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336 commits

Author SHA1 Message Date
Ricardo Wurmus
97b9da6897
gnu: Add discrover. 
* gnu/packages/bioinformatics.scm (discrover): New variable.
 2016-08-03 17:20:26 +02:00
Ben Woodcroft
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
Ricardo Wurmus
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
Ricardo Wurmus
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Leo Famulari
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
Ben Woodcroft
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
Ricardo Wurmus
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
Ricardo Wurmus
6619f9c769
gnu: Add eigensoft. 
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
 2016-07-14 08:58:35 +02:00
Ricardo Wurmus
17dc32a400
gnu: Add Ribotaper. 
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
 2016-07-12 12:19:39 +02:00
Ricardo Wurmus
9a8f309cf1
gnu: Add bedtools-2.18. 
* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
 2016-07-12 12:19:15 +02:00
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ricardo Wurmus
274da826f9
gnu: Add r-seqinr. 
* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
 2016-07-07 10:46:17 +02:00
Efraim Flashner
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
Ricardo Wurmus
5fb5dffbd4
gnu: Add multiqc. 
* gnu/packages/bioinformatics.scm (multiqc): New variable.
 2016-07-05 16:32:37 +02:00
Ricardo Wurmus
1f1b20b8be
gnu: Add bits. 
* gnu/packages/bioinformatics.scm (bits): New variable.
 2016-07-05 15:43:36 +02:00
Ricardo Wurmus
66e40e0065
gnu: Add EMBOSS. 
* gnu/packages/bioinformatics.scm (emboss): New variable.
 2016-07-05 12:32:12 +02:00
Roel Janssen
744004a31f
gnu: Add r-edger. 
* gnu/packages/bioinformatics.scm (r-edger): New variable.
 2016-07-04 14:49:07 +02:00
Roel Janssen
7d4224d794
gnu: Add r-limma. 
* gnu/packages/bioinformatics.scm (r-limma):  New variable.
 2016-07-04 14:39:16 +02:00
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ricardo Wurmus
ec9466388e
gnu: Add SEEK. 
* gnu/packages/bioinformatics.scm (seek): New variable.
 2016-06-28 22:49:05 +02:00
Ben Woodcroft
d6e374a0d9
gnu: mafft: Update to 7.299. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
 2016-06-28 21:42:15 +10:00
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
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
Ben Woodcroft
9ded145717
gnu: Add python-screed. 
* gnu/packages/bioinformatics.scm (python-screed, python2-screed):
New variables.
 2016-06-27 21:16:39 +10:00
Ben Woodcroft
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