ed8fbe5e62
gnu: r-rcas: Update to 1.0.0.
...
* gnu/packages/bioinformatics.scm (r-rcas): Update to 1.0.0.
2016-11-03 19:01:46 +01:00
16a8bd3194
gnu: r-rtracklayer: Update to 1.34.1.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.1.
2016-11-03 19:01:46 +01:00
c15ae9b008
gnu: r-biocparallel: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.8.1.
2016-11-03 19:01:46 +01:00
5b3b2d2f02
gnu: r-limma: Update to 3.30.2.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.30.2.
2016-11-03 19:01:46 +01:00
ed3054231d
gnu: r-edger: Update to 3.16.1.
...
* gnu/packages/bioinformatics.scm (r-edger): Update to 3.16.1.
2016-11-03 19:01:45 +01:00
044ac8d294
gnu: python-twobitreader: Update to 3.1.4.
...
* gnu/packages/bioinformatics.scm (python-twobitreader, python2-twobitreader):
Update to 3.1.4.
2016-10-28 13:59:11 -04:00
900fb8d005
gnu: python-twobitreader: Disable the test suite.
...
The tests were silently skipped with Python 3.4. With Python 3.5, this caused
the build of python-twobitreader to fail.
* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader)[arguments]: Disable the tests.
2016-10-28 13:59:11 -04:00
7500e42b3e
gnu: Add r-mutationalpatterns.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): New variable.
2016-10-27 20:07:05 +02:00
a46cc723ff
gnu: r-seqinr: Update to 3.3-3.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.3-3.
2016-10-26 16:23:26 +02:00
c70271ec48
gnu: bioperl-minimal: Update to 1.7.0.
...
* gnu/packages/bioinformatics.scm (bioperl-minimal): Update to 1.7.0.
2016-10-26 16:23:24 +02:00
59198f8fff
gnu: r-genomationdata: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
e357bec836
gnu: r-bamsignals: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): Update to 1.6.0.
2016-10-26 09:28:23 +02:00
53ca52f013
gnu: r-rhtslib: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): Update to 1.6.0.
[native-inputs]: Add autoconf.
2016-10-26 09:28:23 +02:00
da22da862b
gnu: r-zlibbioc: Update to 1.20.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.20.0.
2016-10-26 09:28:22 +02:00
809251e164
gnu: r-motifrg: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.18.0.
2016-10-26 09:28:22 +02:00
21d6c7a3e1
gnu: r-seqlogo: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.40.0.
2016-10-26 09:28:22 +02:00
51c3c4900f
gnu: r-genomation: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.6.0.
[propagated-inputs]: Add r-rcpp, r-htslib, r-runit, r-s4vectors.
[inputs]: Add zlib.
2016-10-26 09:28:21 +02:00
e92dd6f5e0
gnu: r-seqpattern: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.6.0.
[propagated-inputs]: Add r-kernsmooth.
2016-10-26 09:28:21 +02:00
acf6f7e0c3
gnu: r-impute: Update to 1.48.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.48.0.
2016-10-26 09:28:21 +02:00
3d74c04451
gnu: r-bsgenome: Update to 1.42.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.42.0.
2016-10-26 09:28:20 +02:00
30ec4de738
gnu: r-topgo: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.26.0.
[propagated-inputs]: Add r-dbi.
2016-10-26 09:28:20 +02:00
3587b464fc
gnu: r-graph: Update to 1.52.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.52.0.
2016-10-26 09:28:19 +02:00
d1b1587cad
gnu: r-go-db: Update to 3.4.0.
...
* gnu/packages/bioinformatics.scm (r-go-db): Update to 3.4.0.
2016-10-26 09:28:19 +02:00
b17aac083e
gnu: r-genomicfeatures: Update to 1.26.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.26.0.
2016-10-26 09:28:18 +02:00
6a45fd9aea
gnu: r-rtracklayer: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.34.0.
2016-10-26 09:28:18 +02:00
4ab32f0cd6
gnu: r-genomicalignments: Update to 1.10.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.10.0.
2016-10-26 09:28:18 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
4644644ace
gnu: Add r-bioccheck.
...
* gnu/packages/bioinformatics.scm (r-bioccheck): New variable.
2016-10-20 09:53:02 +02:00
99df12cd19
gnu: Add r-biocstyle.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): New variable.
