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* gnu: Add fraggenescan.Ben Woodcroft2015-12-29
| | | | * gnu/packages/bioinformatics.scm (fraggenescan): New variable.
* gnu: Add GenomicRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): New variable.
* gnu: Add XVector.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-xvector): New variable.
* gnu: Add GenomeInfoDb.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-genomeinfodb): New variable.
* gnu: Add IRanges.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-iranges): New variable.
* gnu: Add S4Vectors.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): New variable.
* gnu: Add BiocGenerics.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-biocgenerics): New variable.
* gnu: Add r-acsnminer.Ricardo Wurmus2015-12-21
| | | | * gnu/packages/bioinformatics.scm (r-acsnminer): New variable.
* gnu: mafft: Update to 7.267.Ben Woodcroft2015-12-21
| | | | | | | * gnu/packages/bioinformatics.scm (mafft): Update to 7.267. [arguments]: Don't include mafft-homologs manpage. [inputs]: Add gawk and grep. [propagated-inputs]: Add coreutils.
* gnu: Add snap-aligner.Ben Woodcroft2015-12-11
| | | | * gnu/packages/bioinformatics.scm (snap-aligner): New variable.
* gnu: python-biopython, python2-biopython: Update to 1.66.Ben Woodcroft2015-12-10
| | | | | * gnu/packages/bioinformatics.scm (python-biopython, python2-biopython): Update to 1.66. [source]: Use PyPi instead of biopython.org.
* gnu: preseq: Update to 2.0.Ricardo Wurmus2015-11-20
| | | | | | | | | | | * 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.
* gnu: Add smithlab-cpp.Ricardo Wurmus2015-11-20
| | | | * gnu/packages/bioinformatics.scm (smithlab-cpp): New variable.
* gnu: edirect: Update home page.Ricardo Wurmus2015-11-20
| | | | | * gnu/packages/bioinformatics.scm (edirect)[home-page]: Append trailing slash to home page.
* gnu: sra-tools: Update to 2.5.4.Ricardo Wurmus2015-11-20
| | | | * gnu/packages/bioinformatics.scm (sra-tools): Update to 2.5.4.
* gnu: ncbi-vdb: Update to 2.5.4.Ricardo Wurmus2015-11-20
| | | | * gnu/packages/bioinformatics.scm (ncbi-vdb): Update to 2.5.4.
* gnu: ngs-java: Update to 1.2.2.Ricardo Wurmus2015-11-20
| | | | | * gnu/packages/bioinformatics.scm (ngs-java): Update to 1.2.2. [arguments]: Remove build phase "fix-java-symlink-installation".
* gnu: ngs-sdk: Update to 1.2.2.Ricardo Wurmus2015-11-20
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Update to 1.2.2.
* gnu: bless: Build only for x86_64.Ricardo Wurmus2015-11-20
| | | | * gnu/packages/bioinformatics.scm (bless): Add supported-systems field.
* gnu: htseq: Propagate numpy.Ricardo Wurmus2015-11-20
| | | | | | * gnu/packages/bioinformatics.scm (htseq)[inputs]: Move python2-numpy from here ... [propagated-inputs]: ... to here.
* gnu: mosaik: Build only on x86_64.Ricardo Wurmus2015-11-12
| | | | | * gnu/packages/bioinformatics.scm (mosaik)[supported-systems]: Add field.
* gnu: bless: Correct indentation and home-page.Ricardo Wurmus2015-11-06
| | | | | * gnu/packages/bioinformatics.scm (bless): Fix indentation. [home-page]: Replace broken URL.
* gnu: Add BLESS.Ricardo Wurmus2015-11-06
| | | | | | * gnu/packages/bioinformatics.scm (bless): New variable. Co-authored-by: Diane Trout <diane@ghic.org>
* gnu: hisat: Disable build on non-x86_64.Ricardo Wurmus2015-11-02
| | | | * gnu/packages/bioinformatics.scm (hisat)[supported-systems]: Add field.
* gnu: Add express-beta-diversity.Ben Woodcroft2015-11-02
| | | | | | * gnu/packages/bioinformatics.scm (express-beta-diversity): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: pbtranscript-tofu: Update to 2.2.3.Ricardo Wurmus2015-10-28
| | | | | | | | | | * 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.
