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Author SHA1 Message Date
Ricardo Wurmus
b87b41a74d
gnu: r-shortread: Update to 1.32.0. 
* gnu/packages/bioinformatics.scm (r-shortread): Update to 1.32.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus
ae6899b683
gnu: r-gostats: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-gostats): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus
816599c1e7
gnu: r-category: Update to 2.40.0. 
* gnu/packages/bioinformatics.scm (r-category): Update to 2.40.0.
 2016-10-26 09:28:10 +02:00
Ricardo Wurmus
558d02c361
gnu: r-gseabase: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-gseabase): Update to 1.36.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus
700c780dcf
gnu: r-rbgl: Update to 1.50.0. 
* gnu/packages/bioinformatics.scm (r-rbgl): Update to 1.50.0.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus
55cd914c3d
gnu: r-annotationforge: Update to 1.16.0. 
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.16.0.
[propagated-inputs]: Add r-rcurl.
 2016-10-26 09:28:09 +02:00
Ricardo Wurmus
e1db8dd813
gnu: r-deseq2: Update to 1.14.0. 
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.14.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus
1e66e71921
gnu: r-genefilter: Update to 1.56.0. 
* gnu/packages/bioinformatics.scm (r-genefilter): Update to 1.56.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus
6faa2a48f0
gnu: r-geneplotter: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-geneplotter): Update to 1.52.0.
 2016-10-26 09:28:08 +02:00
Ricardo Wurmus
9beba74f66
gnu: r-annotate: Update to 1.52.0. 
* gnu/packages/bioinformatics.scm (r-annotate): Update to 1.52.0.
 2016-10-26 09:28:07 +02:00
Roel Janssen
4644644ace
gnu: Add r-bioccheck. 
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
 2016-10-20 09:53:02 +02:00
Roel Janssen
99df12cd19
gnu: Add r-biocstyle. 
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
 2016-10-19 15:22:06 +02:00
Roel Janssen
207ce8fbe5
gnu: Add r-biocviews. 
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
 2016-10-19 15:09:55 +02:00
Roel Janssen
c79ad57a8d
gnu: Add r-optparse. 
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
 2016-10-19 10:48:56 +02:00
Roel Janssen
2acaaee550
gnu: Add r-getopt. 
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
 2016-10-19 09:55:45 +02:00
Ricardo Wurmus
5093729704
gnu: Add rcas-web. 
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
 2016-10-17 18:09:20 +02:00
Ricardo Wurmus
89984be46e
gnu: Add r-rcas. 
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
 2016-10-17 18:09:16 +02:00
Ben Woodcroft
3dd50d974b
gnu: vsearch: Update to 2.3.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.3.0.
 2016-10-11 22:29:48 +10:00
Ben Woodcroft
99c9056141
gnu: diamond: Update to 0.8.23. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.23.
 2016-10-11 19:51:49 +10:00
Ben Woodcroft
9602e3cce9
gnu: python2-dendropy: Fix tests. 
* gnu/packages/bioinformatics.scm (python2-dendropy)[source]: Use unpatched
source.
[arguments]: Use nose to run tests.
[native-inputs]: Add python2-nose.
 2016-10-08 21:38:17 +10:00
Ricardo Wurmus
fc47c7d635
gnu: Add r-bsgenome-celegans-ucsc-ce10. 
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce10): New
variable.
 2016-10-06 10:33:43 +02:00
Ben Woodcroft
2c3eb4b85b
gnu: metabat: Update to 0.32.4-1.cbdca756. 
* gnu/packages/bioinformatics.scm (metabat): Update to 0.32.4-1.cbdca756.
* gnu/packages/patches/metabat-remove-compilation-date.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
 2016-10-04 22:02:52 +10:00
Ben Woodcroft
4bdc3df92d
gnu: vsearch: Update to 2.1.2. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.2.
 2016-10-02 22:25:39 +10:00
Ricardo Wurmus
2320e76b82
gnu: sra-tools: Fix build on i686. 
* gnu/packages/bioinformatics.scm (sra-tools)[arguments]: Pass
"VDB_LIBDIR" in make-flags; dynamically link libmagic.
 2016-09-28 22:30:41 +02:00
Ben J Woodcroft
99caa6f75f
gnu: python-plastid: Update to 1.4.6. 
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): Update to
1.4.6.
[propagated-inputs]: Add python-termcolor.