2016-10-19 15:22:06 +02:00
207ce8fbe5
gnu: Add r-biocviews.
...
* gnu/packages/bioinformatics.scm (r-biocviews): New variable.
2016-10-19 15:09:55 +02:00
c79ad57a8d
gnu: Add r-optparse.
...
* gnu/packages/bioinformatics.scm (r-optparse): New variable.
2016-10-19 10:48:56 +02:00
2acaaee550
gnu: Add r-getopt.
...
* gnu/packages/bioinformatics.scm (r-getopt): New variable.
2016-10-19 09:55:45 +02:00
5093729704
gnu: Add rcas-web.
...
* gnu/packages/bioinformatics.scm (rcas-web): New variable.
2016-10-17 18:09:20 +02:00
89984be46e
gnu: Add r-rcas.
...
* gnu/packages/bioinformatics.scm (r-rcas): New variable.
2016-10-17 18:09:16 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
35aa90a1fd
gnu: Add Infernal.
...
* gnu/packages/bioinformatics.scm (infernal): New variable.
2016-09-02 16:46:37 +02:00
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
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
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
fe02c4c98a
gnu: Add r-bamsignals.
...
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
2016-08-22 16:52:40 +02:00
52765a63ca
gnu: Add r-rhtslib.
...
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
2016-08-22 16:52:22 +02:00
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
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
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
0ed8f0cd4c
gnu: mafft: Update to 7.304.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
2016-08-15 20:59:41 +10:00
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
93b8316e08
gnu: mafft: Update to 7.300.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
2016-08-15 20:51:00 +10:00
a12ba6e878
gnu: Add bamm.
...
* gnu/packages/bioinformatics.scm (bamm): New variable.
2016-08-14 14:55:23 +10:00
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
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
ceb62d5436
gnu: Add roary.
...
* gnu/packages/bioinformatics.scm (roary): New variable.
2016-08-08 22:08:17 +10:00
608dd93267
gnu: Add raxml.
...
* gnu/packages/bioinformatics.scm (raxml): New variable.
2016-08-08 22:08:17 +10:00
024130d258
gnu: Add prank.
...
* gnu/packages/bioinformatics.scm (prank): New variable.
2016-08-08 22:08:17 +10:00
b16728b068
gnu: Add exonerate.
...
* gnu/packages/bioinformatics.scm (exonerate): New variable.
2016-08-08 22:08:17 +10:00
db7a344427
gnu: Add bppsuite.
...
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
2016-08-08 22:08:17 +10:00
159a701678
gnu: Add bpp-popgen.
...
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
2016-08-08 22:08:17 +10:00
8b5f4d5700
gnu: Add bpp-phyl.
...
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
2016-08-08 22:08:17 +10:00
70f1bc051a
gnu: Add bpp-seq.
...
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
2016-08-08 22:08:17 +10:00
985d841144
gnu: Add bpp-core.
...
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
2016-08-08 22:08:17 +10:00
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
97b9da6897
gnu: Add discrover.
...
* gnu/packages/bioinformatics.scm (discrover): New variable.
2016-08-03 17:20:26 +02:00
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
6619f9c769
gnu: Add eigensoft.
...
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
2016-07-14 08:58:35 +02:00
17dc32a400
gnu: Add Ribotaper.
...
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
2016-07-12 12:19:39 +02:00
9a8f309cf1
gnu: Add bedtools-2.18.
...
* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
2016-07-12 12:19:15 +02:00
7f575d3e56
gnu: diamond: Update to 0.8.12.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12.
2016-07-10 22:32:57 +10:00
ec2a67de88
gnu: Add python-dendropy.
...
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New
variables.
* gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New
file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-07-09 08:00:34 +10:00
c11f79a49e
gnu: star: Restrict supported systems to 64-bit systems.
...
* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to
x86_64-linux and mips64el-linux.
2016-07-08 22:10:05 +10:00
d285657eae
gnu: bedtools: Update to 2.26.0.
...
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0.
2016-07-07 23:27:19 +10:00
7c7643a7f0
gnu: diamond: Update to 0.8.11.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11.
2016-07-07 18:21:10 +08:00
274da826f9
gnu: Add r-seqinr.
...
* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
2016-07-07 10:46:17 +02:00
8157af2e09
gnu: khmer: Limit to x86_64 systems only.
...
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field.
2016-07-07 06:33:28 +03:00
5fb5dffbd4
gnu: Add multiqc.