* gnu: subread: Use SSE optimizations on x86_64 only.Ricardo Wurmus2015-10-27
| | | | | * gnu/packages/bioinformatics.scm (subread)[arguments]: Override CC and CCFLAGS conditionally dependent on target system.
* gnu: crossmap: Update to 0.2.1.Ricardo Wurmus2015-10-27
| | | | * gnu/packages/bioinformatics.scm (crossmap): Update to 0.2.1.
* gnu: Add MOSAIK.Ricardo Wurmus2015-10-22
| | | | * gnu/packages/bioinformatics.scm (mosaik): New variable.
* gnu: ngs-sdk: Correct typo.Andreas Enge2015-10-17
| | | | * gnu/packages/bioinformatics.scm (ngs-sdk): Correct typo.
* gnu: ngs-sdk: Remove unsupported systems.Andreas Enge2015-10-17
| | | | | * gnu/packages/bioinformatics.scm (ngs-sdk)[supported-systems]: Keep only x86 based systems.
* gnu: diamond: Restrict supported systems to x86_64-linux.Ben Woodcroft2015-10-14
| | | | | * gnu/packages/bioinformatics.scm (diamond) [supported-systems]: Restrict to x86_64-linux.
* gnu: bwa: Disable on non-x86_64.Ricardo Wurmus2015-10-12
| | | | * gnu/packages/bioinformatics.scm (bwa)[supported-systems]: Add field.
* gnu: vsearch: Restrict supported systems to x86_64-linux.Ben Woodcroft2015-10-03
| | | | | | | * gnu/packages/bioinformatics.scm (vsearch)[supported-systems]: Restrict to x86_64-linux. Signed-off-by: Andreas Enge <andreas@enge.fr>
* gnu: clipper: Add 'file-name' field to source origin.Mark H Weaver2015-10-02
| | | | * gnu/packages/bioinformatics.scm (clipper)[source]: Add file-name.
* gnu: Add vsearch.Ben Woodcroft2015-10-01
| | | | | | * gnu/packages/bioinformatics.scm (vsearch): New variable. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
* gnu: Add bio-blastxmlparser.Pjotr Prins2015-09-28
| | | | * gnu/packages/bioinformatics.scm (bio-blastxmlparser): New variable.
* Merge branch 'core-updates'Ludovic Courtès2015-09-26
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| * Merge branch 'master' into core-updatesMark H Weaver2015-09-22
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| * \ Merge branch 'master' into core-updatesLudovic Courtès2015-09-13
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| * | | gnu: Use 'install-file' instead of 'mkdir-p' and 'copy-file' in obvious cases.Ludovic Courtès2015-08-29
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | * 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.
* | | | gnu: Add seqmagick.Ben Woodcroft2015-09-25
| |_|/ |/| | | | | | | | * gnu/packages/bioinformatics.scm (seqmagick): New variable.
* | | gnu: Add R/qtl.Andreas Enge2015-09-20
| | | | | | | | | | | | | | | | | | * gnu/packages/bioinformatics.scm (r-qtl): New variable. Co-authored-by: Pjotr Prins <pjotr.guix@thebird.nl>
* | | gnu: Add bioruby.Pjotr Prins2015-09-19
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bioruby): New variable.
* | | gnu: Add mafft.Ben Woodcroft2015-09-16
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (mafft): New variable.
* | | gnu: Add bio-locus.Pjotr Prins2015-09-14
| | | | | | | | | | | | * gnu/packages/bioinformatics.scm (bio-locus): New variable.
* | | Revert "gnu: Add bio-locus."David Thompson2015-09-14
| | | | | | | | | | | | This reverts commit b429c4fbb06299ce10ecc113a7818bf777c63a6e.
* | | gnu: Add bio-locus.Pjotr Prins2015-09-14
| |/ |/| | | | | * gnu/packages/bioinformatics.scm (bio-locus): New variable.
* | gnu: Add deeptools.Ricardo Wurmus2015-09-02
|/ | | | * gnu/packages/bioinformatics.scm (deeptools): New variable.
* gnu: Add BioPerl.Ricardo Wurmus2015-08-26
| | | | * gnu/packages/bioinformatics.scm (bioperl-minimal): New variable.
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