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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.
2016-07-14gnu: Add eigensoft.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (eigensoft): New variable.
2016-07-12gnu: Add Ribotaper.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (ribotaper): New variable.
2016-07-12gnu: Add bedtools-2.18.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bedtools-2.18): New variable.
2016-07-10gnu: diamond: Update to 0.8.12.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.12.
2016-07-09gnu: Add python-dendropy.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-dendropy, python2-dendropy): New variables. * gnu/packages/patches/python-dendropy-exclude-failing-tests.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2016-07-08gnu: star: Restrict supported systems to 64-bit systems.Ben Woodcroft
* gnu/packages/bioinformatics.scm (star)[supported-systems]: Restrict to x86_64-linux and mips64el-linux.
2016-07-07gnu: bedtools: Update to 2.26.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (bedtools): Update to 2.26.0.
2016-07-07gnu: diamond: Update to 0.8.11.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.11.
2016-07-07gnu: Add r-seqinr.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-seqinr): New variable.
2016-07-07gnu: khmer: Limit to x86_64 systems only.Efraim Flashner
* gnu/packages/bioinformatics.scm (khmer)[supported-systems]: New field.
2016-07-05gnu: Add multiqc.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (multiqc): New variable.
2016-07-05gnu: Add bits.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (bits): New variable.
2016-07-05gnu: Add EMBOSS.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (emboss): New variable.
2016-07-04gnu: Add r-edger.Roel Janssen
* gnu/packages/bioinformatics.scm (r-edger): New variable.
2016-07-04gnu: Add r-limma.Roel Janssen
* gnu/packages/bioinformatics.scm (r-limma): New variable.
2016-07-01gnu: vsearch: Update to 2.0.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.1.
2016-06-29gnu: blast+: Update to 2.4.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (blast+): Update to 2.4.0.
2016-06-29gnu: star: Update to 2.5.2a.Ben Woodcroft
* gnu/packages/bioinformatics.scm (star): Update to 2.5.2a.
2016-06-29gnu: htslib: Update to 1.3.1.Ben Woodcroft
* gnu/packages/bioinformatics.scm (htslib): Update to 1.3.1.
2016-06-28gnu: Add SEEK.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (seek): New variable.
2016-06-28gnu: mafft: Update to 7.299.Ben Woodcroft
* gnu/packages/bioinformatics.scm (mafft): Update to 7.299.
2016-06-28gnu: metabat: Update to 0.26.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (metabat): Update to 0.26.3. [arguments]: Update include and linking paths accordingly.
2016-06-28gnu: diamond: Update to 0.8.9.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.9.
2016-06-27gnu: Add khmer.Ben Woodcroft
* gnu/packages/bioinformatics.scm (khmer): New variable. * gnu/packages/patches/khmer-use-libraries.patch: New file. * gnu/local.mk (dist_patch_DATA): Add it.
2016-06-27gnu: Add python-screed.Ben Woodcroft
* gnu/packages/bioinformatics.scm (python-screed, python2-screed): New variables.
2016-06-26gnu: vsearch: Update to 2.0.0.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 2.0.0.
2016-06-22gnu: vsearch: Update to 0.11.2.Ben Woodcroft
* gnu/packages/bioinformatics.scm (vsearch): Update to 0.11.2.
2016-06-21gnu: Add r-vegan.Ben Woodcroft
* gnu/packages/bioinformatics.scm (r-vegan): New variable.
2016-06-21gnu: diamond: Update to 0.8.7.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.7.
2016-06-15gnu: Add r-bsgenome-mmusculus-ucsc-mm10.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-bsgenome-mmusculus-ucsc-mm10): New variable.
2016-06-14gnu: Add ruby-bio-kseq.Ben Woodcroft
* gnu/packages/bioinformatics.scm (ruby-bio-kseq): New variable.
2016-06-13gnu: piranha: Update to 1.2.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha): Update to 1.2.1.
2016-06-05gnu: Use full SHA1 commit ids.Hartmut Goebel
* gnu/packages/bioinformatics.scm (pbtranscript-tofu, mosaik, smithlab-cpp, piranha): Use full SHA1 commit ids. * gnu/packages/ci.scm (hydra): Likewise. * gnu/packages/compression.scm (sfarkxtc): Likewise. * gnu/packages/emacs.scm (emacs-ob-ipython): Likewise. * gnu/packages/games.scm (mars, emulation-station): Likewise. * gnu/packages/gnunet.scm (guile-gnunet): Likewise. * gnu/packages/music.scm (non-sequencer): Likewise. * gnu/packages/version-control.scm (git-flow, git-test-sequence): Likewise. * gnu/packages/xorg.scm (xf86-video-intel): Likewise. Signed-off-by: Ludovic Courtès <ludo@gnu.org>
2016-06-04gnu: diamond: Update to 0.8.5.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.5.
2016-05-31gnu: Add r-genomationdata.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomationdata): New variable.
2016-05-28gnu: Update diamond to 0.8.3.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond): Update to 0.8.3.
2016-05-23gnu: Add ParDRe.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (pardre): New variable.
2016-05-20gnu: r-genomation: Update to 1.4.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomation): Update to 1.4.2.
2016-05-20gnu: r-genomicfeatures: Update to 1.24.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomicfeatures): Update to 1.24.2.
2016-05-20gnu: r-summarizedexperiment: Update to 1.2.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-summarizedexperiment): Update to 1.2.2.
2016-05-20gnu: r-biocparallel: Update to 1.6.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-biocparallel): Update to 1.6.2.
2016-05-20gnu: r-annotationdbi: Update to 1.34.2.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-annotationdbi): Update to 1.34.2.
2016-05-20gnu: r-variantannotation: Update to 1.18.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-variantannotation): Update to 1.18.1.
2016-05-20gnu: r-genomeinfodb: Update to 1.8.1.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (r-genomeinfodb): Update to 1.8.1.
2016-05-18gnu: diamond: Do not specify target architecture.Ben Woodcroft
* gnu/packages/bioinformatics.scm (diamond)[arguments]: Do not specify target architecture.
2016-05-18gnu: Add Piranha.Ricardo Wurmus
* gnu/packages/bioinformatics.scm (piranha): New variable.
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