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* gnu: metabat: Update to 2.11.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (metabat): Update to 2.11.1. [source]: Add patch to fix compilation. [arguments]: Adjust regular expressions modifying 'SConstruct'. * gnu/packages/patches/metabat-fix-compilation.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* gnu: python-plastid: Update to 0.4.8.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-plastid): Update to 0.4.8.
* gnu: bcftools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.5. [origin]: Remove fix-makefile patch. [arguments]: Add configure flags, add LIBS make flag. Do not delete configure phase. * gnu/packages/patches/bcftools-fix-makefile.patch: Remove file. * gnu/local.mk (dist_patch_DATA): Remove it.
* gnu: samtools: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.5.
* gnu: htslib: Update to 1.5.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.5.
* gnu: python-pysam: Update to 0.11.2.2.Ben Woodcroft2017-07-23
| | | | * gnu/packages/bioinformatics.scm (python-pysam): Update to 0.11.2.2.
* gnu: bamm: Use htslib-1.3.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics (htslib-1.3): New variable. (bamm)[inputs]: Replace htslib with htslib-1.3.
* gnu: bcftools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | | | * gnu/packages/bioinformatics.scm (bcftools): Update to 1.4.1. [arguments]: Move Makefile modifications from here ... [source]: ... to added patch. Adjust patch for update to 1.4. * gnu/packages/patches/bcftools-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Register it.
* gnu: samtools: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | | * gnu/packages/bioinformatics.scm (samtools): Update to 1.4.1. [arguments]: Add '--with-htslib=system' configure flag. [inputs]: Add htslib.
* gnu: htslib: Update to 1.4.1.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (htslib): Update to 1.4.1. [inputs]: Add curl, openssl.
* gnu: samtools: Use "modify-phases" syntax.Ben Woodcroft2017-07-23
| | | | | * gnu/packages/bioinformatics.scm (samtools)[arguments]: Use "modify-phases" syntax.
* gnu: r-s4vectors: Update to 0.14.3.Ricardo Wurmus2017-07-22
| | | | * gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.14.3.
* gnu: r-genomicranges: Update to 1.28.4.Ricardo Wurmus2017-07-22
| | | | * gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.28.4.
* gnu: r-bsgenome-hsapiens-ucsc-hg19: Update hash.Ricardo Wurmus2017-07-19
| | | | | * gnu/packages/bioinformatics.scm (r-bsgenome-hsapiens-ucsc-hg19)[source]: Update hash because the tarball changed in place.
* gnu: sortmerna: Limit support to x86_64 and i686 only.Efraim Flashner2017-07-19
| | | | * gnu/packages/bioinformatics.scm (sortmerna)[supported-systems]: New field.
* gnu: raxml: Limit to x86_64 and i686 only.Efraim Flashner2017-07-18
| | | | * gnu/packages/bioinformatics.scm (raxml)[supported-systems]: New field.
* gnu: bowtie: Use 'modify-phases'.Ben Woodcroft2017-07-14
| | | | | * gnu/packages/bioinformatics.scm (bowtie)[arguments]: Use 'modify-phases' syntax.
* gnu: bowtie: Update to 2.3.2.Ben Woodcroft2017-07-14
| | | | | * gnu/packages/bioinformatics.scm (bowtie): Update to 2.3.2. [inputs]: Add zlib.
* gnu: deeptools: Update to 2.5.1.Ricardo Wurmus2017-07-09
| | | | | | | * gnu/packages/bioinformatics.scm (deeptools): Update to 2.5.1. [arguments]: Remove. [native-inputs]: Use "python-" instead of "python2-" variants. [inputs]: Likewise; add python-py2bit.
* gnu: Add python-py2bit.Ricardo Wurmus2017-07-09
| | | | * gnu/packages/bioinformatics.scm (python-py2bit): New variable.
* gnu: blast+: Update to 2.6.0.Ben Woodcroft2017-07-08
| | | | | | | | | * gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. Add patch. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python. * gnu/packages/patches/blast+-fix-makefile.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
* Revert "gnu: blast+: Update to 2.6.0."Leo Famulari2017-07-06
| | | | This reverts commit 18dea67dc3a42d782b34b551304748346f173184.
* gnu: gemma: Fix building on non-Intel architectures.Efraim Flashner2017-07-04
| | | | | | | * gnu/packages/patches/gemma-intel-compat.patch: New file. * gnu/packages/bioinformatics.scm (gemma)[source]: Add patch. [arguments]: Add NO_INTEL_COMPAT flag on non-Intel architectures. * gnu/local.mk (dist_patch_DATA): Register patch.
