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122 Commits

Author SHA1 Message Date
Ben Woodcroft 5f7e17bef7 gnu: Add snap-aligner. 
* gnu/packages/bioinformatics.scm (snap-aligner): New variable.
 2015-12-11 14:34:51 +01:00
Ben Woodcroft e815c094f7 gnu: python-biopython, python2-biopython: Update to 1.66. 
* gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66.
[source]: Use PyPi instead of biopython.org.
 2015-12-10 14:35:56 +01:00
Ricardo Wurmus b49c5a58dc gnu: preseq: Update to 2.0. 
* gnu/packages/bioinformatics.scm (preseq): Update to 2.0.
[source]: Add file-name field, remove patches.
[arguments]: Remove unused build phases, add make flags.
[inputs]: Add smithlab-cpp.
* gnu/packages/patches/preseq-1.0.2-link-with-libbam.patch: Remove file.
* gnu/packages/patches/preseq-1.0.2-install-to-PREFIX.patch: Remove
  file.
* gnu-system.am (dist_patch_DATA): Remove them.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus c6a24d6e92 gnu: Add smithlab-cpp. 
* gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
 2015-11-20 15:22:06 +01:00
Ricardo Wurmus 3d51ec919e gnu: edirect: Update home page. 
* gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing
  slash to home page.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus c52a382c4a gnu: sra-tools: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 9e5ef614aa gnu: ncbi-vdb: Update to 2.5.4. 
* gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 614a8977cb gnu: ngs-java: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2.
[arguments]: Remove build phase "fix-java-symlink-installation".
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus d6a1cd7cae gnu: ngs-sdk: Update to 1.2.2. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
 2015-11-20 15:21:24 +01:00
Ricardo Wurmus 9641a89957 gnu: bless: Build only for x86_64. 
* gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus 0536727efe gnu: htseq: Propagate numpy. 
* gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy
  from here ...
[propagated-inputs]: ... to here.
 2015-11-20 11:32:32 +01:00
Ricardo Wurmus 029d9f77ab gnu: mosaik: Build only on x86_64. 
* gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add
  field.
 2015-11-12 12:36:40 +01:00
Ricardo Wurmus 4d75e03ac9 gnu: bless: Correct indentation and home-page. 
* gnu/packages/bioinformatics.scm (bless): Fix indentation.
  [home-page]: Replace broken URL.
 2015-11-06 22:31:29 +01:00
Ricardo Wurmus 6c2b26e21e gnu: Add BLESS. 
* gnu/packages/bioinformatics.scm (bless): New variable.

Co-authored-by: Diane Trout <diane@ghic.org>
 2015-11-06 18:20:50 +01:00
Ricardo Wurmus 60af3d8241 gnu: hisat: Disable build on non-x86_64. 
* gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
 2015-11-02 14:37:52 +01:00
Ben Woodcroft f3674b1c80 gnu: Add express-beta-diversity. 
* gnu/packages/bioinformatics.scm (express-beta-diversity): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-11-02 09:54:21 +01:00
Ricardo Wurmus 9a067efdb2 gnu: pbtranscript-tofu: Update to 2.2.3. 
* gnu/packages/bioinformatics.scm (pbtranscript-tofu): Update to 2.2.3.
  [source]: Remove bundled Cython sources in a snippet.  Replace
  ".tar.gz" extension in file-name field with "-checkout".
  [arguments]: Replace "enter-directory-and-clean-up" phase with
  "enter-directory" phase, and add "patch-setuppy" phase.
  [inputs]: Add python2-h5py.  Move python2-cython ...
  [native-inputs]: ... to this field.
 2015-10-28 16:26:58 +01:00
Ricardo Wurmus 104c1986ac gnu: subread: Use SSE optimizations on x86_64 only. 
* gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and
  CCFLAGS conditionally dependent on target system.
 2015-10-27 12:06:55 +01:00
Ricardo Wurmus 61d5fd03bf gnu: crossmap: Update to 0.2.1. 
* gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
 2015-10-27 11:14:13 +01:00
Ricardo Wurmus fe4c37c244 gnu: Add MOSAIK. 
* gnu/packages/bioinformatics.scm (mosaik): New variable.
 2015-10-22 11:11:09 +02:00
Andreas Enge ab29be81c5 gnu: ngs-sdk: Correct typo. 
* gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
 2015-10-17 22:51:12 +02:00
Andreas Enge a0dadf0cb1 gnu: ngs-sdk: Remove unsupported systems. 
* gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86
  based systems.
 2015-10-17 22:43:14 +02:00
Ben Woodcroft d9c44e9c6a gnu: diamond: Restrict supported systems to x86_64-linux. 
* gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to
  x86_64-linux.
 2015-10-14 20:02:25 +03:00
Ricardo Wurmus db94f8c734 gnu: bwa: Disable on non-x86_64. 
* gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
 2015-10-12 15:50:33 +02:00
Ben Woodcroft 6f04e51560 gnu: vsearch: Restrict supported systems to x86_64-linux. 
* gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict
  to x86_64-linux.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2015-10-03 13:59:11 +02:00
Mark H Weaver 9ab5ea449e gnu: clipper: Add 'file-name' field to source origin. 
* gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
 2015-10-02 10:55:57 -04:00
Ben Woodcroft a2950fa4dc gnu: Add vsearch. 
* gnu/packages/bioinformatics.scm (vsearch): New variable.