...
* gnu/packages/bioinformatics.scm (multiqc): New variable.
2016-07-05 16:32:37 +02:00
1f1b20b8be
gnu: Add bits.
...
* gnu/packages/bioinformatics.scm (bits): New variable.
2016-07-05 15:43:36 +02:00
66e40e0065
gnu: Add EMBOSS.
...
* gnu/packages/bioinformatics.scm (emboss): New variable.
2016-07-05 12:32:12 +02:00
744004a31f
gnu: Add r-edger.
...
* gnu/packages/bioinformatics.scm (r-edger): New variable.
2016-07-04 14:49:07 +02:00
7d4224d794
gnu: Add r-limma.
...
* gnu/packages/bioinformatics.scm (r-limma): New variable.
2016-07-04 14:39:16 +02:00
71830f0e49
gnu: vsearch: Update to 2.0.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1.
2016-07-01 09:01:28 +10:00
8dec2229a2
gnu: blast+: Update to 2.4.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
2016-06-29 22:42:47 +10:00
3bce0f14b2
gnu: star: Update to 2.5.2a.
...
* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
2016-06-29 10:14:22 +10:00
6c737963f6
gnu: htslib: Update to 1.3.1.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
2016-06-29 10:14:22 +10:00
ec9466388e
gnu: Add SEEK.
...
* gnu/packages/bioinformatics.scm (seek): New variable.
2016-06-28 22:49:05 +02:00
d6e374a0d9
gnu: mafft: Update to 7.299.
...
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
2016-06-28 21:42:15 +10:00
45469ebe52
gnu: metabat: Update to 0.26.3.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3.
[arguments]: Update include and linking paths accordingly.
2016-06-28 21:28:06 +10:00
af45244e36
gnu: diamond: Update to 0.8.9.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
2016-06-28 19:31:25 +10:00
94ff31572d
gnu: Add khmer.
...
* gnu/packages/bioinformatics.scm (khmer): New variable.
* gnu/packages/patches/khmer-use-libraries.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2016-06-27 21:35:16 +10:00
9ded145717
gnu: Add python-screed.
...
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
2016-06-27 21:16:39 +10:00
c2e575185b
gnu: vsearch: Update to 2.0.0.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
2016-06-26 12:43:39 +10:00
69af462496
gnu: vsearch: Update to 0.11.2.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
2016-06-22 07:51:12 +10:00
7b3df1e56e
gnu: Add r-vegan.
...
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
2016-06-21 21:29:17 +10:00
cec2653bb4
gnu: diamond: Update to 0.8.7.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7.
2016-06-21 20:00:38 +10:00
4714d521e3
gnu: Add r-bsgenome-mmusculus-ucsc-mm10.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New
variable.
2016-06-15 17:08:08 +02:00
e4a44a6aa5
gnu: Add ruby-bio-kseq.
...
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
2016-06-14 07:57:09 +10:00
883302daf2
gnu: piranha: Update to 1.2.1.
...
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
2016-06-13 11:53:38 +02:00
698bd29799
gnu: Use full SHA1 commit ids.
...
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik,
smithlab-cpp, piranha): Use full SHA1 commit ids.
* gnu/packages/ci.scm (hydra): Likewise.
* gnu/packages/compression.scm (sfarkxtc): Likewise.
* gnu/packages/emacs.scm (emacs-ob-ipython): Likewise.
* gnu/packages/games.scm (mars, emulation-station): Likewise.
* gnu/packages/gnunet.scm (guile-gnunet): Likewise.
* gnu/packages/music.scm (non-sequencer): Likewise.
* gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise.
* gnu/packages/xorg.scm (xf86-video-intel): Likewise.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-06-05 00:05:38 +02:00
6ac0a0fbe7
gnu: diamond: Update to 0.8.5.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
2016-06-04 09:28:54 +10:00
64efa3078a
gnu: Add r-genomationdata.
...
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-31 16:29:37 +02:00
9fcc3509a7
gnu: Update diamond to 0.8.3.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
2016-05-28 23:44:16 +10:00
0783787436
gnu: Add ParDRe.
...
