| Commit message (Expand) | Author | Age | Files | Lines |
|---|
| * | gnu: bowtie: Use 'modify-phases'.•••* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
| Ben Woodcroft | 2017-07-14 | 1 | -10/+8 |
| * | gnu: bowtie: Update to 2.3.2.•••* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
| Ben Woodcroft | 2017-07-14 | 1 | -8/+10 |
| * | gnu: deeptools: Update to 2.5.1.•••* 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.
| Ricardo Wurmus | 2017-07-09 | 1 | -14/+12 |
| * | gnu: Add python-py2bit.•••* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
| Ricardo Wurmus | 2017-07-09 | 1 | -0/+18 |
| * | gnu: blast+: Update to 2.6.0.•••* 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.
| Ben Woodcroft | 2017-07-08 | 1 | -9/+16 |
| * | Revert "gnu: blast+: Update to 2.6.0."•••This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
| Leo Famulari | 2017-07-06 | 1 | -16/+9 |
| * | gnu: gemma: Fix building on non-Intel architectures.•••* 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.
| Efraim Flashner | 2017-07-04 | 1 | -8/+11 |
| * | gnu: diamond: Update to 0.9.9.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
| Ben J Woodcroft | 2017-07-04 | 1 | -2/+2 |
| * | gnu: blast+: Update to 2.6.0.•••* 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.
| Ben Woodcroft | 2017-07-04 | 1 | -9/+16 |
| * | gnu: cd-hit: Update to 4.6.8.•••* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
| Ben Woodcroft | 2017-07-01 | 1 | -4/+5 |
| * | gnu: bwa: Update to 0.7.15.•••* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
| Ben Woodcroft | 2017-07-01 | 1 | -2/+2 |
| * | gnu: Add f-seq.•••* gnu/packages/bioinformatics.scm (f-seq): New variable.
| Ricardo Wurmus | 2017-06-25 | 1 | -0/+52 |
| * | gnu: orfm: Update to 0.7.1.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
| Ben Woodcroft | 2017-06-24 | 1 | -2/+2 |
| * | gnu: orfm: Update to 0.7.0.•••* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
| Ben Woodcroft | 2017-06-23 | 1 | -2/+2 |
| * | gnu: Add kentutils.•••* gnu/packages/bioinformatics.scm (kentutils): New variable.
| Ricardo Wurmus | 2017-06-23 | 1 | -0/+115 |
| * | gnu: python2-bx-python: Update to 0.7.3.•••* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
| Ricardo Wurmus | 2017-06-22 | 1 | -5/+3 |
| * | gnu: Move contents of zip module into compression module.•••* 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.
| Arun Isaac | 2017-06-20 | 1 | -1/+0 |
| * | gnu: diamond: Update to 0.9.8.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
| Ben Woodcroft | 2017-06-17 | 1 | -2/+2 |
| * | gnu: tadbit: Fix typo in description.•••* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
| Tobias Geerinckx-Rice | 2017-06-16 | 1 | -1/+1 |
| * | gnu: gemma: Fix indentation.•••* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
| Efraim Flashner | 2017-06-15 | 1 | -9/+9 |
| * | gnu: gemma: Fix building on 32-bit architectures.•••* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
| Efraim Flashner | 2017-06-15 | 1 | -4/+12 |
| * | gnu: Add tadbit.•••* gnu/packages/bioinformatics.scm (tadbit): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+58 |
| * | gnu: Add imp.•••* gnu/packages/bioinformatics.scm (imp): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+48 |
| * | gnu: Add phylip.•••* gnu/packages/bioinformatics.scm (phylip): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+37 |
| * | gnu: Add gess.•••* gnu/packages/bioinformatics.scm (gess): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+61 |
| * | gnu: Add trim-galore.•••* gnu/packages/bioinformatics.scm (trim-galore): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+60 |
| * | gnu: Add ritornello.•••* gnu/packages/bioinformatics.scm (ritornello): New variable.
| Ricardo Wurmus | 2017-06-09 | 1 | -0/+45 |
| * | gnu: diamond: Update to 0.9.6.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
| Ben Woodcroft | 2017-06-08 | 1 | -2/+2 |
| * | gnu: Add kaiju.•••* gnu/packages/bioinformatics.scm (kaiju): New variable.
| Roel Janssen | 2017-06-02 | 1 | -0/+38 |
| * | gnu: diamond: Update to 0.9.3.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
| Ben Woodcroft | 2017-05-28 | 1 | -2/+2 |
| * | gnu: diamond: Update to 0.9.2.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
| Ben Woodcroft | 2017-05-27 | 1 | -2/+2 |
| * | gnu: diamond: Update to 0.9.1.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
| Ben Woodcroft | 2017-05-22 | 1 | -2/+2 |
| * | gnu: Add r-edaseq.•••* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
| Ricardo Wurmus | 2017-05-22 | 1 | -0/+38 |
| * | gnu: Add r-deseq.•••* gnu/packages/bioinformatics.scm (r-deseq): New variable.
| Ricardo Wurmus | 2017-05-22 | 1 | -0/+31 |
| * | gnu: Add r-aroma-light.•••* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
| Ricardo Wurmus | 2017-05-22 | 1 | -0/+27 |
| * | gnu: fraggenescan: Update to 1.30.•••* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure. Add new test
case.
| Ben Woodcroft | 2017-05-22 | 1 | -11/+14 |
| * | gnu: roary: Update to 3.8.2.•••* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
| Ben Woodcroft | 2017-05-22 | 1 | -2/+2 |
| * | gnu: taxtastic: Update to 0.6.4.•••* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
| Ben Woodcroft | 2017-05-22 | 1 | -8/+3 |
| * | gnu: r-mutationalpatterns: Update to 1.2.1.•••* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
| Roel Janssen | 2017-05-22 | 1 | -2/+2 |
| * | gnu: diamond: Update to 0.9.0.•••* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
| Ben Woodcroft | 2017-05-21 | 1 | -4/+3 |
| * | gnu: fasttree: Update to 2.1.10.•••* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
| Ben Woodcroft | 2017-05-21 | 1 | -2/+2 |
| * | gnu: python-biom-format: Update to 2.1.6.•••* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
| Ben Woodcroft | 2017-05-21 | 1 | -3/+4 |
| * | gnu: Add gemma.•••* gnu/packages/bioinformatics.scm (gemma): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
| Pjotr Prins | 2017-05-18 | 1 | -0/+40 |
| * | gnu: guile-json: Rename "guile2.2-json" to "guile-json".•••* 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.
| Ludovic Courtès | 2017-05-13 | 1 | -1/+1 |
| * | gnu: Add pplacer.•••* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
| Ben Woodcroft | 2017-05-10 | 1 | -0/+125 |
| * | gnu: Add taxtastic.•••* gnu/packages/bioinformatics.scm (taxtastic): New variable.
| Ben Woodcroft | 2017-05-10 | 1 | -0/+36 |
| * | gnu: Avoid circular dependencies by Perl license.•••* 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>
| Petter | 2017-05-02 | 1 | -1/+1 |
| * | gnu: vcftools: Update to 0.1.15.•••* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
| Roel Janssen | 2017-05-01 | 1 | -2/+2 |
| * | gnu: r-genomeinfodbdata: Fix source url.•••* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use
source uri and not bioconductor-uri shortener.
| Efraim Flashner | 2017-04-29 | 1 | -1/+5 |
| * | gnu: r-msnid: Update to 1.10.0.•••* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
| Roel Janssen | 2017-04-28 | 1 | -2/+2 |
