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
Ricardo Wurmus