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-23 12:55:09 +02:00
7740f58128
gnu: r-genomation: Update to 1.4.2.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
2016-05-20 15:18:23 +02:00
8ede249e0a
gnu: r-genomicfeatures: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
2016-05-20 15:18:23 +02:00
192e1ea8d1
gnu: r-summarizedexperiment: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20 15:18:23 +02:00
d7420566a9
gnu: r-biocparallel: Update to 1.6.2.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20 15:18:23 +02:00
73af676feb
gnu: r-annotationdbi: Update to 1.34.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20 15:18:23 +02:00
679e670b36
gnu: r-variantannotation: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20 15:18:23 +02:00
186ed87337
gnu: r-genomeinfodb: Update to 1.8.1.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-20 15:18:23 +02:00
7c544991dc
gnu: diamond: Do not specify target architecture.
...
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not
specify target architecture.
2016-05-18 21:25:06 +10:00
e62ffce538
gnu: Add Piranha.
...
* gnu/packages/bioinformatics.scm (piranha): New variable.
2016-05-18 11:59:34 +02:00
849485f5a0
gnu: sortmerna: Update to 2.1b.
...
* gnu/packages/bioinformatics.scm (sortmerna): Update to 2.1b.
[inputs]: New field.
2016-05-17 21:45:49 +10:00
daaeed765a
gnu: vsearch: Update to 1.11.1.
...
* gnu/packages/bioinformatics.scm (vsearch): Update to 1.11.1.
2016-05-17 21:36:46 +10:00
122395f9fc
gnu: diamond: Update to 0.8.1.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.1.
[source]: Remove 'snippet'.
[build-system]: Use cmake-build-system.
[arguments]: Remove modifications to phases.
[native-inputs]: Remove field.
[inputs]: Remove 'boost'.
2016-05-17 21:07:00 +10:00
96101b6718
gnu: r-zlibbioc: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): Update to 1.18.0.
2016-05-16 20:59:50 +02:00
a0fe3aeecf
gnu: r-motifrg: Update to 1.16.0.
...
* gnu/packages/bioinformatics.scm (r-motifrg): Update to 1.16.0.
2016-05-16 20:59:38 +02:00
1f5786a918
gnu: r-seqlogo: Update to 1.38.0.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): Update to 1.38.0.
2016-05-16 20:59:27 +02:00
8adc3b628d
gnu: r-genomation: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.0.
2016-05-16 20:59:14 +02:00
7555817c2b
gnu: r-seqpattern: Update to 1.4.0.
...
* gnu/packages/bioinformatics.scm (r-seqpattern): Update to 1.4.0.
2016-05-16 20:59:04 +02:00
d1bff89d26
gnu: r-impute: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-impute): Update to 1.46.0.
2016-05-16 20:58:49 +02:00
5190ed1751
gnu: r-bsgenome: Update to 1.40.0.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.0.
2016-05-16 20:58:35 +02:00
e48e88c217
gnu: r-topgo: Update to 2.24.0.
...
* gnu/packages/bioinformatics.scm (r-topgo): Update to 2.24.0.
[propagated-inputs]: Add r-matrixstats.
2016-05-16 20:58:24 +02:00
0c56023557
gnu: r-graph: Update to 1.50.0.
...
* gnu/packages/bioinformatics.scm (r-graph): Update to 1.50.0.
2016-05-16 20:58:08 +02:00
c12b0a5a30
gnu: r-genomicfeatures: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.0.
2016-05-16 20:57:55 +02:00
d23fbf1eb9
gnu: r-rtracklayer: Update to 1.32.0.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.0.
2016-05-16 20:57:43 +02:00
3cd551ea7b
gnu: r-genomicalignments: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.0.
2016-05-16 20:57:30 +02:00
d848ed7cf2
gnu: r-summarizedexperiment: Update to 1.2.0.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.0.
2016-05-16 20:57:21 +02:00
b4c5a0db22
gnu: r-rsamtools: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-rsamtools): Update to 1.24.0.
2016-05-16 20:57:10 +02:00
2477d9773a
gnu: r-biostrings: Update to 2.40.0.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.0.
2016-05-16 20:56:58 +02:00
6a2a0de1ab
gnu: r-biocparallel: Update to 1.6.0.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.0.
2016-05-16 20:56:39 +02:00
63cea37234
gnu: r-biomart: Update to 2.28.0.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.28.0.
2016-05-16 20:56:29 +02:00
c4a4e17938
gnu: r-annotationdbi: Update to 1.34.0.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.0.
2016-05-16 20:56:19 +02:00
4466a02c9f
gnu: r-biobase: Update to 2.32.0.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.32.0.
