cc294bcee6
Merge branch 'master' into core-updates
2017-08-09 17:25:31 -04:00
1b22ecdac4
gnu: r-wgcna: Update to 1.61.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.61.
[propagated-inputs]: Add r-rcpp, r-robust, r-survival.
2017-08-09 20:08:13 +02:00
18f5d2a70a
gnu: Add reference to (gnu packages graph).
...
This is a follow-up to 1738138cb3
2017-08-09 15:43:35 +02:00
2d9495da23
Merge branch 'master' into core-updates
2017-08-07 16:45:16 -04:00
9d217d277e
gnu: r-bsgenome-hsapiens-ucsc-hg19: Restore original hash.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Restore hash from before the tarball changed in place. It changed back.
This reverts commit fd40857938
2017-08-07 01:58:39 +02:00
f167595ba1
Merge branch 'master' into core-updates
2017-08-06 00:23:20 -04:00
a56bf101c6
gnu: perl: Work around more "dotless @INC" build issues.
...
* gnu/packages/web.scm (perl-www-curl)[arguments]: Add 'set-search-path'
phase.
* gnu/packages/bioinformatics.scm (ngs-sdk)[arguments]: Augment
'configure' phase to set PERL5LIB.
* gnu/packages/image.scm (steghide)[arguments]: Add #:phases argument.
2017-08-05 00:31:26 +02:00
7cb6155088
gnu: bioinformatics.scm: Use (gnu packages cran) module.
...
This is a follow up to a8cba9dd11
2017-08-03 21:39:12 +03:00
5e0de29892
gnu: r-seqminer: Update to 6.0.
...
* gnu/packages/bioinformatics.scm (r-seqminer): Update to 6.0.
2017-08-03 17:53:54 +02:00
4e0c847d59
gnu: r-wgcna: Update to 1.60.
...
* gnu/packages/bioinformatics.scm (r-wgcna): Update to 1.60.
2017-08-03 17:53:54 +02:00
c8a9b2bcbf
gnu: r-qtl: Update to 1.41-6.
...
* gnu/packages/bioinformatics.scm (r-qtl): Update to 1.41-6.
2017-08-03 17:53:54 +02:00
023aa8ff58
gnu: r-seqinr: Update to 3.4-5.
...
* gnu/packages/bioinformatics.scm (r-seqinr): Update to 3.4-5.
2017-08-03 17:53:54 +02:00
7150f1c30c
gnu: r-optparse: Update to 1.4.4.
...
* gnu/packages/bioinformatics.scm (r-optparse): Update to 1.4.4.
2017-08-03 17:53:53 +02:00
3f6ec083ec
gnu: r-bookdown: Update to 0.4.
...
* gnu/packages/bioinformatics.scm (r-bookdown): Update to 0.4.
2017-08-03 17:53:53 +02:00
75e6639f36
gnu: htseq: Use PyPI URI.
...
This is a follow-up to 92971d68ac
2017-08-03 21:08:13 +10:00
92971d68ac
gnu: htseq: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (htseq): Update to 0.9.1.
[arguments]: Use python-3 by removing field.
[native-inputs]: Add 'python-cython'.
[propagated-inputs]: Use python3 numpy package.
[inputs]: Use python3 pysam package. Add 'python-matplotlib'.
(python2-htseq): New variable.
(clipper)[inputs]: Use it.
2017-08-03 21:02:30 +10:00
f1915a5dd0
gnu: r-deseq2: Update to 1.16.1.
...
* gnu/packages/bioinformatics.scm (r-deseq2): Update to 1.16.1.
2017-08-02 00:33:23 +02:00
fd215c2978
gnu: r-annotationforge: Update to 1.18.1.
...
* gnu/packages/bioinformatics.scm (r-annotationforge): Update to 1.18.1.
2017-08-02 00:33:07 +02:00
bd4a0bab5f
gnu: r-category: Update to 2.42.1.
...
* gnu/packages/bioinformatics.scm (r-category): Update to 2.42.1.
2017-08-02 00:32:46 +02:00
0ff478344b
gnu: r-biocstyle: Update to 2.4.1.
...
* gnu/packages/bioinformatics.scm (r-biocstyle): Update to 2.4.1.
2017-08-02 00:32:31 +02:00
9c4348d8c4
gnu: r-dnacopy: Update to 1.50.1.
...
* gnu/packages/bioinformatics.scm (r-dnacopy): Update to 1.50.1.
2017-08-02 00:32:11 +02:00
3ec25eb2a8
gnu: r-iranges: Update to 2.10.2.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.10.2.
