-06-15gnu: gemma: Fix building on 32-bit architectures.Efraim Flashner
* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit architectures add 'FORCE_32BIT' flag.
2017-06-09gnu: Add tadbit.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (tadbit): New variable.
2017-06-09gnu: Add imp.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (imp): New variable.
2017-06-09gnu: Add phylip.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (phylip): New variable.
2017-06-09gnu: Add gess.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (gess): New variable.
2017-06-09gnu: Add trim-galore.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
2017-06-09gnu: Add ritornello.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ritornello): New variable.
2017-06-08gnu: diamond: Update to 0.9.6.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
2017-06-02gnu: Add kaiju.Roel Janssen
* gnu/packages/bioinformatics.scm (kaiju): New variable.
2017-05-28gnu: diamond: Update to 0.9.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
2017-05-27gnu: diamond: Update to 0.9.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
2017-05-22gnu: diamond: Update to 0.9.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
2017-05-22gnu: Add r-edaseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22gnu: Add r-deseq.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
2017-05-22gnu: Add r-aroma-light.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
2017-05-22gnu: fraggenescan: Update to 1.30.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30. [arguments]: Update patching of paths, install procedure. Add new test case.
2017-05-22gnu: roary: Update to 3.8.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
2017-05-22gnu: taxtastic: Update to 0.6.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI.
2017-05-22gnu: r-mutationalpatterns: Update to 1.2.1.Roel Janssen
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
2017-05-21gnu: diamond: Update to 0.9.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0. [license]: Change to AGPL3+.
2017-05-21gnu: fasttree: Update to 2.1.10.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
2017-05-21gnu: python-biom-format: Update to 2.1.6.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6. [propagated-inputs]: Add python-pandas.
2017-05-18gnu: Add gemma.Pjotr Prins
* gnu/packages/bioinformatics.scm (gemma): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-13gnu: guile-json: Rename "guile2.2-json" to "guile-json".Ludovic Courtès
* 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.
2017-05-10gnu: Add pplacer.Ben Woodcroft
* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
2017-05-10gnu: Add taxtastic.Ben Woodcroft
* gnu/packages/bioinformatics.scm (taxtastic): New variable.
2017-05-02gnu: Avoid circular dependencies by Perl license.Petter
* 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>
2017-05-01gnu: vcftools: Update to 0.1.15.Roel Janssen
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
2017-04-29gnu: r-genomeinfodbdata: Fix source url.Efraim Flashner
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use source uri and not bioconductor-uri shortener.
2017-04-28gnu: r-msnid: Update to 1.10.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
2017-04-28gnu: r-msnbase: Update to 2.2.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
2017-04-28gnu: r-pcamethods: Update to 1.68.0.Roel Janssen
* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
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