2016-05-16 20:56:09 +02:00
828980cad6
gnu: r-genomicranges: Update to 1.24.0.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.0.
2016-05-16 20:55:58 +02:00
e782ca3e97
gnu: r-xvector: Update to 0.12.0.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.0.
2016-05-16 20:55:46 +02:00
052ee32b24
gnu: r-variantannotation: Update to 1.18.0.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to
1.18.0.
2016-05-16 20:55:32 +02:00
d1ab3d8fa5
gnu: r-genomeinfodb: Update to 1.8.0.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.0.
2016-05-16 20:55:20 +02:00
952ff8c862
gnu: r-iranges: Update to 2.6.0.
...
* gnu/packages/bioinformatics (r-iranges): Update to 2.6.0.
2016-05-16 20:55:11 +02:00
3654a61146
gnu: r-s4vectors: Update to 0.10.0.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.0.
2016-05-16 20:54:59 +02:00
a936bf59ea
gnu: r-dnacopy: Update to 1.46.0.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.46.0.
2016-05-16 20:54:37 +02:00
dbfeba5209
gnu: r-biocgenerics: Update to 0.18.0.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics): Update to 0.18.0.
2016-05-16 20:53:48 +02:00
a83e604662
gnu: hmmer: Update urls.
...
* gnu/packages/bioinformatics.scm (hmmer)[source]: Project has moved to
eddylab, with their downloads.
[home-page]: Update to new homepage.
2016-05-16 14:28:53 +03:00
99828fa788
gnu: Update module imports for asciidoc and doxygen.
...
This is a followup to commit 0573a923de
2016-05-12 20:18:15 -04:00
83b84fa812
gnu: edirect: Update to 4.10.
...
* gnu/packages/bioinformatics.scm (edirect): Update to 4.10.
2016-05-04 16:45:43 +02:00
324efb8888
gnu: Add muscle.
...
* gnu/packages/bioinformatics.scm (muscle): New variable.
2016-04-30 15:46:24 +10:00
fb868e3395
gnu: r-acsnminer: Update to 0.16.01.29.
...
* gnu/packages/bioinformatics.scm (r-acsnminer): Update to 0.16.01.29.
2016-04-26 17:06:17 +02:00
e1c2ad6777
gnu: r-qtl: Update to 1.39-5.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.39-5.
2016-04-26 17:06:17 +02:00
6b49a37e6b
gnu: Add filevercmp.
...
* gnu/packages/bioinformatics.scm (filevercmp): New variable.
2016-04-26 16:41:15 +02:00
79b555edeb
gnu: samtools: Update to 1.3.1.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.3.1.
2016-04-24 09:45:07 +10:00
1ad15c1669
gnu: Rename Java packages to match new naming specification.
...
* gnu/packages/bioinformatics.scm (htsjdk): Rename to...
(java-htsjdk): ...this.
(ngs-java): Rename to...
(java-ngs): ...this.
(ncbi-vdb)[arguments,inputs]: Use new name.
* gnu/packages/java.scm (swt): Rename to...
(java-swt): ...this.
* gnu/packages/music.scm (tuxguitar)[make-flags,inputs,arguments]: Use
new name of package "swt".
2016-04-19 16:55:03 +02:00
4d16cc5133
gnu: python2-plastid: Propagate setuptools.
...
* gnu/packages/bioinformatics.scm (python2-plastid)[native-inputs]: Move
python2-setuptools from here...
[propagated-inputs]: ...to here.
2016-04-19 16:12:51 +02:00
f94bf1983b
gnu: Add python-plastid.
...
* gnu/packages/bioinformatics.scm (python-plastid, python2-plastid): New
variables.
2016-04-19 12:16:01 +02:00
4db9433aa0
gnu: Add python-twobitreader.
...
* gnu/packages/bioinformatics.scm (python-twobitreader,
python2-twobitreader): New variables.
2016-04-19 12:16:01 +02:00
fc1adab148
gnu: packages: Use 'search-patches' everywhere.
...
* gnu/packages/abiword.scm: Use 'search-patches' for 'patches' field.
* gnu/packages/acl.scm: Likewise.
* gnu/packages/admin.scm: Likewise.
* gnu/packages/algebra.scm: Likewise.
* gnu/packages/animation.scm: Likewise.
* gnu/packages/apr.scm: Likewise.
