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75 commits

Author SHA1 Message Date
Ricardo Wurmus
9f04196d88 gnu: preseq: Move "use-samtools-headers" phase. 
* gnu/packages/bioinformatics.scm (preseq)[arguments]: Move phase
  "use-samtools-headers" after "enter-dir" phase.
 2015-07-09 12:12:07 +02:00
Ricardo Wurmus
56e373ef75 gnu: Add preseq. 
* gnu/packages/bioinformatics.scm (preseq): New variable.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: New file.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: New file.
* gnu-system.am (dist_patch_DATA): Add them.
 2015-07-08 17:05:00 +02:00
Ricardo Wurmus
5bdda30b32 gnu: samtools: Install headers. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-headers" to install header files.
 2015-07-08 17:05:00 +02:00
Ricardo Wurmus
795c01f31d gnu: samtools: Update to 1.2. 
* gnu/packages/bioinformatics.scm (samtools): Update to 1.2.
 2015-07-07 14:43:07 +02:00
Ben Woodcroft
af86047537 gnu: Add prodigal. 
* gnu/packages/bioinformatics.scm (prodigal): New variable.
 2015-07-05 02:56:53 -04:00
Ricardo Wurmus
151714ca8c gnu: shogun: Build with install RPATH. 
* gnu/packages/bioinformatics.scm (shogun)[arguments]: Add configure flag to
  build with install RPATH.
 2015-07-04 17:55:30 +02:00
Ricardo Wurmus
c61fe02cc0 gnu: Add WarpedLMM. 
* gnu/packages/bioinformatics.scm (python2-warpedlmm): New variable.
 2015-07-02 11:16:46 +02:00
Ricardo Wurmus
82c370dea1 gnu: Add Blast+. 
* gnu/packages/bioinformatics.scm (blast+): New variable.
 2015-06-29 16:13:28 +02:00
Ricardo Wurmus
cc6ed47737 gnu: Add plink. 
* gnu/packages/bioinformatics.scm (plink): New variable.
* gnu/packages/patches/plink-1.07-unclobber-i.patch: New file.
 2015-06-29 12:54:48 +02:00
Ben Woodcroft
c684629f7c gnu: Add hmmer. 
* gnu/packages/bioinformatics.scm (hmmer): New variable.
 2015-06-24 00:39:22 -04:00
Ricardo Wurmus
4758eaaa2d gnu: star: Update to 2.4.2a. 
* gnu/packages/bioinformatics.scm (star): Update to 2.4.2a.
 2015-06-23 18:37:16 +02:00
Ricardo Wurmus
0ec8b206d4 gnu: miso: Install executables. 
* gnu/packages/bioinformatics.scm (miso)[source]: Patch "setup.py" to use
  "setuptools" so that executables are built.
* gnu/packages/bioinformatics.scm (miso)[native-inputs]: Add "python2-mock"
  and "python2-pytz".
 2015-06-23 13:13:03 +02:00
Ricardo Wurmus
c4325f6269 gnu: Add idr. 
* gnu/packages/bioinformatics.scm (idr): New variable.
 2015-06-23 10:55:52 +02:00
Ben Woodcroft
12b04cbee6 gnu: Add fasttree. 
* gnu/packages/bioinformatics.scm (fasttree): New variable.
 2015-06-21 03:30:40 -04:00
Ben Woodcroft
684bf7c7f1 gnu: Add diamond. 
* gnu/packages/bioinformatics.scm (diamond): New variable.
 2015-06-17 19:43:54 -04:00
Ricardo Wurmus
86517de69c gnu: miso: Use HTTPS URL. 
* gnu/packages/bioinformatics.scm (miso)[source]: Use "https" protocol for
  downloading the source tarball.
 2015-06-17 15:28:43 +02:00
Ricardo Wurmus
1bbc3b1d2c gnu: bedops: Update to 2.4.14. 
* gnu/packages/bioinformatics.scm (bedops): Update to 2.4.14.
 2015-06-17 14:37:29 +02:00
Ricardo Wurmus
a98c6eccf8 gnu: orfm: Update to 0.4.1. 
* gnu/packages/bioinformatics.scm (orfm): Update to 0.4.1.
 2015-06-15 10:36:42 +02:00
Ben Woodcroft
1e44cf8b0f gnu: Add OrfM. 
* gnu/packages/bioinformatics.scm (orfm): New variable.

Signed-off-by: Ricardo Wurmus <ricardo.wurmus@mdc-berlin.de>
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus
36742f4389 gnu: Add Couger. 
* gnu/packages/bioinformatics.scm (couger): New variable.
 2015-06-12 12:57:30 +02:00
Ricardo Wurmus
e0a02cb21f gnu: ngs-sdk: Update to version 1.1.1. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to version 1.1.1.
 2015-06-12 12:57:29 +02:00
Ricardo Wurmus
e7c097306d gnu: Add HTSlib. 
* gnu/packages/bioinformatics.scm (htslib): New variable.
 2015-06-02 14:30:14 +02:00
Ricardo Wurmus
132b4c8c23 gnu: ncbi-vdb: Use "i386" instead of "i686" in directory name. 
* gnu/packages/bioinformatics.scm (ncbi-vdb)[arguments]: Copy libraries from
  "linux/gcc/i386" directory instead of "linux/gcc/i686" when building on
  i686.
 2015-06-02 14:26:14 +02:00
Ricardo Wurmus
365c815389 gnu: Add edirect. 
* gnu/packages/bioinformatics.scm (edirect): New variable.
