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354 Commits (316a5d02b07cefbe8d54880a0c2effe563ca0661)

Author SHA1 Message Date
Marius Bakke 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
Ben Woodcroft 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
Ben Woodcroft 0ed8f0cd4c
gnu: mafft: Update to 7.304. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
 2016-08-15 20:59:41 +10:00
Ben Woodcroft 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
Ben Woodcroft 93b8316e08
gnu: mafft: Update to 7.300. 
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
 2016-08-15 20:51:00 +10:00
Ben Woodcroft a12ba6e878
gnu: Add bamm. 
* gnu/packages/bioinformatics.scm (bamm): New variable.
 2016-08-14 14:55:23 +10:00
Efraim Flashner 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
Ben Woodcroft 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
Ben Woodcroft ceb62d5436
gnu: Add roary. 
* gnu/packages/bioinformatics.scm (roary): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 608dd93267
gnu: Add raxml. 
* gnu/packages/bioinformatics.scm (raxml): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 024130d258
gnu: Add prank. 
* gnu/packages/bioinformatics.scm (prank): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft b16728b068
gnu: Add exonerate. 
* gnu/packages/bioinformatics.scm (exonerate): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft db7a344427
gnu: Add bppsuite. 
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 159a701678
gnu: Add bpp-popgen. 
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 8b5f4d5700
gnu: Add bpp-phyl. 
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 70f1bc051a
gnu: Add bpp-seq. 
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 985d841144
gnu: Add bpp-core. 
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
 2016-08-08 22:08:17 +10:00
Ben Woodcroft 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
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