* gnu/packages/audacity.scm: Likewise.
* gnu/packages/audio.scm: Likewise.
* gnu/packages/autotools.scm: Likewise.
* gnu/packages/avahi.scm: Likewise.
* gnu/packages/backup.scm: Likewise.
* gnu/packages/base.scm: Likewise.
* gnu/packages/bash.scm: Likewise.
* gnu/packages/bioinformatics.scm: Likewise.
* gnu/packages/cdrom.scm: Likewise.
* gnu/packages/ci.scm: Likewise.
* gnu/packages/cmake.scm: Likewise.
* gnu/packages/cpio.scm: Likewise.
* gnu/packages/cross-base.scm: Likewise.
* gnu/packages/dico.scm: Likewise.
* gnu/packages/doxygen.scm: Likewise.
* gnu/packages/ebook.scm: Likewise.
* gnu/packages/elf.scm: Likewise.
* gnu/packages/emacs.scm: Likewise.
* gnu/packages/engineering.scm: Likewise.
* gnu/packages/firmware.scm: Likewise.
* gnu/packages/flashing-tools.scm: Likewise.
* gnu/packages/fltk.scm: Likewise.
* gnu/packages/ftp.scm: Likewise.
* gnu/packages/games.scm: Likewise.
* gnu/packages/gawk.scm: Likewise.
* gnu/packages/gcc.scm: Likewise.
* gnu/packages/gd.scm: Likewise.
* gnu/packages/ghostscript.scm: Likewise.
* gnu/packages/glib.scm: Likewise.
* gnu/packages/gnome.scm: Likewise.
* gnu/packages/gnucash.scm: Likewise.
* gnu/packages/gnunet.scm: Likewise.
* gnu/packages/gnupg.scm: Likewise.
* gnu/packages/gnuzilla.scm: Likewise.
* gnu/packages/graphics.scm: Likewise.
* gnu/packages/grub.scm: Likewise.
* gnu/packages/gtk.scm: Likewise.
* gnu/packages/guile.scm: Likewise.
* gnu/packages/icu4c.scm: Likewise.
* gnu/packages/idutils.scm: Likewise.
* gnu/packages/image.scm: Likewise.
* gnu/packages/imagemagick.scm: Likewise.
* gnu/packages/irc.scm: Likewise.
* gnu/packages/ldc.scm: Likewise.
* gnu/packages/libcanberra.scm: Likewise.
* gnu/packages/libevent.scm: Likewise.
* gnu/packages/libreoffice.scm: Likewise.
* gnu/packages/libunwind.scm: Likewise.
* gnu/packages/libusb.scm: Likewise.
* gnu/packages/linux.scm: Likewise.
* gnu/packages/lirc.scm: Likewise.
* gnu/packages/llvm.scm: Likewise.
* gnu/packages/lsh.scm: Likewise.
* gnu/packages/lua.scm: Likewise.
* gnu/packages/lxqt.scm: Likewise.
* gnu/packages/mail.scm: Likewise.
* gnu/packages/maths.scm: Likewise.
* gnu/packages/mcrypt.scm: Likewise.
* gnu/packages/messaging.scm: Likewise.
* gnu/packages/mit-krb5.scm: Likewise.
* gnu/packages/mp3.scm: Likewise.
* gnu/packages/multiprecision.scm: Likewise.
* gnu/packages/music.scm: Likewise.
* gnu/packages/ninja.scm: Likewise.
* gnu/packages/nvi.scm: Likewise.
* gnu/packages/ocaml.scm: Likewise.
* gnu/packages/orpheus.scm: Likewise.
* gnu/packages/ots.scm: Likewise.
* gnu/packages/parallel.scm: Likewise.
* gnu/packages/patchutils.scm: Likewise.
* gnu/packages/pcre.scm: Likewise.
* gnu/packages/pdf.scm: Likewise.
* gnu/packages/perl.scm: Likewise.
* gnu/packages/plotutils.scm: Likewise.
* gnu/packages/polkit.scm: Likewise.
* gnu/packages/pulseaudio.scm: Likewise.
* gnu/packages/python.scm: Likewise.
* gnu/packages/qemu.scm: Likewise.
* gnu/packages/qt.scm: Likewise.
* gnu/packages/ratpoison.scm: Likewise.
* gnu/packages/rdf.scm: Likewise.
* gnu/packages/readline.scm: Likewise.