2017-08-02 00:31:46 +02:00
6252dd0f15
gnu: r-genomeinfodb: Update to 1.12.2.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.12.2.
2017-08-02 00:31:28 +02:00
48f5d283b2
gnu: r-variantannotation: Update to 1.22.3.
...
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.22.3.
2017-08-02 00:31:08 +02:00
1b4738e23c
gnu: r-limma: Update to 3.32.5.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.32.5.
2017-08-02 00:30:49 +02:00
1898a7832f
gnu: r-biobase: Update to 2.36.2.
...
* gnu/packages/bioinformatics.scm (r-biobase): Update to 2.36.2.
2017-08-02 00:30:27 +02:00
62eb93a7d0
gnu: r-annotationdbi: Update to 1.38.2.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.38.2.
2017-08-02 00:28:32 +02:00
0c6494a1db
gnu: r-biomart: Update to 2.32.1.
...
* gnu/packages/bioinformatics.scm (r-biomart): Update to 2.32.1.
2017-08-02 00:28:16 +02:00
1ff74d074e
gnu: r-biocparallel: Update to 1.10.1.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.10.1.
2017-08-02 00:27:57 +02:00
5077bc3e2e
gnu: r-biostrings: Update to 2.44.2.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.44.2.
2017-08-02 00:27:35 +02:00
adf5d0a0bc
gnu: r-delayedarray: Update to 0.2.7.
...
* gnu/packages/bioinformatics.scm (r-delayedarray): Update to 0.2.7.
2017-08-02 00:27:16 +02:00
f41150f13d
gnu: r-summarizedexperiment: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.6.3.
2017-08-02 00:26:55 +02:00
26760c80cd
gnu: r-genomicalignments: Update to 1.12.1.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.12.1.
2017-08-02 00:26:33 +02:00
15afa9bf8f
gnu: r-rtracklayer: Update to 1.36.4.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.36.4.
2017-08-02 00:26:00 +02:00
8cfaa9ab4e
gnu: r-genomicfeatures: Update to 1.28.4.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.28.4.
2017-08-02 00:25:26 +02:00
9eb2714625
gnu: r-copywriter: Update to 2.8.1.
...
* gnu/packages/bioinformatics.scm (r-copywriter): Update to 2.8.1.
2017-08-02 00:25:00 +02:00
bfa0d1e773
gnu: r-sva: Update to 3.24.4.
...
* gnu/packages/bioinformatics.scm (r-sva): Update to 3.24.4.
2017-08-02 00:24:27 +02:00
aa9780daf9
Merge branch 'master' into core-updates
2017-08-01 23:42:28 +02:00
d931a4bbeb
gnu: metabat: Limit to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (metabat)[supported-systems]: New field.
2017-08-01 17:28:35 +03:00
a9085f0c5c
gnu: metabat: Update to 2.11.2.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.2.
2017-07-29 22:37:47 +10:00
d3dce32216
gnu: metabat: Fix boost-related compilation issue.
...
Reported by Leo Famulari.
* gnu/packages/patches/metabat-fix-boost-issue.patch: New file.
* gnu/packages/bioinformatics.scm (metabat): Use it.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 22:35:52 +10:00
f3f68a442c
gnu: metabat: Update to 2.11.1.
...
* gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1.
[source]: Add patch to fix compilation.
[arguments]: Adjust regular expressions modifying 'SConstruct'.
* gnu/packages/patches/metabat-fix-compilation.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-23 10:29:36 +10:00
897ab082b2
gnu: python-plastid: Update to 0.4.8.
...
* gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
2017-07-23 10:29:36 +10:00
0620387a59
gnu: bcftools: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.5.
[origin]: Remove fix-makefile patch.
[arguments]: Add configure flags, add LIBS make flag. Do not delete
configure phase.
* gnu/packages/patches/bcftools-fix-makefile.patch: Remove file.
* gnu/local.mk (dist_patch_DATA): Remove it.
2017-07-23 10:29:36 +10:00
63fa0ffcd4
gnu: samtools: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
2017-07-23 10:29:36 +10:00
4fb6d1280e
gnu: htslib: Update to 1.5.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
2017-07-23 10:29:35 +10:00
60739965da
gnu: python-pysam: Update to 0.11.2.2.
...
* gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
2017-07-23 10:29:35 +10:00
bca2c57658
gnu: bamm: Use htslib-1.3.
...
* gnu/packages/bioinformatics (htslib-1.3): New variable.
(bamm)[inputs]: Replace htslib with htslib-1.3.
2017-07-23 10:29:35 +10:00
98593f9f51
gnu: bcftools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1.
[arguments]: Move Makefile modifications from here ...
