ae32c58e28
gnu: r-bsgenome: Update to 1.40.1.
...
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28 21:35:40 +10:00
e426cd7421
gnu: r-iranges: Update to 2.6.1.
...
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28 21:35:40 +10:00
1c4ad6076c
gnu: r-limma: Update to 3.28.17.
...
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28 21:35:40 +10:00
bd0cc37834
gnu: r-xvector: Update to 0.12.1.
...
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28 21:35:40 +10:00
362f39d667
gnu: r-genomicranges: Update to 1.24.2.
...
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28 21:35:40 +10:00
ae60f3801a
gnu: r-annotationdbi: Update to 1.34.4.
...
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28 21:35:40 +10:00
7a0594fb5d
gnu: r-biocparallel: Update to 1.6.3.
...
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28 21:35:40 +10:00
658f36e569
gnu: r-biostrings: Update to 2.40.2.
...
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28 21:35:40 +10:00
0d159d84e2
gnu: r-summarizedexperiment: Update to 1.2.3.
...
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28 21:35:40 +10:00
722b4c919d
gnu: r-genomicalignments: Update to 1.8.4.
...
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28 21:35:40 +10:00
380d3f8657
gnu: r-rtracklayer: Update to 1.32.2.
...
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28 21:35:40 +10:00
303163c7b9
gnu: r-genomeinfodb: Update to 1.8.3.
...
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28 21:35:40 +10:00
2d88825183
gnu: r-genomicfeatures: Update to 1.24.5.
...
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28 21:35:40 +10:00
d6dfc39f68
gnu: r-s4vectors: Update to 0.10.2.
...
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-28 12:31:22 +02:00
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
Ben Woodcroft