 2015-05-27 17:42:40 +02:00
Ricardo Wurmus
628bd9b8a7 gnu: shogun: Remove non-free source files. 
* gnu/packages/bioinformatics.scm (shogun)[source]: Add snippet to remove
  non-free sources.
 2015-05-27 10:56:27 +02:00
Ricardo Wurmus
66e3eff1e3 gnu: Add rsem. 
* gnu/packages/bioinformatics.scm (rsem): New variable.
* gnu/packages/patches/rsem-makefile.patch: New file.
 2015-05-22 13:14:29 +02:00
Ricardo Wurmus
7c3958e15a gnu: vcftools: Remove "-m64" from CFLAGS. 
* gnu/packages/bioinformatics.scm (vcftools): Explicitly set CFLAGS to
  remove "-m64" flag.
 2015-05-05 10:20:21 +02:00
Ricardo Wurmus
4702cec246 gnu: bamtools: Set rpath via LDFLAGS. 
* gnu/packages/bioinformatics.scm (bamtools): Add a pre-configure phase
  setting $LDFLAGS to set the rpath to $out/lib/bamtools.
 2015-05-04 11:29:41 +02:00
Ricardo Wurmus
0b84a0aaca gnu: Add samtools-0.1.19. 
* gnu/packages/bioinformatics.scm (samtools-0.1): New variable.
 2015-05-04 10:28:27 +02:00
Ricardo Wurmus
41dd712657 gnu: samtools: Install libbam.a library. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Add phase
  "install-library" to install the libbam.a library.
 2015-05-04 10:28:26 +02:00
Ricardo Wurmus
0a75450c14 gnu: samtools: Remove patch-makefile-curses phase. 
* gnu/packages/bioinformatics.scm (samtools)[arguments]: Remove
  patch-makefile-curses phase, use make-flags instead.
 2015-05-04 10:28:26 +02:00
Ricardo Wurmus
4ca009c036 gnu: flexbar: Enable tests. 
* gnu/packages/bioinformatics.scm (flexbar): Enable tests.
 2015-04-27 15:12:47 +02:00
Ricardo Wurmus
e4e5a4d88f gnu: Add eXpress. 
* gnu/packages/bioinformatics.scm (express): New variable.
 2015-04-21 17:57:22 +02:00
Ricardo Wurmus
9794180d5e gnu: Add bamtools. 
* gnu/packages/bioinformatics.scm (bamtools): New variable.
 2015-04-21 17:57:22 +02:00
Ricardo Wurmus
dbf4ed7c91 gnu: Add subread. 
* gnu/packages/bioinformatics.scm (subread): New variable.
 2015-04-21 10:46:23 +02:00
Ricardo Wurmus
51c649992e gnu: Add sra-tools. 
* gnu/packages/bioinformatics.scm (sra-tools): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus
75dd242480 gnu: Add NCBI VDB. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): New variable.
 2015-04-20 15:29:17 +02:00
Ricardo Wurmus
2651a5e695 gnu: Add NGS Java bindings. 
* gnu/packages/bioinformatics.scm (ngs-java): New variable.
 2015-04-20 15:29:16 +02:00
Ricardo Wurmus
282c5087b4 gnu: Add NGS SDK. 
* gnu/packages/bioinformatics.scm (ngs-sdk): New variable.
 2015-04-20 15:28:58 +02:00
Ricardo Wurmus
85c37e29a4 gnu: Add Biopython. 
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): New
  variables.
 2015-04-20 15:23:23 +02:00
Ricardo Wurmus
2127cedb23 gnu: Add FASTX Toolkit. 
* gnu/packages/bioinformatics.scm (fastx-toolkit): New variable.
 2015-04-16 10:28:37 +02:00
Ricardo Wurmus
8214b7fbea gnu: rseqc: Update hash. 
* gnu/packages/bioinformatics.scm (rseqc): Update hash.
 2015-04-13 15:39:02 +02:00
Ricardo Wurmus
5854f6858b gnu: Add GRIT. 
* gnu/packages/bioinformatics.scm (grit): New variable.
 2015-04-10 14:35:48 +02:00
Ricardo Wurmus
c833ab556f gnu: Add Shogun. 
* gnu/packages/bioinformatics.scm (shogun): New variable.
 2015-04-09 15:05:12 +02:00
Ricardo Wurmus
bfe3c68572 gnu: Add clustal omega. 
* gnu/packages/bioinformatics.scm (clustal-omega): New variable.
 2015-04-01 11:39:39 +02:00
Ricardo Wurmus
c5372108f2 gnu: pbtranscript-tofu: Add missing inputs. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[inputs]: Add missing
  runtime inputs.
 2015-03-31 20:04:41 +02:00
Ricardo Wurmus
49261e45d8 gnu: pbtranscript-tofu: Delete pre-built libraries. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu)[arguments]: Delete
  "build" directory and any shared objects after unpacking.
 2015-03-31 20:04:32 +02:00
Ricardo Wurmus
de07c0db4a gnu: Add vcftools. 
* gnu/packages/bioinformatics.scm (vcftools): New variable.
 2015-03-31 17:43:52 +02:00
Ricardo Wurmus
8e913213d9 gnu: Add cutadapt. 
* gnu/packages/bioinformatics.scm (cutadapt): New variable.
 2015-03-31 17:38:56 +02:00
Ricardo Wurmus
2c16316ef4 gnu: Add pbtranscript-tofu. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): New variable.
 2015-03-24 16:59:47 +01:00