 2016-09-27 20:07:12 +10:00
Marius Bakke
f536dce522
gnu: python-pysam: Enable tests. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Change from
PyPi to source archive due to missing test data.
[arguments]: Add check phase after install.
[native-inputs]: Add python-nose, samtools and bcftools.
 2016-09-27 20:06:00 +10:00
Marius Bakke
dff26b2363
gnu: python-pysam: Delete bundled htslib. 
* gnu/packages/bioinformatics.scm (python-pysam)[source]: Add snippet
to delete htslib.
[arguments]: Add htslib flags in 'set-flags phase.
[propagated-inputs]: New field. Add htslib.
 2016-09-27 20:06:00 +10:00
Marius Bakke
397d463a12
gnu: python-pysam: Use 'modify-phases'. 
* gnu/packages/bioinformatics.scm (python-pysam)[arguments]: Use
'modify-phases'.
 2016-09-27 20:06:00 +10:00
Marius Bakke
bdc7be59eb
gnu: Add bcftools. 
* gnu/packages/bioinformatics.scm (bcftools): New variable.
 2016-09-27 20:06:00 +10:00
Marius Bakke
e301bfc886
gnu: python2-pbcore: Update to 1.2.10. 
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.10.
[propagated-inputs]: New field. Add python2-pyxb.
 2016-09-27 20:06:00 +10:00
Marius Bakke
fd49eb213f
gnu: python-pysam: Update to 0.9.1.4. 
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam): Update
to 0.9.1.4.
 2016-09-27 20:05:57 +10:00
Ricardo Wurmus
675d7ae26f
gnu: ncbi-vdb: Only build on i686 and x86_64. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[supported-systems]: Only
build on i686 and x86_64.
[arguments]: Add mandatory "-msse2" flag to CFLAGS.
 2016-09-26 14:30:59 +02:00
Ben Woodcroft
af8de20386
gnu: vsearch: Update to 2.1.1. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.1.
 2016-09-26 20:35:32 +10:00
Ricardo Wurmus
f3cfe4515a
gnu: Add r-txdb-hsapiens-ucsc-hg19-knowngene. 
* gnu/packages/bioinformatics.scm (r-txdb-hsapiens-ucsc-hg19-knowngene):
  New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
684f29bd2e
gnu: Add r-grohmm. 
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
7f903d7300
gnu: Add r-systempiper. 
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
 2016-09-26 07:47:55 +02:00
Ricardo Wurmus
cb99d457f0
gnu: Add r-shortread. 
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
89f40c5e4e
gnu: Add r-gostats. 
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
1a1931f7e0
gnu: Add r-category. 
* gnu/packages/bioinformatics.scm (r-category): New variable.
 2016-09-26 07:47:54 +02:00
Ricardo Wurmus
ad740ff818
gnu: Add r-gseabase. 
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
 2016-09-26 07:47:53 +02:00
Ricardo Wurmus
cd9e7dc7ff
gnu: Add r-rbgl. 
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
 2016-09-26 03:25:23 +02:00
Ricardo Wurmus
e816377374
gnu: Add r-annotationforge. 
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
 2016-09-26 03:25:17 +02:00
Ricardo Wurmus
ad34f0ac96
gnu: Add r-deseq2. 
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
 2016-09-26 03:21:27 +02:00
Ricardo Wurmus
2301fd3e4d
gnu: Add r-genefilter. 
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
 2016-09-26 03:21:19 +02:00
Ricardo Wurmus
07a664cde0
gnu: Add r-geneplotter. 
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
 2016-09-26 03:21:07 +02:00
Ricardo Wurmus
8c6de58849
gnu: Add r-annotate. 
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
 2016-09-26 03:20:59 +02:00
Ricardo Wurmus
646a84338d
gnu: sra-tools: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.7.0.
 2016-09-23 11:46:53 +02:00
Ricardo Wurmus
40974c933e
gnu: ncbi-vdb: Update to 2.7.0. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.7.0.
 2016-09-23 11:46:26 +02:00
Ricardo Wurmus
48b419ebd6
gnu: ngs-sdk: Update to 1.2.5. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.5.
 2016-09-23 11:45:24 +02:00
Efraim Flashner
0dbb7ac2df
gnu: plink: Set endian-ness on more architectures. 
* gnu/packages/patches/plink-endian-detection.patch: New file.
* gnu/packages/bioinformatics.scm (plink)[source]: Use it.
* gnu/local.mk (dist_patch_DATA): Register it.
 2016-09-22 22:42:37 +03:00