8ab6f241ea
gnu: r-rbgl: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.52.0.
2017-04-28 11:04:16 +02:00
46972a4427
gnu: r-annotationforge: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.0.
2017-04-28 11:04:12 +02:00
3ae74e451c
gnu: r-deseq2: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.0.
2017-04-28 11:04:09 +02:00
b5bc3a3963
gnu: r-genefilter: Update to 1.58.0.
...
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.58.0.
2017-04-28 11:04:06 +02:00
97a50e4f34
gnu: r-geneplotter: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.54.0.
2017-04-28 11:03:59 +02:00
dbab99b6d2
gnu: r-annotate: Update to 1.54.0.
...
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.54.0.
2017-04-28 11:03:47 +02:00
ffef27f3d2
gnu: Add r-genomeinfodbdata.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodbdata): New variable.
2017-04-28 10:17:06 +02:00
71e34e6b5b
gnu: Add r-delayedarray.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): New variable.
2017-04-28 10:15:12 +02:00
2abfc5b827
gnu: Add r-bookdown.
...
* gnu/packages/bioinformatics.scm (r-bookdown): New variable.
2017-04-28 10:09:31 +02:00
31c374e081
gnu: python-pysam: Disable tests.
...
* gnu/packages/bioinformatics.scm (python-pysam): Disable tests.
2017-04-25 14:05:59 +02:00
b2955e224e
gnu: python-pysam: Fix tests, again.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Run nosetests
explicitly with a single process.
2017-04-24 18:46:28 +02:00
c136240efc
gnu: diamond: Enable building on all architectures.
...
* gnu/packages/bioinformatics.scm (diamond)[supported-systems]: Remove
field.
2017-04-24 19:30:10 +03:00
1a84edeb0b
gnu: r-seqminer: Update to 5.9.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.9.
2017-04-22 23:30:31 +02:00
a7d12a9e71
gnu: proteinortho: Update to 5.16.
...
* gnu/packages/bioinformatics.scm (proteinortho): Update to 5.16.
2017-04-21 23:03:56 +10:00
37199768e8
gnu: diamond: Update to 0.8.38.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.38.
2017-04-21 23:03:55 +10:00
d1e4ad1b02
gnu: Fix typos in descriptions.
...
* gnu/packages/admin.scm (di)[description]: Likewise.
* gnu/packages/bioinformatics.scm (r-annotate)[description]: Likewise.
* gnu/packages/datastructures.scm (sparsehash)[description]: Likewise.
* gnu/packages/dns.scm (knot)[description]: Likewise.
* gnu/packages/emacs.scm (emacs-idle-highlight)[synopsis, description]:
Likewise.
* gnu/packages/gnome.scm (libpeas)[description]: Likewise.
* gnu/packages/gtk.scm (python2-pygtk)[description]: Likewise.
* gnu/packages/kde-frameworks.scm (kactivities)[description]: Fix typo.
* gnu/packages/libevent.scm (perl-anyevent)[description]: Likewise.
* gnu/packages/machine-learning.scm (ghmm)[description]: Likewise.
* gnu/packages/mail.scm (mlmmj)[description]: Likewise.
* gnu/packages/maths.scm (vc)[description]: Likewise.
* gnu/packages/music.scm (gx-super-fuzz-lv2)[description]: Likewise.
* gnu/packages/networking.scm (nload)[description]: Likewise.
* gnu/packages/python.scm (python-execnet)[description]: Likewise.
* gnu/packages/terminals.scm (tilda)[description]: Likewise.
* gnu/packages/python.scm (python-execnet, python-tables)
(python2-coverage-test-runner, python2-rope)[description]: Likewise.
2017-04-17 02:04:08 +02:00
88eb119f95
gnu: mafft: Update to 7.310.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.310.
2017-04-14 15:19:37 +10:00
e9e0fab079
gnu: raxml: Update to 8.2.10.
...
* gnu/packages/bioinformatics.scm (raxml): Update to 8.2.10.
2017-04-09 21:44:14 +10:00
6acdff5875
gnu: r-rsamtools: Update to 1.26.2.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.2.
2017-04-09 13:34:53 +02:00
dc8ebe43af
gnu: r-biocparallel: Update to 1.8.2.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.2.
2017-04-09 13:34:53 +02:00
1d65b5379b
gnu: r-vegan: Update to 2.4-3.
...
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-3.
[arguments]: Remove build phase "revert-test-deletion".
[native-inputs]: Remove "r-vegan-delete-tests-patch".
2017-04-08 10:25:50 +02:00
37982693ca
gnu: vsearch: Update to 2.4.3.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.4.3.
2017-04-07 21:35:07 +10:00
e18c731ba0
gnu: r-seqinr: Update to 3.3-6.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-6.
2017-04-06 14:39:22 +02:00
0685fe3c86
gnu: r-rcpparmadillo: Update to 0.7.700.0.0.
...
* gnu/packages/statistics.scm (r-rcpparmadillo): Update to 0.7.700.0.0.
[source]: Do not delete bundled armadillo sources, because upstream no longer
hosts previous versions.