Signed-off-by: Ludovic Courtès <ludo@gnu.org>
 2015-10-01 10:51:28 +02:00
Pjotr Prins b2bddb07ef gnu: Add bio-blastxmlparser. 
* gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
 2015-09-28 12:22:47 +02:00
Ludovic Courtès e1556533d3 Merge branch 'core-updates' 2015-09-26 15:14:53 +02:00
Ben Woodcroft d708b7a973 gnu: Add seqmagick. 
* gnu/packages/bioinformatics.scm (seqmagick): New variable.
 2015-09-25 16:16:28 +02:00
Mark H Weaver bd90127ad4 Merge branch 'master' into core-updates 2015-09-22 16:38:48 -04:00
Andreas Enge a5002ae77c gnu: Add R/qtl. 
* gnu/packages/bioinformatics.scm (r-qtl): New variable.

Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
 2015-09-20 00:32:45 +02:00
Pjotr Prins edb15985f1 gnu: Add bioruby. 
* gnu/packages/bioinformatics.scm (bioruby): New variable.
 2015-09-19 12:41:52 -04:00
Ben Woodcroft 41ddebdd2a gnu: Add mafft. 
* gnu/packages/bioinformatics.scm (mafft): New variable.
 2015-09-16 23:06:14 +02:00
Pjotr Prins 9c38b54027 gnu: Add bio-locus. 
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
 2015-09-14 12:06:04 -04:00
David Thompson 801a0a2219 Revert "gnu: Add bio-locus." 
This reverts commit b429c4fbb0.
 2015-09-14 12:05:15 -04:00
Pjotr Prins b429c4fbb0 gnu: Add bio-locus. 
* gnu/packages/bioinformatics.scm (bio-locus): New variable.
 2015-09-14 11:36:30 -04:00
Ludovic Courtès 75710da667 Merge branch 'master' into core-updates 2015-09-13 21:28:01 +02:00
Ricardo Wurmus 1921b1de07 gnu: Add deeptools. 
* gnu/packages/bioinformatics.scm (deeptools): New variable.
 2015-09-02 10:38:43 +02:00
Ludovic Courtès 96c4621056 gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases. 
* gnu/packages/bioinformatics.scm (bedtools, bowtie, bwa, hisat, samtools,
  plink, star): Use 'install-file' instead of 'mkdir-p' + 'copy-file'.
* gnu/packages/check.scm (catch-framework): Likewise.
* gnu/packages/code.scm (global): Likewise.
* gnu/packages/emacs.scm (magit-svn, haskell-mode, emacs-pdf-tools):
  Likewise.
* gnu/packages/engineering.scm (fastcap, fasthenry): Likewise.
* gnu/packages/gnuzilla.scm (nss): Likewise.
* gnu/packages/guile.scm (guile-minikanren): Likewise.
* gnu/packages/java.scm (swt): Likewise.
* gnu/packages/make-bootstrap.scm (%static-binaries): Likewise.
* gnu/packages/maths.scm (lpsolve): Likewise.
* gnu/packages/mp3.scm (mpc123): Likewise.
* gnu/packages/ninja.scm (ninja): Likewise.
* gnu/packages/python.scm (python-numpy, python-pyparsing): Likewise.
* gnu/packages/screen.scm (dtach): Likewise.
* gnu/packages/synergy.scm (synergy): Likewise.
* gnu/packages/textutils.scm (utf8proc): Likewise.
* gnu/packages/version-control.scm (git-test-sequence): Likewise.
* gnu/packages/wicd.scm (wicd): Likewise.
 2015-08-29 01:25:08 +02:00
Ricardo Wurmus f7283db37d gnu: Add BioPerl. 
* gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
 2015-08-26 17:54:52 +02:00
Ricardo Wurmus c1670a8196 gnu: shogun: Move package to machine-learning.scm. 
* gnu/packages/bioinformatics.scm (shogun): Move from here...
* gnu/packages/machine-learning.scm (shogun): ...to here.
 2015-08-14 17:17:05 +02:00
Ben Woodcroft b81cb1f2f3 gnu: bedtools: Add patch to fix compilation on 32 bit systems. 
* gnu/packages/patches/bedtools-32bit-compilation.patch: New file.
* gnu/packages/bioinformatics.scm (bedtools)[source]: Add patch.
* gnu-system.am (dist_patch_DATA): Register patch.

Signed-off-by: Andreas Enge <andreas@enge.fr>
 2015-07-25 19:16:49 +02:00
Ben Woodcroft bd4af2f940 gnu: bedtools: Update to 2.24.0. 
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.24.0.
 2015-07-25 00:02:54 -04:00
Ben Woodcroft 8dc797fa28 gnu: Add aragorn. 
* gnu/packages/bioinformatics.scm (aragorn): New variable.
 2015-07-21 16:39:38 +02:00
Mark H Weaver 5ede5f2f1c gnu: metabat: Minor tweaks. 
* gnu/packages/bioinformatics.scm (metabat)[arguments]: Fix indentation in
  'fix-includes' phase.
  [license]: Fix misspelling.
 2015-07-19 15:27:15 -04:00
Ben Woodcroft 8fd790eb87 gnu: Add metabat. 
* gnu/packages/bioinformatics.scm (metabat): New variable.
 2015-07-19 15:17:08 -04:00
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