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* gnu: bowtie: Use 'modify-phases'.Ben Woodcroft2017-07-141-10/+8
| | | | | * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases' syntax.
* gnu: bowtie: Update to 2.3.2.Ben Woodcroft2017-07-141-8/+10
| | | | | * gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2. [inputs]: Add zlib.
* gnu: deeptools: Update to 2.5.1.Ricardo Wurmus2017-07-091-14/+12
| | | | | | | * 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.
* gnu: Add python-py2bit.Ricardo Wurmus2017-07-091-0/+18
| | | | * gnu/packages/bioinformatics.scm (python-py2bit): New variable.
* gnu: blast+: Update to 2.6.0.Ben Woodcroft2017-07-081-9/+16
| | | | | | | | | * 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.
* Revert "gnu: blast+: Update to 2.6.0."Leo Famulari2017-07-061-16/+9
| | | | This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
* gnu: gemma: Fix building on non-Intel architectures.Efraim Flashner2017-07-041-8/+11
| | | | | | | * 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.
* gnu: diamond: Update to 0.9.9.Ben J Woodcroft2017-07-041-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
* gnu: blast+: Update to 2.6.0.Ben Woodcroft2017-07-041-9/+16
| | | | | | | * 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.
* gnu: cd-hit: Update to 4.6.8.Ben Woodcroft2017-07-011-4/+5
| | | | * gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
* gnu: bwa: Update to 0.7.15.Ben Woodcroft2017-07-011-2/+2
| | | | * gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
* gnu: Add f-seq.Ricardo Wurmus2017-06-251-0/+52
| | | | * gnu/packages/bioinformatics.scm (f-seq): New variable.
* gnu: orfm: Update to 0.7.1.Ben Woodcroft2017-06-241-2/+2
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
* gnu: orfm: Update to 0.7.0.Ben Woodcroft2017-06-231-2/+2
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
* gnu: Add kentutils.Ricardo Wurmus2017-06-231-0/+115
| | | | * gnu/packages/bioinformatics.scm (kentutils): New variable.
* gnu: python2-bx-python: Update to 0.7.3.Ricardo Wurmus2017-06-221-5/+3
| | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
* gnu: Move contents of zip module into compression module.Arun Isaac2017-06-201-1/+0
| | | | | | | | | | | | | | | * 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 Woodcroft2017-06-171-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
* gnu: tadbit: Fix typo in description.Tobias Geerinckx-Rice2017-06-161-1/+1
| | | | * gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
* gnu: gemma: Fix indentation.Efraim Flashner2017-06-151-9/+9
| | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
* gnu: gemma: Fix building on 32-bit architectures.Efraim Flashner2017-06-151-4/+12
| | | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit architectures add 'FORCE_32BIT' flag.
* gnu: Add tadbit.Ricardo Wurmus2017-06-091-0/+58
| | | | * gnu/packages/bioinformatics.scm (tadbit): New variable.
* gnu: Add imp.Ricardo Wurmus2017-06-091-0/+48
| | | | * gnu/packages/bioinformatics.scm (imp): New variable.
* gnu: Add phylip.Ricardo Wurmus2017-06-091-0/+37
| | | | * gnu/packages/bioinformatics.scm (phylip): New variable.
* gnu: Add gess.Ricardo Wurmus2017-06-091-0/+61
| | | | * gnu/packages/bioinformatics.scm (gess): New variable.
* gnu: Add trim-galore.Ricardo Wurmus2017-06-091-0/+60
| | | | * gnu/packages/bioinformatics.scm (trim-galore): New variable.
* gnu: Add ritornello.Ricardo Wurmus2017-06-091-0/+45
| | | | * gnu/packages/bioinformatics.scm (ritornello): New variable.
* gnu: diamond: Update to 0.9.6.Ben Woodcroft2017-06-081-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
* gnu: Add kaiju.Roel Janssen2017-06-021-0/+38
| | | | * gnu/packages/bioinformatics.scm (kaiju): New variable.
* gnu: diamond: Update to 0.9.3.Ben Woodcroft2017-05-281-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
* gnu: diamond: Update to 0.9.2.Ben Woodcroft2017-05-271-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
* gnu: diamond: Update to 0.9.1.Ben Woodcroft2017-05-221-2/+2
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
* gnu: Add r-edaseq.Ricardo Wurmus2017-05-221-0/+38
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): New variable.
* gnu: Add r-deseq.Ricardo Wurmus2017-05-221-0/+31
| | | | * gnu/packages/bioinformatics.scm (r-deseq): New variable.
* gnu: Add r-aroma-light.Ricardo Wurmus2017-05-221-0/+27
| | | | * gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
* gnu: fraggenescan: Update to 1.30.Ben Woodcroft2017-05-221-11/+14
| | | | | | * 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 Woodcroft2017-05-221-2/+2
| | | | * gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
* gnu: taxtastic: Update to 0.6.4.Ben Woodcroft2017-05-221-8/+3
| | | | | * gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4. [source]: Use PyPI URI.
* gnu: r-mutationalpatterns: Update to 1.2.1.Roel Janssen2017-05-221-2/+2
| | | | * gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
* gnu: diamond: Update to 0.9.0.Ben Woodcroft2017-05-211-4/+3
| | | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0. [license]: Change to AGPL3+.
* gnu: fasttree: Update to 2.1.10.Ben Woodcroft2017-05-211-2/+2
| | | | * gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
* gnu: python-biom-format: Update to 2.1.6.Ben Woodcroft2017-05-211-3/+4
| | | | | * gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6. [propagated-inputs]: Add python-pandas.
* gnu: Add gemma.Pjotr Prins2017-05-181-0/+40
| | | | | | * 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 Courtès2017-05-131-1/+1
| | | | | | | | | | * 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 Woodcroft2017-05-101-0/+125
| | | | | * gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New variables.
* gnu: Add taxtastic.Ben Woodcroft2017-05-101-0/+36
| | | | * gnu/packages/bioinformatics.scm (taxtastic): New variable.
* gnu: Avoid circular dependencies by Perl license.Petter2017-05-021-1/+1
| | | | | | | | | | | | | | | | | | | | | | | | | * 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 Janssen2017-05-011-2/+2
| | | | * gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
* gnu: r-genomeinfodbdata: Fix source url.Efraim Flashner2017-04-291-1/+5
| | | | | * gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use source uri and not bioconductor-uri shortener.
* gnu: r-msnid: Update to 1.10.0.Roel Janssen2017-04-281-2/+2
| | | | * gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
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