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314 commits

Author SHA1 Message Date
Ludovic Courtès
da6dd842d0 gnu: Remove now unneeded 'unpack' phases for unzip. 
This is a followup to commit cd0385b.

* gnu/packages/bioinformatics.scm (hisat)[arguments]: Remove 'unpack'
  phase.
* gnu/packages/image.scm (freeimage): Likewise.
* gnu/packages/python.scm (python2-cssutils): Likewise.
 2015-02-27 15:08:37 +01:00
Ricardo Wurmus
85652f599a gnu: Add HTSeq. 
* gnu/packages/bioinformatics.scm (htseq): New variable.
 2015-02-20 19:31:53 +01:00
Ricardo Wurmus
8622a07280 gnu: Add RSeQC. 
* gnu/packages/bioinformatics.scm (rseqc): New variable.
 2015-02-19 13:41:38 +01:00
Ricardo Wurmus
8dd4ff1133 gnu: Add bedops. 
* gnu/packages/bioinformatics.scm (bedops): New variable.
 2015-02-13 15:51:10 +01:00
Ricardo Wurmus
e58d01faf5 gnu: hisat: fix build on non-x86_64. 
* 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
Ricardo Wurmus
ce7155d5dd gnu: Add STAR. 
* gnu/packages/bioinformatics.scm (star): New variable.
 2015-02-10 14:37:14 +01:00
Ricardo Wurmus
346a829a85 gnu: Add HISAT. 
* gnu/packages/bioinformatics.scm (hisat): New variable.
 2015-02-10 14:37:13 +01:00
Ricardo Wurmus
d7678942f9 gnu: Add flexbar. 
* gnu/packages/bioinformatics.scm (flexbar): New variable.
 2015-02-09 10:26:28 +01:00
Ricardo Wurmus
d3517eda25 gnu: Add seqan. 
* gnu/packages/bioinformatics.scm (seqan): New variable.
 2015-02-09 10:26:20 +01:00
Ricardo Wurmus
241e122193 gnu: bowtie: fix build errors 
* 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
Ricardo Wurmus
2c7ee16720 gnu: Add bowtie 
* gnu/packages/bioinformatics.scm (bowtie): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-19 18:50:28 +01:00
Ricardo Wurmus
81de56479a gnu: Add bedtools 
* gnu/packages/bioinformatics.scm (bedtools): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2014-12-16 18:17:15 +01:00
Ricardo Wurmus
f3cd952b45 gnu: samtools: disable tests for non-64-bit systems 
* 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
Ricardo Wurmus
4e10a22168 gnu: Add samtools 
* 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