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
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
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
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
bdc7be59eb
gnu: Add bcftools.
...
* gnu/packages/bioinformatics.scm (bcftools): New variable.
2016-09-27 20:06:00 +10:00
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
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
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
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
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
684f29bd2e
gnu: Add r-grohmm.
...
* gnu/packages/bioinformatics.scm (r-grohmm): New variable.
2016-09-26 07:47:55 +02:00
7f903d7300
gnu: Add r-systempiper.
...
* gnu/packages/bioinformatics.scm (r-systempiper): New variable.
2016-09-26 07:47:55 +02:00
cb99d457f0
gnu: Add r-shortread.
...
* gnu/packages/bioinformatics.scm (r-shortread): New variable.
2016-09-26 07:47:54 +02:00
89f40c5e4e
gnu: Add r-gostats.
...
* gnu/packages/bioinformatics.scm (r-gostats): New variable.
2016-09-26 07:47:54 +02:00
1a1931f7e0
gnu: Add r-category.
...
* gnu/packages/bioinformatics.scm (r-category): New variable.
2016-09-26 07:47:54 +02:00
ad740ff818
gnu: Add r-gseabase.
...
* gnu/packages/bioinformatics.scm (r-gseabase): New variable.
2016-09-26 07:47:53 +02:00
cd9e7dc7ff
gnu: Add r-rbgl.
...
* gnu/packages/bioinformatics.scm (r-rbgl): New variable.
2016-09-26 03:25:23 +02:00
e816377374
gnu: Add r-annotationforge.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): New variable.
2016-09-26 03:25:17 +02:00
ad34f0ac96
gnu: Add r-deseq2.
...
* gnu/packages/bioinformatics.scm (r-deseq2): New variable.
2016-09-26 03:21:27 +02:00
2301fd3e4d
gnu: Add r-genefilter.
...
* gnu/packages/bioinformatics.scm (r-genefilter): New variable.
2016-09-26 03:21:19 +02:00
07a664cde0
gnu: Add r-geneplotter.
...
* gnu/packages/bioinformatics.scm (r-geneplotter): New variable.
2016-09-26 03:21:07 +02:00
8c6de58849
gnu: Add r-annotate.
...
* gnu/packages/bioinformatics.scm (r-annotate): New variable.
2016-09-26 03:20:59 +02:00
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
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
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
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
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
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
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
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
eb24341ffb
gnu: Add r-biocinstaller.
...
* gnu/packages/bioinformatics.scm (r-biocinstaller): New variable.
2016-09-19 11:56:44 +02:00
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
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
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
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
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
66daf78c0a
gnu: Add seqtk.
...
* gnu/packages/bioinformatics.scm (seqtk): New variable.
2016-09-13 20:27:29 +10:00
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
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
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
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
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
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
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
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
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
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
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
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
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
Ben J Woodcroft