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2016-09-04gnu: infernal: Limit to i686 and x86_64 systems.Efraim Flashner
* gnu/packages/bioinformatics.scm (infernal)[supported-systems]: The package requires VMX or SSE capability for parallel instructions, so limit it to those supported systems.
2016-09-02gnu: Add Infernal.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (infernal): New variable.
2016-08-31gnu: subread: Update to 1.5.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (subread): Update to 1.5.1.
2016-08-31gnu: aragorn: Update to 1.2.37.Ben Woodcroft
* gnu/packages/bioinformatics.scm (aragorn): Update to 1.2.37.
2016-08-30gnu: diamond: Update to 0.8.20.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.20.
2016-08-22gnu: Add r-bamsignals.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bamsignals): New variable.
2016-08-22gnu: Add r-rhtslib.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-rhtslib): New variable.
2016-08-17gnu: clipper: Update to 1.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (clipper): Update to 1.1. [source]: Delete pre-built libraries. [inputs]: Add python2-pandas.
2016-08-17gnu: Add minced.Marius Bakke
* gnu/packages/bioinformatics.scm (minced): New variable. Signed-off-by: Ben Woodcroft <donttrustben@gmail.com>
2016-08-16gnu: mafft: Update to 7.305.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.305. [inputs]: Add ruby.
2016-08-15gnu: mafft: Update to 7.304.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.304.
2016-08-15gnu: mafft: Wrap programs.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft)[arguments]: Add 'wrap-programs' phase. [propagated-inputs]: Move coreutils from here ... [inputs]: ... to here.
2016-08-15gnu: mafft: Update to 7.300.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.300.
2016-08-14gnu: Add bamm.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bamm): New variable.
2016-08-11gnu: snap-aligner: Limit to x86_64.Efraim Flashner
* gnu/packages/bioinformatics.scm (snap-aligner)[supported-systems]: Add note explaining why we build for x86_64 only.
2016-08-11gnu: diamond: Update to 0.8.18.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.18.
2016-08-08gnu: Add roary.Ben Woodcroft
* gnu/packages/bioinformatics.scm (roary): New variable.
2016-08-08gnu: Add raxml.Ben Woodcroft
* gnu/packages/bioinformatics.scm (raxml): New variable.
2016-08-08gnu: Add prank.Ben Woodcroft
* gnu/packages/bioinformatics.scm (prank): New variable.
2016-08-08gnu: Add exonerate.Ben Woodcroft
* gnu/packages/bioinformatics.scm (exonerate): New variable.
2016-08-08gnu: Add bppsuite.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bppsuite): New variable.
2016-08-08gnu: Add bpp-popgen.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bpp-popgen): New variable.
2016-08-08gnu: Add bpp-phyl.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bpp-phyl): New variable.
2016-08-08gnu: Add bpp-seq.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bpp-seq): New variable.
2016-08-08gnu: Add bpp-core.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bpp-core): New variable.
2016-08-06gnu: Add python-biom-format.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-biom-format, python2-biom-format): New variables.
2016-08-03gnu: Add discrover.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (discrover): New variable.
2016-08-03gnu: fxtract: Restrict to x86_64-linux.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fxtract)[supported-systems]: Restrict to x86_64-linux.
2016-08-02gnu: r-variantannotation: Update to 1.18.6.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.6.
2016-08-02gnu: r-genomationdata: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): Update to 1.4.2.
2016-07-30gnu: diamond: Update to 0.8.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.17.
2016-07-28gnu: r-genomicfeatures: Update to 1.24.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.5.
2016-07-28gnu: r-bsgenome: Update to 1.40.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-bsgenome): Update to 1.40.1.
2016-07-28gnu: r-iranges: Update to 2.6.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-iranges): Update to 2.6.1.
2016-07-28gnu: r-limma: Update to 3.28.17.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-limma): Update to 3.28.17.
2016-07-28gnu: r-xvector: Update to 0.12.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-xvector): Update to 0.12.1.