[source]: ... to added patch. Adjust patch for update to 1.4.
* gnu/packages/patches/bcftools-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Register it.
2017-07-23 10:29:35 +10:00
4ab1644049
gnu: samtools: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1.
[arguments]: Add '--with-htslib=system' configure flag.
[inputs]: Add htslib.
2017-07-23 10:29:34 +10:00
a9e4a1e641
gnu: htslib: Update to 1.4.1.
...
* gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1.
[inputs]: Add curl, openssl.
2017-07-23 10:29:34 +10:00
c842d42593
gnu: samtools: Use "modify-phases" syntax.
...
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases"
syntax.
2017-07-23 10:29:34 +10:00
3a4b0b126b
gnu: r-s4vectors: Update to 0.14.3.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
2017-07-22 17:31:19 +02:00
a35a1e9c13
gnu: r-genomicranges: Update to 1.28.4.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
2017-07-22 17:22:07 +02:00
fd40857938
gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.
...
* gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]:
Update hash because the tarball changed in place.
2017-07-19 14:39:37 +02:00
2324541bd0
gnu: sortmerna: Limit support to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
2017-07-19 14:37:47 +03:00
2805f9b2a0
gnu: raxml: Limit to x86_64 and i686 only.
...
* gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
2017-07-18 09:00:10 +03:00
06e372360e
gnu: bowtie: Use 'modify-phases'.
...
* gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases'
syntax.
2017-07-14 19:23:37 +10:00
d6e63cf31c
gnu: bowtie: Update to 2.3.2.
...
* gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2.
[inputs]: Add zlib.
2017-07-14 18:54:10 +10:00
fed7200862
gnu: deeptools: Update to 2.5.1.
...
* gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1.
[arguments]: Remove.
[native-inputs]: Use "python-" instead of "python2-" variants.
[inputs]: Likewise; add python-py2bit.
2017-07-09 17:07:27 +02:00
eb2200f3bd
gnu: Add python-py2bit.
...
* gnu/packages/bioinformatics.scm (python-py2bit): New variable.
2017-07-09 17:07:23 +02:00
4732e6ee84
gnu: blast+: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre. Add patch.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
* gnu/packages/patches/blast+-fix-makefile.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
2017-07-08 12:05:59 +10:00
0a66c38764
Revert "gnu: blast+: Update to 2.6.0."
...
This reverts commit 18dea67dc3
2017-07-06 19:38:55 -04:00
ce7e361fa3
gnu: gemma: Fix building on non-Intel architectures.
...
* gnu/packages/patches/gemma-intel-compat.patch: New file.
* gnu/packages/bioinformatics.scm (gemma)[source]: Add patch.
[arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures.
* gnu/local.mk (dist_patch_DATA): Register patch.
2017-07-04 22:55:44 +03:00
a522517cdb
gnu: diamond: Update to 0.9.9.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
2017-07-04 19:59:01 +10:00
18dea67dc3
gnu: blast+: Update to 2.6.0.
...
* gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0.
[origin]: Remove bundled pcre.
[arguments]: Replace paths in run_with_lock.c. Configure with pcre.
[inputs]: Add pcre, perl, python.
2017-07-04 19:58:42 +10:00
ba773f65f0
gnu: cd-hit: Update to 4.6.8.
...
* gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
2017-07-01 10:49:37 +10:00
fd99d95b3f
gnu: bwa: Update to 0.7.15.
...
* gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
2017-07-01 09:48:20 +10:00
7ceb0a83e3
gnu: Add f-seq.
...
* gnu/packages/bioinformatics.scm (f-seq): New variable.
2017-06-25 22:26:07 +02:00
dfc83eadaf
gnu: orfm: Update to 0.7.1.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
2017-06-24 14:46:46 +10:00
ab8d728144
gnu: orfm: Update to 0.7.0.
...
* gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
2017-06-23 22:22:50 +10:00
94820951d6
gnu: Add kentutils.
...
* gnu/packages/bioinformatics.scm (kentutils): New variable.
2017-06-23 08:09:33 +02:00
c1dfe8c30b
gnu: python2-bx-python: Update to 0.7.3.
...
* gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
2017-06-22 17:25:40 +02:00
148585c240
gnu: Move contents of zip module into compression module.
...
* gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to...
* gnu/packages/compression.scm: ...here.
* gnu/packages/zip.scm: Delete file.
* gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file.
* po/packages/POTFILES.in: Unregister deleted file.
* gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression,
docbook, documentation, fonts, fpga, game-development, games, gl, gnome,
gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice,
markup, maths, mc, monitoring, music, php, pretty-print, python, scheme,
smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml,
zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm:
Adapt module import.
