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Author SHA1 Message Date
Ricardo Wurmus 08da08d296
gnu: r-summarizedexperiment: Update to 1.4.0. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.4.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus c0ccef41ae
gnu: r-rsamtools: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.26.1.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 47d39b6e7a
gnu: r-biostrings: Update to 2.42.0. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.42.0.
 2016-10-26 09:28:17 +02:00
Ricardo Wurmus 89559a124e
gnu: r-biocparallel: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 9405333186
gnu: r-biomart: Update to 2.30.0. 
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.30.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus e45dc05781
gnu: r-annotationdbi: Update to 1.36.0. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.36.0.
 2016-10-26 09:28:16 +02:00
Ricardo Wurmus 464870caf7
gnu: r-biobase: Update to 2.34.0. 
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.34.0.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 92a740afac
gnu: r-genomicranges: Update to 1.26.1. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.26.1.
[propagated-inputs]: Add r-iranges, r-s4vectors.
 2016-10-26 09:28:15 +02:00
Ricardo Wurmus 1d048589ca
gnu: r-xvector: Update to 0.14.0. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.14.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 753bc32b8e
gnu: r-limma: Update to 3.30.0. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.0.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 37d96f1dde
gnu: r-variantannotation: Update to 1.20.0. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.20.0.
[propagated-inputs]: Add r-biobase, r-biostrings, r-iranges,
r-rtracklayer, r-s4vectors, r-xvector.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus 5e48005fa9
gnu: r-edger: Update to 3.16.0. 
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.0.
[propagated-inputs]: Add r-locfit.
 2016-10-26 09:28:14 +02:00
Ricardo Wurmus dece310a25
gnu: r-genomeinfodb: Update to 1.10.0. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.10.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 7f354dafb1
gnu: r-iranges: Update to 2.8.0. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.8.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus b120c5f3a2
gnu: r-s4vectors: Update to 0.12.0. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.12.0.
 2016-10-26 09:28:13 +02:00
Ricardo Wurmus 22c5d736af
gnu: r-dnacopy: Update to 1.48.0. 
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.48.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus 5c7b04e0c3
gnu: r-biocinstaller: Update to 1.24.0. 
* gnu/packages/bioinformatics.scm (r-biocinstaller): Update to 1.24.0.
 2016-10-26 09:28:12 +02:00
Ricardo Wurmus f0b297e17b
gnu: r-biocgenerics: Update to 0.20.0. 
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.20.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus c9b5046a18
gnu: r-grohmm: Update to 1.8.0. 
* gnu/packages/bioinformatics.scm (r-grohmm): Update to 1.8.0.
 2016-10-26 09:28:11 +02:00
Ricardo Wurmus 1265d3877b
gnu: r-systempiper: Update to 1.8.1. 
* gnu/packages/bioinformatics.scm (r-systempiper): Update to 1.8.1.
 2016-10-26 09:28:11 +02:00
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
Efraim Flashner 62d00095c2
gnu: prank: Allow building on 32-bit machines. 
* gnu/packages/bioinformatics.scm (prank)[arguments]: Add a phase
removing the '-m64' compiler flag.
 2016-09-22 19:21:16 +03:00
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
Ben Woodcroft 70f1bc051a
gnu: Add bpp-seq. 
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 985d841144
gnu: Add bpp-core. 
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 9e12eba866
gnu: Add python-biom-format. 
* gnu/packages/bioinformatics.scm (python-biom-format,
python2-biom-format): New variables.
 2016-08-06 09:44:28 +10:00
Ricardo Wurmus 97b9da6897
gnu: Add discrover. 
* gnu/packages/bioinformatics.scm (discrover): New variable.
 2016-08-03 17:20:26 +02:00
Ben Woodcroft afde1a264b
gnu: fxtract: Restrict to x86_64-linux. 
* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to
  x86_64-linux.
 2016-08-03 21:22:02 +10:00
Ricardo Wurmus dda3627141
gnu: r-variantannotation: Update to 1.18.6. 
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
 2016-08-02 14:47:46 +02:00
Ricardo Wurmus 005ca42396
gnu: r-genomationdata: Update to 1.4.2. 
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
 2016-08-02 14:47:46 +02:00
Ben Woodcroft c4382cd18f
gnu: diamond: Update to 0.8.17. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
 2016-07-30 23:02:57 +10:00
Ben Woodcroft 6547708f71
gnu: r-genomicfeatures: Update to 1.24.5. 
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
 2016-07-28 21:54:44 +10:00
Ben Woodcroft 2c9f6251fc
gnu: r-bsgenome: Update to 1.40.1. 
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft b0f0778a7c
gnu: r-iranges: Update to 2.6.1. 
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
 2016-07-28 21:45:17 +10:00
Ben Woodcroft f403941f81
gnu: r-limma: Update to 3.28.17. 
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft 2b2ff0bd91
gnu: r-xvector: Update to 0.12.1. 
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft a463055862
gnu: r-genomicranges: Update to 1.24.2. 
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
 2016-07-28 21:45:16 +10:00
Ben Woodcroft bab15ccec4
gnu: r-annotationdbi: Update to 1.34.4. 
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft a22999f245
gnu: r-biocparallel: Update to 1.6.3. 
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft d104fc607d
gnu: r-biostrings: Update to 2.40.2. 
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 1864e051c9
gnu: r-summarizedexperiment: Update to 1.2.3. 
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
 2016-07-28 21:45:15 +10:00
Ben Woodcroft 29b0cc8ad5
gnu: r-genomicalignments: Update to 1.8.4. 
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 5131e21064
gnu: r-rtracklayer: Update to 1.32.2. 
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft 2a3e325f5e
gnu: r-genomeinfodb: Update to 1.8.3. 
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
 2016-07-28 21:45:14 +10:00
Ben Woodcroft f2e791750b
gnu: r-s4vectors: Update to 0.10.2. 
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
 2016-07-28 20:13:42 +10:00
Ben Woodcroft 12c8f210ee
gnu: diamond: Update to 0.8.16. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
 2016-07-27 23:17:57 +10:00
Ben Woodcroft e03a515304
gnu: fasttree: Update to 2.1.9. 
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9.
 2016-07-23 15:15:12 +10:00
Leo Famulari de67e92288
gnu: Update URLs for sourceforge.net. 
* gnu/packages/admin.scm: Update URLs pointing to sourceforge.net.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/boost.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/code.scm: Likewise.
* gnu/packages/compression.scm: Likewise.
* gnu/packages/cups.scm: Likewise.
* gnu/packages/djvu.scm: Likewise.
* gnu/packages/docbook.scm: Likewise.
* gnu/packages/documentation.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fonts.scm: Likewise.
* gnu/packages/fontutils.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/gl.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/graphviz.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/networking.scm: Likewise.
* gnu/packages/onc-rpc.scm: Likewise.
* gnu/packages/password-utils.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/photo.scm: Likewise.
* gnu/packages/popt.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/rdesktop.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/swig.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
 2016-07-21 18:09:40 -04:00
Ben Woodcroft 7593e50b26
gnu: diamond: Update to 0.8.15. 
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15.
 2016-07-18 00:06:21 +10:00
Ricardo Wurmus 2c0d8e0d09
gnu: eigensoft: Do not refer to "lapacke" output. 
* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference
  to non-existing "lapacke" output.
 2016-07-17 12:04:04 +02:00
Ricardo Wurmus 6619f9c769
gnu: Add eigensoft. 
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
 2016-07-14 08:58:35 +02:00
Ricardo Wurmus 17dc32a400
gnu: Add Ribotaper. 
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
 2016-07-12 12:19:39 +02:00