2016-07-28gnu: r-genomicranges: Update to 1.24.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicranges): Update to 1.24.2.
2016-07-28gnu: r-annotationdbi: Update to 1.34.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.4.
2016-07-28gnu: r-biocparallel: Update to 1.6.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.3.
2016-07-28gnu: r-biostrings: Update to 2.40.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-biostrings): Update to 2.40.2.
2016-07-28gnu: r-summarizedexperiment: Update to 1.2.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.3.
2016-07-28gnu: r-genomicalignments: Update to 1.8.4.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomicalignments): Update to 1.8.4.
2016-07-28gnu: r-rtracklayer: Update to 1.32.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-rtracklayer): Update to 1.32.2.
2016-07-28gnu: r-genomeinfodb: Update to 1.8.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.3.
2016-07-28gnu: r-s4vectors: Update to 0.10.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-s4vectors): Update to 0.10.2.
2016-07-27gnu: diamond: Update to 0.8.16.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.16.
2016-07-23gnu: fasttree: Update to 2.1.9.Ben Woodcroft
* gnu/packages/bioinformatics.scm (fasttree): Update to 2.1.9.
2016-07-21gnu: Update URLs for sourceforge.net.Leo Famulari
* gnu/packages/admin.scm: Update URLs pointing to sourceforge.net. * gnu/packages/audacity.scm: Likewise. * gnu/packages/audio.scm: Likewise. * gnu/packages/bioinformatics.scm: Likewise. * gnu/packages/boost.scm: Likewise. * gnu/packages/cdrom.scm: Likewise. * gnu/packages/code.scm: Likewise. * gnu/packages/compression.scm: Likewise. * gnu/packages/cups.scm: Likewise. * gnu/packages/djvu.scm: Likewise. * gnu/packages/docbook.scm: Likewise. * gnu/packages/documentation.scm: Likewise. * gnu/packages/flashing-tools.scm: Likewise. * gnu/packages/fonts.scm: Likewise. * gnu/packages/fontutils.scm: Likewise. * gnu/packages/games.scm: Likewise. * gnu/packages/ghostscript.scm: Likewise. * gnu/packages/gl.scm: Likewise. * gnu/packages/gnucash.scm: Likewise. * gnu/packages/graphviz.scm: Likewise. * gnu/packages/image.scm: Likewise. * gnu/packages/libreoffice.scm: Likewise. * gnu/packages/libusb.scm: Likewise. * gnu/packages/linux.scm: Likewise. * gnu/packages/lirc.scm: Likewise. * gnu/packages/maths.scm: Likewise. * gnu/packages/mcrypt.scm: Likewise. * gnu/packages/mp3.scm: Likewise. * gnu/packages/music.scm: Likewise. * gnu/packages/networking.scm: Likewise. * gnu/packages/onc-rpc.scm: Likewise. * gnu/packages/password-utils.scm: Likewise. * gnu/packages/pdf.scm: Likewise. * gnu/packages/perl.scm: Likewise. * gnu/packages/photo.scm: Likewise. * gnu/packages/popt.scm: Likewise. * gnu/packages/python.scm: Likewise. * gnu/packages/rdesktop.scm: Likewise. * gnu/packages/screen.scm: Likewise. * gnu/packages/swig.scm: Likewise. * gnu/packages/tcl.scm: Likewise. * gnu/packages/version-control.scm: Likewise. * gnu/packages/video.scm: Likewise. * gnu/packages/w3m.scm: Likewise. * gnu/packages/web.scm: Likewise. * gnu/packages/wm.scm: Likewise. * gnu/packages/xdisorg.scm: Likewise. * gnu/packages/xml.scm: Likewise.
2016-07-18gnu: diamond: Update to 0.8.15.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.15.
2016-07-17gnu: eigensoft: Do not refer to "lapacke" output.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eigensoft)[inputs]: Remove reference to non-existing "lapacke" output.
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