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Author SHA1 Message Date
Ben Woodcroft
951da521a9
gnu: diamond: Update to 0.8.22. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.22.
 2016-09-22 16:36:00 +10:00
Efraim Flashner
6e8faf7794
gnu: jellyfish: Limit to x86_64. 
* gnu/packages/bioinformatics.scm (jellyfish)[supported-systems}: New
field, limit support to x86_64.
 2016-09-21 22:36:52 +03:00
Ben Woodcroft
79558df220
gnu: vsearch: Update to 2.1.0. 
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.1.0.
 2016-09-21 18:44:22 +10:00
Roel Janssen
eb24341ffb
gnu: Add r-biocinstaller. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable.
 2016-09-19 11:56:44 +02:00
Ben Woodcroft
de96ea286d
gnu: python-biom-format: Move inputs to propagated-inputs. 
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format)
[inputs]: Move all from here ...
[propagated-inputs]: ... to here.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft
7bba95b769
gnu: seqmagick: Use BioPython 1.66. 
* gnu/packages/bioinformatics.scm (seqmagick)[inputs]: Use
python2-biopython-1.66 instead of python2-biopython.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft
4b1a152826
gnu: Add python2-biopython-1.66. 
* gnu/packages/bioinformatics.scm (python2-biopython-1.66): New variable.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft
8c8da1389e
gnu: python-biopython: Use 'python2-variant'. 
* gnu/packages/bioinformatics.scm (python-biopython)[properties]: New field.
[native-inputs]: Remove field.
(python-biopython): Use 'strip-python-variant'.
 2016-09-19 15:44:20 +10:00
Ben Woodcroft
4ce6030588
gnu: python-biopython: Update to 1.68. 
* gnu/packages/bioinformatics.scm (python-biopython): Update to 1.68.
[arguments]: New field.
 2016-09-19 15:44:18 +10:00
Ben J Woodcroft
66daf78c0a
gnu: Add seqtk. 
* gnu/packages/bioinformatics.scm (seqtk): New variable.
 2016-09-13 20:27:29 +10:00
Leo Famulari
2642231b39
gnu: bowtie: Update to 2.2.9. 
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.2.9.
 2016-09-12 14:19:37 -04:00
Ricardo Wurmus
d108c21228
gnu: r-org-mm-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-mm-eg-db): Update to 3.3.0.
 2016-09-12 17:44:49 +02:00
Ricardo Wurmus
6ab7ca24f2
gnu: r-org-dm-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-dm-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus
019be09060
gnu: r-org-ce-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-ce-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus
5cc7cff6ef
gnu: r-org-hs-eg-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-org-hs-eg-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus
401528b2b5
gnu: r-go-db: Update to 3.3.0. 
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.3.0.
 2016-09-12 17:44:48 +02:00
Ricardo Wurmus
44f711dbe6
gnu: r-biocparallel: Update to 1.6.6. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.6.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus
10e479a7c0
gnu: r-genomicranges: Update to 1.24.3. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.3.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus
01ebbb1b76
gnu: r-limma: Update to 3.28.21. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.21.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus
bbf53cb527
gnu: r-variantannotation: Update to 1.18.7. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.7.
 2016-09-12 17:44:42 +02:00
Ricardo Wurmus
4fa7091d54
gnu: r-genomeinfodb: Update to 1.8.7. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.7.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus
3b851cd4ac
gnu: r-seqinr: Update to 3.3-1. 
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-1.
[propagated-inputs]: Add "r-segmented".
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus
2b1cc79d98
gnu: r-s4vectors: Update to 0.10.3. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.3.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus
0b54b4c986
gnu: r-acsnminer: Update to 0.16.8.25. 
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.8.25.
 2016-09-12 17:44:41 +02:00
Ricardo Wurmus
2c575bb9a2
gnu: r-vegan: Update to 2.4-1. 
* gnu/packages/bioinformatics.scm (r-vegan): Update to 2.4-1.
 2016-09-12 17:44:40 +02:00
Marius Bakke
84be3b9920
gnu: Add mash. 
* gnu/packages/bioinformatics.scm (mash): New variable.