* gnu: diamond: Update to 0.9.9.Ben J Woodcroft2017-07-04
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.9.
* gnu: blast+: Update to 2.6.0.Ben Woodcroft2017-07-04
| | | | | | | * gnu/packages/bioinformatics.scm (blast+): Update to 2.6.0. [origin]: Remove bundled pcre. [arguments]: Replace paths in run_with_lock.c. Configure with pcre. [inputs]: Add pcre, perl, python.
* gnu: cd-hit: Update to 4.6.8.Ben Woodcroft2017-07-01
| | | | * gnu/packages/bioinformatics.scm (cd-hit): Update to 4.6.8.
* gnu: bwa: Update to 0.7.15.Ben Woodcroft2017-07-01
| | | | * gnu/packages/bioinformatics.scm (bwa): Update to 0.7.15.
* gnu: Add f-seq.Ricardo Wurmus2017-06-25
| | | | * gnu/packages/bioinformatics.scm (f-seq): New variable.
* gnu: orfm: Update to 0.7.1.Ben Woodcroft2017-06-24
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.1.
* gnu: orfm: Update to 0.7.0.Ben Woodcroft2017-06-23
| | | | * gnu/packages/bioinformatics.scm (orfm): Update to 0.7.0.
* gnu: Add kentutils.Ricardo Wurmus2017-06-23
| | | | * gnu/packages/bioinformatics.scm (kentutils): New variable.
* gnu: python2-bx-python: Update to 0.7.3.Ricardo Wurmus2017-06-22
| | | | * gnu/packages/bioinformatics.scm (python2-bx-python): Update to 0.7.3.
* gnu: Move contents of zip module into compression module.Arun Isaac2017-06-20
| | | | | | | | | | | | | | | * gnu/packages/zip.scm (zip, unzip, zziplib, perl-zip): Move to... * gnu/packages/compression.scm: ...here. * gnu/packages/zip.scm: Delete file. * gnu/local.mk (GNU_SYSTEM_MODULES): Unregister deleted file. * po/packages/POTFILES.in: Unregister deleted file. * gnu/packages/{audio, avr, bioinformatics, busybox, cdrom, ci, compression, docbook, documentation, fonts, fpga, game-development, games, gl, gnome, gnuzilla, graphics, guile, haskell, image, java, kodi, ldc, libreoffice, markup, maths, mc, monitoring, music, php, pretty-print, python, scheme, smalltalk, statistics, synergy, tex, textutils, video, web-browsers, xml, zip}.scm, guix/build-system/{ant, font}.scm, guix/{download, packages}.scm: Adapt module import.
* gnu: diamond: Update to 0.9.8.Ben Woodcroft2017-06-17
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.8.
* gnu: tadbit: Fix typo in description.Tobias Geerinckx-Rice2017-06-16
| | | | * gnu/packages/bioinformatics.scm (tadbit)[description]: Fix typo.
* gnu: gemma: Fix indentation.Efraim Flashner2017-06-15
| | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: Fix indentation.
* gnu: gemma: Fix building on 32-bit architectures.Efraim Flashner2017-06-15
| | | | | * gnu/packages/bioinformatics.scm (gemma)[arguments]: On 32-bit architectures add 'FORCE_32BIT' flag.
* gnu: Add tadbit.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (tadbit): New variable.
* gnu: Add imp.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (imp): New variable.
* gnu: Add phylip.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (phylip): New variable.
* gnu: Add gess.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (gess): New variable.
* gnu: Add trim-galore.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (trim-galore): New variable.
* gnu: Add ritornello.Ricardo Wurmus2017-06-09
| | | | * gnu/packages/bioinformatics.scm (ritornello): New variable.
* gnu: diamond: Update to 0.9.6.Ben Woodcroft2017-06-08
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.6.
* gnu: Add kaiju.Roel Janssen2017-06-02
| | | | * gnu/packages/bioinformatics.scm (kaiju): New variable.
* gnu: diamond: Update to 0.9.3.Ben Woodcroft2017-05-28
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.3.
* gnu: diamond: Update to 0.9.2.Ben Woodcroft2017-05-27
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.2.
* gnu: diamond: Update to 0.9.1.Ben Woodcroft2017-05-22
| | | | * gnu/packages/bioinformatics.scm (diamond): Update to 0.9.1.
* gnu: Add r-edaseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-edaseq): New variable.
* gnu: Add r-deseq.Ricardo Wurmus2017-05-22
| | | | * gnu/packages/bioinformatics.scm (r-deseq): New variable.
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