| Commit message (Collapse) | Author | Age |
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* 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.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
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* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
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* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
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* gnu/packages/bioinformatics.scm (tadbit): New variable.
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* gnu/packages/bioinformatics.scm (imp): New variable.
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* gnu/packages/bioinformatics.scm (phylip): New variable.
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* gnu/packages/bioinformatics.scm (gess): New variable.
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* gnu/packages/bioinformatics.scm (trim-galore): New variable.
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* gnu/packages/bioinformatics.scm (ritornello): New variable.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
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* gnu/packages/bioinformatics.scm (kaiju): New variable.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
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* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
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* gnu/packages/bioinformatics.scm (r-deseq): New variable.
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* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
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* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure. Add new test
case.
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* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
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* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
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* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
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* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
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* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
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* gnu/packages/bioinformatics.scm (gemma): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
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* 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.
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* gnu/packages/bioinformatics.scm (pplacer, pplacer-scripts): New
variables.
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* gnu/packages/bioinformatics.scm (taxtastic): New variable.
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* 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>
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* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.15.
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* gnu/packages/bioinformatics.scm (r-genomeinfodbdata)[source]: Use
source uri and not bioconductor-uri shortener.
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* gnu/packages/bioinformatics.scm (r-msnid): Update to 1.10.0.
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* gnu/packages/bioinformatics.scm (r-msnbase): Update to 2.2.0.
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* gnu/packages/bioinformatics.scm (r-pcamethods): Update to 1.68.0.
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* gnu/packages/bioinformatics.scm (r-mzid): Update to 1.14.0.
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* gnu/packages/bioinformatics.scm (r-vsn):
[source]: Update to 3.44.0,
[propagated-inputs]: Add r-hexbin.
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* gnu/packages/bioinformatics.scm (r-affy): Update to 1.54.0.
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* gnu/packages/bioinformatics.scm (r-affyio): Update to 1.46.0.
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* gnu/packages/bioinformatics.scm (r-mzr): Update to 2.10.0.
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* gnu/packages/bioinformatics.scm (r-protgenerics): Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.0.
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* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.0.
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* gnu/packages/bioinformatics.scm (r-chipseq): Update to 1.26.0.
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* gnu/packages/bioinformatics.scm (r-rhdf5): Update to 2.20.0.
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* gnu/packages/bioinformatics.scm (r-tximport): Update to 1.4.0.
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* gnu/packages/bioinformatics.scm (r-mutationalpatterns):
[source]: Update to 1.2.0,
[propagated-inputs]: Add r-bsgenome-hsapiens-1000genomes-hs37d5,
r-bsgenome-hsapiens-ucsc-hg19.
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* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.8.0.
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* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.8.0.
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