Signed-off-by: Leo Famulari <leo@famulari.name>
 2016-09-10 17:41:38 -04:00
Ben Woodcroft
4b6da268ff
gnu: bamm: Update to 1.7.3. 
* gnu/packages/bioinformatics.scm (bamm): Update to 1.7.3.
 2016-09-10 09:47:42 +10:00
Efraim Flashner
48409ef269
gnu: infernal: Limit to i686 and x86_64 systems. 
* gnu/packages/bioinformatics.scm (infernal)[supported-systems]: The
package requires VMX or SSE capability for parallel instructions, so
limit it to those supported systems.
 2016-09-04 12:43:10 +03:00
Ricardo Wurmus
35aa90a1fd
gnu: Add Infernal. 
* gnu/packages/bioinformatics.scm (infernal): New variable.
 2016-09-02 16:46:37 +02:00
Ricardo Wurmus
c180533bb5
gnu: subread: Update to 1.5.1. 
* gnu/packages/bioinformatics.scm (subread): Update to 1.5.1.
 2016-08-31 15:23:03 +02:00
Ben Woodcroft
7d57ebaa7c
gnu: aragorn: Update to 1.2.37. 
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.37.
 2016-08-31 15:52:49 +10:00
Ben Woodcroft
caa9bc7dc5
gnu: diamond: Update to 0.8.20. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.20.
 2016-08-30 10:46:30 +10:00
Ricardo Wurmus
fe02c4c98a
gnu: Add r-bamsignals. 
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
 2016-08-22 16:52:40 +02:00
Ricardo Wurmus
52765a63ca
gnu: Add r-rhtslib. 
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
 2016-08-22 16:52:22 +02:00
Ricardo Wurmus
433530a5fc
gnu: clipper: Update to 1.1. 
* gnu/packages/bioinformatics.scm (clipper): Update to 1.1.
[source]: Delete pre-built libraries.
[inputs]: Add python2-pandas.
 2016-08-17 19:35:05 +02:00
Marius Bakke
318c0aee1e
gnu: Add minced. 
* gnu/packages/bioinformatics.scm (minced): New variable.

Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
 2016-08-17 20:56:21 +10:00
Ben Woodcroft
71461f88ee
gnu: mafft: Update to 7.305. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.305.
[inputs]: Add ruby.
 2016-08-16 19:49:15 +10:00
Ben Woodcroft
0ed8f0cd4c
gnu: mafft: Update to 7.304. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
 2016-08-15 20:59:41 +10:00
Ben Woodcroft
101e8f7171
gnu: mafft: Wrap programs. 
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Add 'wrap-programs'
phase.
[propagated-inputs]: Move coreutils from here ...
[inputs]: ... to here.
 2016-08-15 20:51:00 +10:00
Ben Woodcroft
93b8316e08
gnu: mafft: Update to 7.300. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
 2016-08-15 20:51:00 +10:00
Ben Woodcroft
a12ba6e878
gnu: Add bamm. 
* gnu/packages/bioinformatics.scm (bamm): New variable.
 2016-08-14 14:55:23 +10:00
Efraim Flashner
3e6fdd5f8a
gnu: snap-aligner: Limit to x86_64. 
* gnu/packages/bioinformatics.scm (snap-aligner)[supported-systems]: Add
note explaining why we build for x86_64 only.
 2016-08-11 22:44:07 +03:00
Ben Woodcroft
7024aeaaaa
gnu: diamond: Update to 0.8.18. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.18.
 2016-08-11 20:39:54 +10:00
Ben Woodcroft
ceb62d5436
gnu: Add roary. 
* gnu/packages/bioinformatics.scm (roary): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
608dd93267
gnu: Add raxml. 
* gnu/packages/bioinformatics.scm (raxml): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
024130d258
gnu: Add prank. 
* gnu/packages/bioinformatics.scm (prank): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
b16728b068
gnu: Add exonerate. 
* gnu/packages/bioinformatics.scm (exonerate): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
db7a344427
gnu: Add bppsuite. 
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
159a701678
gnu: Add bpp-popgen. 
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft
8b5f4d5700
gnu: Add bpp-phyl. 
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
 2016-08-08 22:08:17 +10:00