* gnu/packages/rush.scm: Likewise.
* gnu/packages/scheme.scm: Likewise.
* gnu/packages/screen.scm: Likewise.
* gnu/packages/sdl.scm: Likewise.
* gnu/packages/slim.scm: Likewise.
* gnu/packages/ssh.scm: Likewise.
* gnu/packages/tcl.scm: Likewise.
* gnu/packages/tcsh.scm: Likewise.
* gnu/packages/texinfo.scm: Likewise.
* gnu/packages/tls.scm: Likewise.
* gnu/packages/tor.scm: Likewise.
* gnu/packages/tv.scm: Likewise.
* gnu/packages/valgrind.scm: Likewise.
* gnu/packages/version-control.scm: Likewise.
* gnu/packages/video.scm: Likewise.
* gnu/packages/vpn.scm: Likewise.
* gnu/packages/vtk.scm: Likewise.
* gnu/packages/w3m.scm: Likewise.
* gnu/packages/web.scm: Likewise.
* gnu/packages/wicd.scm: Likewise.
* gnu/packages/wm.scm: Likewise.
* gnu/packages/xdisorg.scm: Likewise.
* gnu/packages/xfce.scm: Likewise.
* gnu/packages/xiph.scm: Likewise.
* gnu/packages/xml.scm: Likewise.
* gnu/packages/xorg.scm: Likewise.
* gnu/packages/zip.scm: Likewise.
2016-04-14 10:38:21 +03:00
6dc6099853
gnu: Add r-bsgenome-dmelanogaster-ucsc-dm3.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-dmelanogaster-ucsc-dm3):
New variable.
2016-04-11 15:11:16 +02:00
943bd6279f
gnu: Add r-bsgenome-celegans-ucsc-ce6.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-celegans-ucsc-ce6): New
variable.
2016-04-11 15:11:16 +02:00
a3e9028770
gnu: Add r-bsgenome-mmusculus-ucsc-mm9.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm9): New
variable.
2016-04-11 15:11:15 +02:00
ae2462f7dd
gnu: Add r-motifrg.
...
* gnu/packages/bioinformatics.scm (r-motifrg): New variable.
2016-04-11 11:03:27 +02:00
c90a4baff6
gnu: Add r-bsgenome-hsapiens-ucsc-hg19.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19): New
variable.
2016-04-11 11:03:27 +02:00
936e7d6774
gnu: Add r-seqlogo.
...
* gnu/packages/bioinformatics.scm (r-seqlogo): New variable.
2016-04-11 11:03:27 +02:00
9e3ba31c53
gnu: Add r-zlibbioc.
...
* gnu/packages/bioinformatics.scm (r-zlibbioc): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
b669d9c4c8
gnu: Add r-variantannotation.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-04-06 17:38:42 -04:00
9b36e25607
gnu: vcftools: Update to 0.1.14.
...
* gnu/packages/bioinformatics.scm (vcftools): Update to 0.1.14.
[arguments]: Do not modify phases as it is not needed anymore.
[native-inputs]: Add 'pkg-config'.
[home-page]: Update to new location.
Signed-off-by: Alex Kost <alezost@gmail.com>
2016-04-05 11:29:32 +03:00
ddb8312911
gnu: python2-pbcore: Update to 1.2.8.
...
* gnu/packages/bioinformatics.scm (python2-pbcore): Update to 1.2.8.
[native-inputs]: Add python2-docutils, python2-nose, python2-sphinx.
2016-03-30 22:45:35 +03:00
f315f4fcab
gnu: r-genomation: Update to 1.2.2.
...
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.2.2.
2016-03-30 11:59:16 +02:00
571f0b63d5
gnu: r-genomicfeatures: Update to 1.22.13.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to
1.22.13.
2016-03-30 11:59:16 +02:00
ffaf72ad96
gnu: r-rtracklayer: Update to 1.30.4.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.30.4.
2016-03-30 11:59:15 +02:00
ac2d8b0fb8
gnu: r-genomicalignments: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to
1.6.3.
2016-03-30 11:59:15 +02:00
7eade1c5f9
gnu: r-summarizedexperiment: Update to 1.0.2.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to
1.0.2.
2016-03-30 11:59:15 +02:00
53fd0f5e1d
gnu: r-biostrings: Update to 2.38.4.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.38.4.