2017-06-20 18:10:35 +05:30
0002be1d0b
gnu: diamond: Update to 0.9.8.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
2017-06-17 13:05:08 +10:00
a147fadd3b
gnu: tadbit: Fix typo in description.
...
* gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
2017-06-16 00:29:21 +02:00
07bf6929b9
gnu: gemma: Fix indentation.
...
* gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
2017-06-15 10:32:03 +03:00
2c9232ae69
gnu: gemma: Fix building on 32-bit architectures.
...
* gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit
architectures add 'FORCE_32BIT' flag.
2017-06-15 10:31:44 +03:00
8befd0940b
gnu: Add tadbit.
...
* gnu/packages/bioinformatics.scm (tadbit): New variable.
2017-06-09 03:32:23 +02:00
aa163424b2
gnu: Add imp.
...
* gnu/packages/bioinformatics.scm (imp): New variable.
2017-06-09 03:31:51 +02:00
282b01515b
gnu: Add phylip.
...
* gnu/packages/bioinformatics.scm (phylip): New variable.
2017-06-09 03:31:50 +02:00
3420c905cd
gnu: Add gess.
...
* gnu/packages/bioinformatics.scm (gess): New variable.
2017-06-09 03:31:50 +02:00
44f6c88909
gnu: Add trim-galore.
...
* gnu/packages/bioinformatics.scm (trim-galore): New variable.
2017-06-09 03:31:50 +02:00
b8fffd3a53
gnu: Add ritornello.
...
* gnu/packages/bioinformatics.scm (ritornello): New variable.
2017-06-09 03:31:50 +02:00
f69ff11af7
gnu: diamond: Update to 0.9.6.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
2017-06-08 09:39:23 +10:00
b9a601d9db
gnu: Add kaiju.
...
* gnu/packages/bioinformatics.scm (kaiju): New variable.
2017-06-02 12:38:23 +02:00
0d2b2fd4f4
gnu: diamond: Update to 0.9.3.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
2017-05-28 21:06:06 -04:00
ca40d4e7c5
gnu: diamond: Update to 0.9.2.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
2017-05-27 22:03:00 -04:00
b608765a2c
gnu: diamond: Update to 0.9.1.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
2017-05-22 21:17:41 +01:00
296b3c631c
gnu: Add r-edaseq.
...
* gnu/packages/bioinformatics.scm (r-edaseq): New variable.
2017-05-22 18:54:59 +02:00
7b46532779
gnu: Add r-deseq.
...
* gnu/packages/bioinformatics.scm (r-deseq): New variable.
2017-05-22 18:54:59 +02:00
d4b83651d1
gnu: Add r-aroma-light.
...
* gnu/packages/bioinformatics.scm (r-aroma-light): New variable.
2017-05-22 18:54:58 +02:00
74297231be
gnu: fraggenescan: Update to 1.30.
...
* gnu/packages/bioinformatics.scm (fraggenescan): Update to 1.30.
[arguments]: Update patching of paths, install procedure. Add new test
case.
2017-05-22 11:44:20 +01:00
7569613076
gnu: roary: Update to 3.8.2.
...
* gnu/packages/bioinformatics.scm (roary): Update to 3.8.2.
2017-05-22 11:44:20 +01:00
3cbfc149c3
gnu: taxtastic: Update to 0.6.4.
...
* gnu/packages/bioinformatics.scm (taxtastic): Update to 0.6.4.
[source]: Use PyPI URI.
2017-05-22 11:44:19 +01:00
b458413721
gnu: r-mutationalpatterns: Update to 1.2.1.
...
* gnu/packages/bioinformatics.scm (r-mutationalpatterns): Update to 1.2.1.
2017-05-22 09:44:08 +02:00
ef81341f0e
gnu: diamond: Update to 0.9.0.
...
* gnu/packages/bioinformatics.scm (diamond): Update to 0.9.0.
[license]: Change to AGPL3+.
2017-05-21 16:08:03 +01:00
88682c9a72
gnu: fasttree: Update to 2.1.10.
...
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.10.
2017-05-21 15:42:08 +01:00
abc08cbae6
gnu: python-biom-format: Update to 2.1.6.
...
* gnu/packages/bioinformatics.scm (python-biom-format): Update to 2.1.6.
[propagated-inputs]: Add python-pandas.
2017-05-21 15:42:08 +01:00
2b18ad054c
gnu: Add gemma.
...
* gnu/packages/bioinformatics.scm (gemma): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2017-05-18 14:22:03 +02:00
Mark H Weaver