[propagated-inputs]: Remove "armadillo-for-rcpparmadillo".
[arguments]: Remove because we no longer need to link with the armadillo
library.
* gnu/packages/bioinformatics.scm (r-deseq2)[arguments]: Remove because we no
longer need to link with armadillo library.
2017-04-06 14:39:22 +02:00
a3656b11d2
gnu: r-annotationforge: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.1.
2017-04-06 14:39:22 +02:00
e0d7b31820
gnu: r-shortread: Update to 1.32.1.
...
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.1.
2017-04-06 14:39:21 +02:00
2cea968e41
gnu: r-s4vectors: Update to 0.12.2.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.2.
2017-04-06 14:39:21 +02:00
7d05eb2dcc
gnu: r-iranges: Update to 2.8.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.2.
2017-04-06 14:39:21 +02:00
e89cf15091
gnu: r-variantannotation: Update to 1.20.3.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.20.3.
2017-04-06 14:39:21 +02:00
3506a62762
gnu: r-limma: Update to 3.30.13.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.13.
2017-04-06 14:39:21 +02:00
4cd4721dbb
gnu: r-genomicranges: Update to 1.26.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
69b356efce
gnu: r-annotationdbi: Update to 1.36.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.2.
2017-04-06 14:39:20 +02:00
5cc3b7a548
gnu: r-genomicalignments: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.10.1.
2017-04-06 14:39:20 +02:00
25d8854723
gnu: r-rtracklayer: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.2.
2017-04-06 14:39:20 +02:00
9ce6cb082e
gnu: r-genomicfeatures: Update to 1.26.4.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.4.
2017-04-06 14:39:20 +02:00
57ac1d2f03
gnu: r-seqminer: Update to 5.7.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 5.7.
2017-04-06 14:39:19 +02:00
e8bec95e69
gnu: r-maldiquant: Update to 1.16.2.
...
* gnu/packages/bioinformatics.scm (r-maldiquant): Update to 1.16.2.
2017-04-06 14:39:19 +02:00
4cd07e487e
gnu: r-genomeinfodb: Update to 1.10.3.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.3.
[propagated-inputs]: Add "r-rcurl".
2017-04-06 14:39:11 +02:00
acbeb2d56b
gnu: r-xvector: Update to 0.14.1.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.1.
2017-04-06 14:39:11 +02:00
da250f733a
gnu: r-bioccheck: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): Update to 1.10.1.
[propagated-inputs]: Remove "r-knitr" and "r-devtools".
2017-04-06 14:39:11 +02:00
1108a920bd
gnu: sra-tools: Fix glibc naming conflict.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Add build phase
"patch-away-glibc-conflict" to fix a definition conflict with glibc 2.25.
2017-04-05 18:06:51 +02:00
beebe43176
gnu: sra-tools: Use "modify-phases" syntax.
...
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Use "modify-phases"
syntax.
2017-04-05 18:06:51 +02:00
fc5b12879f
gnu: diamond: Update to 0.8.37.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.37.
2017-04-05 22:49:01 +10:00
7bf837fd43
gnu: Use HTTPS URLs for GitHub home-pages.
...
* gnu/packages/bioinformatics.scm, gnu/packages/emacs.scm,
gnu/packages/haskell.scm, gnu/packages/libffi.scm, gnu/packages/lisp.scm,
gnu/packages/ocaml.scm, gnu/packages/openstack.scm, gnu/packages/python.scm,
gnu/packages/ruby.scm, gnu/packages/shells.scm, gnu/packages/statistics.scm,
gnu/packages/xdisorg.scm: Use HTTPS URLs for all packages with a home-page on
GitHub.
2017-04-02 20:00:51 -04:00
cf1d581464
gnu: khmer: Build with gcc-4.
...
* gnu/packages/bioinformatics.scm (khmer)[inputs]: Add gcc-4.9.
2017-04-02 10:14:17 +10:00
84157bb8bf
Merge branch 'master' into core-updates
...
Most conflicts are from 6fd52309b8
2017-03-30 22:59:53 +02:00
fa702e1a29
gnu: discrover: Add missing includes.
...
* gnu/packages/bioinformatics.scm (discrover)[arguments]: Add build phase
"add-missing-includes" to include "random" headers.
2017-03-30 10:35:54 +02:00
0d2c0562b8
gnu: stringtie: Remove typedef conflict.
...
* gnu/packages/bioinformatics.scm (stringtie)[arguments]: Remove conflicting
typedef in a new build phase "remove-duplicate-typedef".
2017-03-30 10:35:53 +02:00
e1f02f92e9
Replace (compose not PROC) with simpler idioms.
...
* gnu/packages/bioinformatics.scm (python-pysam)[arguments] <check>:
Use (negate proc) instead of (compose not proc).
* guix/import/cran.scm (recursive-import): Likewise.
* guix/import/elpa.scm (filter-dependencies): Use 'remove' instead of
'(filter (compose not proc) ...)'.
2017-03-28 22:15:44 +02:00
939b6b113b
gnu: star: Update to 2.5.3a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.5.3a.
2017-03-23 11:21:08 +01:00
Roel Janssen