2016-03-30 11:59:15 +02:00
5fe3115415
gnu: r-genomicranges: Update to 1.22.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.22.4.
2016-03-30 11:59:15 +02:00
9cc22d28d8
gnu: r-genomeinfodb: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.6.3.
2016-03-30 11:59:15 +02:00
1d216b6ec9
gnu: Remove "r-repository" property.
...
* gnu/packages/bioinformatics.scm (r-biocgenerics, r-s4vectors,
r-iranges, r-genomeinfodb, r-xvector, r-genomicranges)[properties]:
Remove "r-repository" property.
2016-03-24 16:18:01 +01:00
5697fdc366
gnu: r-dnacopy: Fix home page URL.
...
* gnu/packages/bioinformatics.scm (r-dnacopy)[home-page]: Add missing
URI scheme.
2016-03-18 23:00:04 +01:00
953c12232f
gnu: bless: Remove bundled sources for sparsehash.
...
* gnu/packages/bioinformatics.scm (bless)[source]: Delete
"google-sparsehash" sources.
[inputs]: Add "sparsehash".
2016-03-17 13:01:31 +01:00
6c1305f9ec
gnu: Add CD-HIT.
...
* gnu/packages/bioinformatics.scm (cd-hit): New variable.
2016-03-17 13:01:31 +01:00
247d498aaa
gnu: Add r-dnacopy.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): New variable.
2016-03-16 11:23:27 +01:00
6a35566df7
gnu: Add codingquarry.
...
* gnu/packages/bioinformatics.scm (codingquarry): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-16 04:49:27 -04:00
10b4a969be
gnu: htsjdk: Use ant-build-system.
...
* gnu/packages/bioinformatics.scm (htsjdk)[build-system]: Use
ant-build-system.
[arguments]: Adapt for ant-build-system.
2016-03-14 14:30:03 +01:00
846e340954
gnu: Add pyicoteo.
...
* gnu/packages/bioinformatics.scm (pyicoteo): New variable.
2016-03-14 12:36:49 +01:00
a0a71439fa
gnu: Add bioawk.
...
* gnu/packages/bioinformatics.scm (bioawk): New variable.
Signed-off-by: Leo Famulari <leo@famulari.name>
2016-03-10 18:37:25 -05:00
649e9b3b47
gnu: python-pysam: Move cython and setuptools to native inputs.
...
* gnu/packages/bioinformatics.scm (python-pysam)[inputs]: Move
"python-cython" and "python-setuptools" from here...
[native-inputs]: ... to here.
2016-03-03 13:47:19 +01:00
3acb8c857c
gnu: deeptools: Update to 2.1.1.
...
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.1.1.
[inputs]: Add "python2-numpydoc" and "python2-pybigwig".
2016-03-03 13:47:12 +01:00
14bda1ff49
gnu: deeptools: Change "propagated-inputs" to "inputs".
...
* gnu/packages/bioinformatics.scm (deeptools)[propagated-inputs]: Move
all inputs from here...
[inputs]: ...to here.
2016-03-03 13:47:02 +01:00
69e0e03c36
gnu: Add python-pybigwig.
...
* gnu/packages/bioinformatics.scm (python-pybigwig, python2-pybigwig):
New variables.
2016-03-03 13:46:52 +01:00
d454640c38
gnu: python-pysam: Update to 0.8.4.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.8.4.
2016-03-03 13:46:39 +01:00
55a9a8c2b9
gnu: python-pysam, python2-pysam: Move to bioinformatics.scm.
...
* gnu/packages/python.scm (python-pysam, python2-pysam): Move to...
* gnu/packages/bioinformatics.scm (python-pysam, python2-pysam):
...here.
2016-03-03 13:46:26 +01:00
f82c8c3cba
gnu: r-go-db: Bioconductor changed URL for data downloads.
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* gnu/packages/bioinformatics.scm (r-go-db)[source]: Update data URL.
2016-03-01 19:47:26 +02:00
27acfaea4c
gnu: r-iranges: Update to 2.4.8.
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* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.4.8.
2016-03-01 19:47:26 +02:00
8921841da8
gnu: r-s4vectors: Update to 0.8.11.
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* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.8.11.
2016-03-01 19:47:25 +02:00
d1e32822b4
gnu: Add PePr.
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* gnu/packages/bioinformatics.scm (pepr): New variable.
2016-03-01 11:51:24 +01:00
Ricardo Wurmus