2651a5e695
gnu: Add NGS Java bindings.
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* gnu/packages/bioinformatics.scm (ngs-java): New variable.
2015-04-20 15:29:16 +02:00
282c5087b4
gnu: Add NGS SDK.
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* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
2015-04-20 15:28:58 +02:00
85c37e29a4
gnu: Add Biopython.
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* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
variables.
2015-04-20 15:23:23 +02:00
2127cedb23
gnu: Add FASTX Toolkit.
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* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
2015-04-16 10:28:37 +02:00
8214b7fbea
gnu: rseqc: Update hash.
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* gnu/packages/bioinformatics.scm (rseqc): Update hash.
2015-04-13 15:39:02 +02:00
5854f6858b
gnu: Add GRIT.
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* gnu/packages/bioinformatics.scm (grit): New variable.
2015-04-10 14:35:48 +02:00
c833ab556f
gnu: Add Shogun.
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* gnu/packages/bioinformatics.scm (shogun): New variable.
2015-04-09 15:05:12 +02:00
bfe3c68572
gnu: Add clustal omega.
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* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
2015-04-01 11:39:39 +02:00
c5372108f2
gnu: pbtranscript-tofu: Add missing inputs.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
runtime inputs.
2015-03-31 20:04:41 +02:00
49261e45d8
gnu: pbtranscript-tofu: Delete pre-built libraries.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
"build" directory and any shared objects after unpacking.
2015-03-31 20:04:32 +02:00
de07c0db4a
gnu: Add vcftools.
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* gnu/packages/bioinformatics.scm (vcftools): New variable.
2015-03-31 17:43:52 +02:00
8e913213d9
gnu: Add cutadapt.
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* gnu/packages/bioinformatics.scm (cutadapt): New variable.
2015-03-31 17:38:56 +02:00
2c16316ef4
gnu: Add pbtranscript-tofu.
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* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
2015-03-24 16:59:47 +01:00
ad641d53de
gnu: Add python2-bx-python.
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* gnu/packages/bioinformatics.scm (python2-bx-python): New variable.
2015-03-24 15:00:09 +01:00
19ee920144
gnu: Add python2-pbcore.
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* gnu/packages/bioinformatics.scm (python2-pbcore): New variable.
2015-03-24 14:58:47 +01:00
ddd82e0e76
gnu: Add MISO.
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* gnu/packages/bioinformatics.scm (miso): New variable.
2015-03-17 12:29:58 +01:00
9a8336d87b
gnu: Add bwa.
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* gnu/packages/bioinformatics.scm (bwa): New variable.
2015-03-17 12:29:51 +01:00
15a3c3d4f1
gnu: Add htsjdk.
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* gnu/packages/bioinformatics.scm (htsjdk): New variable.
2015-03-10 11:46:49 +01:00
1289062522
Merge branch 'core-updates'.
2015-03-04 14:07:23 +01:00
191c710139
gnu: Add crossmap.
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* gnu/packages/bioinformatics.scm (crossmap): New variable.
* gnu/packages/patches/crossmap-allow-system-pysam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-03-02 17:23:56 +01:00
810cff8557
gnu: Add CLIPper.
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* gnu/packages/bioinformatics.scm (clipper): New variable.
2015-03-02 14:11:54 +01:00
d57e6d0f8e
gnu: Add MACS.
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* gnu/packages/bioinformatics.scm (macs): New variable.
2015-03-02 11:33:13 +01:00
a2fb1492af
gnu: Add pybedtools.
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* gnu/packages/bioinformatics.scm (python2-pybedtools): New variable.
2015-03-02 11:32:10 +01:00
f586c87705
gnu: Add 'file-name' fields for github source tarballs without a name.
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* gnu/packages/aarddict.scm (aarddict), gnu/packages/algebra.scm (arb),
gnu/packages/audio.scm (jack-2, lvtk),
gnu/packages/bioinformatics.scm (bedops, bedtools, bowtie),
gnu/packages/game-development.scm (tiled),
gnu/packages/games.scm (minetest-data, minetest, retroarch),
gnu/packages/jrnl.scm (jrnl), gnu/packages/kde.scm (qjson),
gnu/packages/libevent.scm (libuv), gnu/packages/linux.scm (pflask),
gnu/packages/mail.scm (offlineimap, libetpan),
gnu/packages/maths.scm (arpack-ng), gnu/packages/ninja.scm (ninja),
gnu/packages/nutrition.scm (gourmet),
gnu/packages/python.scm (python-cairocffi), gnu/packages/rdf.scm (lrdf),
gnu/packages/ruby.scm (ruby-i18n), gnu/packages/sxiv.scm (sxiv): Add
'file-name' field to origin.
2015-02-28 09:49:01 -05:00
da6dd842d0
gnu: Remove now unneeded 'unpack' phases for unzip.
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This is a followup to commit cd0385b
2015-02-27 15:08:37 +01:00
85652f599a
gnu: Add HTSeq.
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* gnu/packages/bioinformatics.scm (htseq): New variable.
2015-02-20 19:31:53 +01:00
8622a07280
gnu: Add RSeQC.
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* gnu/packages/bioinformatics.scm (rseqc): New variable.
2015-02-19 13:41:38 +01:00
8dd4ff1133
gnu: Add bedops.
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* gnu/packages/bioinformatics.scm (bedops): New variable.
2015-02-13 15:51:10 +01:00
e58d01faf5
gnu: hisat: fix build on non-x86_64.
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* gnu/packages/bioinformatics.scm (hisat): Add "POPCNT_CAPABILITY=0" to
make-flags on architectures other than x86_64.
2015-02-12 14:09:00 +01:00
ce7155d5dd
gnu: Add STAR.
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* gnu/packages/bioinformatics.scm (star): New variable.
2015-02-10 14:37:14 +01:00
346a829a85
gnu: Add HISAT.
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* gnu/packages/bioinformatics.scm (hisat): New variable.
2015-02-10 14:37:13 +01:00
d7678942f9
gnu: Add flexbar.
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* gnu/packages/bioinformatics.scm (flexbar): New variable.
2015-02-09 10:26:28 +01:00
d3517eda25
gnu: Add seqan.
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* gnu/packages/bioinformatics.scm (seqan): New variable.
2015-02-09 10:26:20 +01:00
241e122193
gnu: bowtie: fix build errors
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* gnu/packages/bioinformatics.scm (bowtie): Add 'supported-systems' field and
add Makefile patch.
* gnu/packages/patches/bowtie-fix-makefile.patch: New file.
* gnu-system.am (dist_patch_DATA): Add it.
2015-01-30 10:45:27 +01:00
2c7ee16720
gnu: Add bowtie
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* gnu/packages/bioinformatics.scm (bowtie): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-19 18:50:28 +01:00
81de56479a
gnu: Add bedtools
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* gnu/packages/bioinformatics.scm (bedtools): New variable.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
f3cd952b45
gnu: samtools: disable tests for non-64-bit systems
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* gnu/packages/bioinformatics.scm (samtools): disable tests for all non-64-bit
systems because of an upstream bug in the test data.
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-16 18:17:15 +01:00
4e10a22168
gnu: Add samtools
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* gnu/packages/bioinformatics.scm: New file
* gnu-system.am (GNU_SYSTEM_MODULES): Add it
Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2014-12-13 00:01:06 +01:00
Ricardo Wurmus